cpg free promoter lucia plasmid Search Results


96
New England Biolabs cpg free vector pcpgl
GRN expression in human lymphoblast cell lines is inversely correlated to its promoter methylation. ( a ) GRN net secretion was measured by ELISA in LCLs derived from neurologically healthy individuals (LCL #1-13), unaffected relatives of FTLD patients (LCL #14, 15, highlighted in blue) and FTLD-patients (LCL#16, 17, highlighted in red). n = 3, mean ± SEM. ( b ) Scheme of GRN promoter region. Red bars depict PCR-amplicons analyzed for DNA methylation levels by MassARRAY. Blue bars indicate full length and short promoter region that was cloned into the <t>pCpGL</t> vector for luciferase assays (compare Figure ). White circles display CpG units in amplicons A-1 to A-5 and A-DAC quantified by MassARRAY. CpG units that were not analyzed are not shown. Asterisks indicate significant correlation between GRN mRNA expression or GRN secretion and GRN methylation at respective CpG unit (*p < 0.05, linear regression analysis, Benjamini Hochberg multiple testing and FDR correction, compare Additional file : Table S3). ( c ) Average DNA methylation levels in amplicons A-1 to A-5 for individual LCLs are plotted. Mean ± SD. Color code as in (a). ( d ) Correlation between GRN mRNA expression and average DNA methylation at CpG units 1, 2, 6, 8 and 11 is shown. GRN mRNA expression was quantified by qPCR and normalized to PGK1 and GAPDH. Relative mRNA expression levels were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a). ( e ) Correlation between GRN secretion and average DNA methylation at CpG units 1, 2, 6, 8 and 11. GRN secretion was determined by ELISA and relative units (R.U.) were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a).
Cpg Free Vector Pcpgl, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pmc03893557-219-26-38?v=New+England+Biolabs
Average 96 stars, based on 1 article reviews
cpg free vector pcpgl - by Bioz Stars, 2026-07
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90
VGXI Inc plasmid pgm169
GRN expression in human lymphoblast cell lines is inversely correlated to its promoter methylation. ( a ) GRN net secretion was measured by ELISA in LCLs derived from neurologically healthy individuals (LCL #1-13), unaffected relatives of FTLD patients (LCL #14, 15, highlighted in blue) and FTLD-patients (LCL#16, 17, highlighted in red). n = 3, mean ± SEM. ( b ) Scheme of GRN promoter region. Red bars depict PCR-amplicons analyzed for DNA methylation levels by MassARRAY. Blue bars indicate full length and short promoter region that was cloned into the <t>pCpGL</t> vector for luciferase assays (compare Figure ). White circles display CpG units in amplicons A-1 to A-5 and A-DAC quantified by MassARRAY. CpG units that were not analyzed are not shown. Asterisks indicate significant correlation between GRN mRNA expression or GRN secretion and GRN methylation at respective CpG unit (*p < 0.05, linear regression analysis, Benjamini Hochberg multiple testing and FDR correction, compare Additional file : Table S3). ( c ) Average DNA methylation levels in amplicons A-1 to A-5 for individual LCLs are plotted. Mean ± SD. Color code as in (a). ( d ) Correlation between GRN mRNA expression and average DNA methylation at CpG units 1, 2, 6, 8 and 11 is shown. GRN mRNA expression was quantified by qPCR and normalized to PGK1 and GAPDH. Relative mRNA expression levels were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a). ( e ) Correlation between GRN secretion and average DNA methylation at CpG units 1, 2, 6, 8 and 11. GRN secretion was determined by ELISA and relative units (R.U.) were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a).
Plasmid Pgm169, supplied by VGXI Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pmc04673100__mmc1-30-1-26?v=VGXI+Inc
Average 90 stars, based on 1 article reviews
plasmid pgm169 - by Bioz Stars, 2026-07
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90
GenScript corporation px458-rela1 (seq id no:8
GRN expression in human lymphoblast cell lines is inversely correlated to its promoter methylation. ( a ) GRN net secretion was measured by ELISA in LCLs derived from neurologically healthy individuals (LCL #1-13), unaffected relatives of FTLD patients (LCL #14, 15, highlighted in blue) and FTLD-patients (LCL#16, 17, highlighted in red). n = 3, mean ± SEM. ( b ) Scheme of GRN promoter region. Red bars depict PCR-amplicons analyzed for DNA methylation levels by MassARRAY. Blue bars indicate full length and short promoter region that was cloned into the <t>pCpGL</t> vector for luciferase assays (compare Figure ). White circles display CpG units in amplicons A-1 to A-5 and A-DAC quantified by MassARRAY. CpG units that were not analyzed are not shown. Asterisks indicate significant correlation between GRN mRNA expression or GRN secretion and GRN methylation at respective CpG unit (*p < 0.05, linear regression analysis, Benjamini Hochberg multiple testing and FDR correction, compare Additional file : Table S3). ( c ) Average DNA methylation levels in amplicons A-1 to A-5 for individual LCLs are plotted. Mean ± SD. Color code as in (a). ( d ) Correlation between GRN mRNA expression and average DNA methylation at CpG units 1, 2, 6, 8 and 11 is shown. GRN mRNA expression was quantified by qPCR and normalized to PGK1 and GAPDH. Relative mRNA expression levels were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a). ( e ) Correlation between GRN secretion and average DNA methylation at CpG units 1, 2, 6, 8 and 11. GRN secretion was determined by ELISA and relative units (R.U.) were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a).
Px458 Rela1 (Seq Id No:8, supplied by GenScript corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/us11541130-399-17-16?v=GenScript+corporation
Average 90 stars, based on 1 article reviews
px458-rela1 (seq id no:8 - by Bioz Stars, 2026-07
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90
GenScript corporation pcpgl-basic
GRN expression in human lymphoblast cell lines is inversely correlated to its promoter methylation. ( a ) GRN net secretion was measured by ELISA in LCLs derived from neurologically healthy individuals (LCL #1-13), unaffected relatives of FTLD patients (LCL #14, 15, highlighted in blue) and FTLD-patients (LCL#16, 17, highlighted in red). n = 3, mean ± SEM. ( b ) Scheme of GRN promoter region. Red bars depict PCR-amplicons analyzed for DNA methylation levels by MassARRAY. Blue bars indicate full length and short promoter region that was cloned into the <t>pCpGL</t> vector for luciferase assays (compare Figure ). White circles display CpG units in amplicons A-1 to A-5 and A-DAC quantified by MassARRAY. CpG units that were not analyzed are not shown. Asterisks indicate significant correlation between GRN mRNA expression or GRN secretion and GRN methylation at respective CpG unit (*p < 0.05, linear regression analysis, Benjamini Hochberg multiple testing and FDR correction, compare Additional file : Table S3). ( c ) Average DNA methylation levels in amplicons A-1 to A-5 for individual LCLs are plotted. Mean ± SD. Color code as in (a). ( d ) Correlation between GRN mRNA expression and average DNA methylation at CpG units 1, 2, 6, 8 and 11 is shown. GRN mRNA expression was quantified by qPCR and normalized to PGK1 and GAPDH. Relative mRNA expression levels were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a). ( e ) Correlation between GRN secretion and average DNA methylation at CpG units 1, 2, 6, 8 and 11. GRN secretion was determined by ELISA and relative units (R.U.) were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a).
Pcpgl Basic, supplied by GenScript corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pmc06332625-98-15-24?v=GenScript+corporation
Average 90 stars, based on 1 article reviews
pcpgl-basic - by Bioz Stars, 2026-07
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93
Novus Biologicals mouse anti firefly luciferase antibodies
FIGURE 1 | H2O2 suppresses NF-kB activity in MEC-1 cells. (A–D). Quantification of the <t>luciferase</t> activity in MEC-1 cells transfected with either NF-AT-luciferase (C) or NF-kB-luciferase (D) reporter constructs and then treated for 6 h with H2O2 at the indicated concentrations. Data are expressed as relative luciferase units (RLU). A combination of A23187 and PMA was used as positive control (n independent experiments = 4). A mix of cells transfected with the two constructs and treated as above were used for the flow cytometric analysis of ROS intracellular content in cells stained with 5 mM CM-H2DCFDA (A) and of cell viability, calculated as the percentage of Annexin V-/PI- cells (B) (n independent experiments = 4). Mean ± SD. Anova two-way test, Multiple Comparison. p ≤0.0001, ****; p ≤0.001, ***; p ≤0.01, **; p ≤0.05, *.
Mouse Anti Firefly Luciferase Antibodies, supplied by Novus Biologicals, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pm35847884-53-27-31?v=Novus+Biologicals
Average 93 stars, based on 1 article reviews
mouse anti firefly luciferase antibodies - by Bioz Stars, 2026-07
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90
GenScript corporation cpg-free firefly luciferase reporter vector
FIGURE 1 | H2O2 suppresses NF-kB activity in MEC-1 cells. (A–D). Quantification of the <t>luciferase</t> activity in MEC-1 cells transfected with either NF-AT-luciferase (C) or NF-kB-luciferase (D) reporter constructs and then treated for 6 h with H2O2 at the indicated concentrations. Data are expressed as relative luciferase units (RLU). A combination of A23187 and PMA was used as positive control (n independent experiments = 4). A mix of cells transfected with the two constructs and treated as above were used for the flow cytometric analysis of ROS intracellular content in cells stained with 5 mM CM-H2DCFDA (A) and of cell viability, calculated as the percentage of Annexin V-/PI- cells (B) (n independent experiments = 4). Mean ± SD. Anova two-way test, Multiple Comparison. p ≤0.0001, ****; p ≤0.001, ***; p ≤0.01, **; p ≤0.05, *.
Cpg Free Firefly Luciferase Reporter Vector, supplied by GenScript corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pm34315727-82-31-37?v=GenScript+corporation
Average 90 stars, based on 1 article reviews
cpg-free firefly luciferase reporter vector - by Bioz Stars, 2026-07
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96
Addgene inc plasmid l myc and lin28 episonal insert pcxle hul

Plasmid L Myc And Lin28 Episonal Insert Pcxle Hul, supplied by Addgene inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pmc08065177-59-0-9?v=Addgene+inc
Average 96 stars, based on 1 article reviews
plasmid l myc and lin28 episonal insert pcxle hul - by Bioz Stars, 2026-07
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90
Lonza episomal plasmid nucleofection

Episomal Plasmid Nucleofection, supplied by Lonza, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/10__1096_slash_fj__201902447r-16-5-8?v=Lonza
Average 90 stars, based on 1 article reviews
episomal plasmid nucleofection - by Bioz Stars, 2026-07
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Lonza episomal plasmids lonza contract

Episomal Plasmids Lonza Contract, supplied by Lonza, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pmc05404968-143-12-14?v=Lonza
Average 90 stars, based on 1 article reviews
episomal plasmids lonza contract - by Bioz Stars, 2026-07
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93
Addgene inc plasmid5

Plasmid5, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pmc06429602__SC___010___C8SC03901A___s001-43-14-15?v=Addgene+inc
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plasmid5 - by Bioz Stars, 2026-07
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Lonza episomal plasmids

Episomal Plasmids, supplied by Lonza, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pm28253233-410-12-14?v=Lonza
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episomal plasmids - by Bioz Stars, 2026-07
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90
Promega episomal tss-mpra plasmid
<t>TSS-MPRA</t> of synthetic regulatory sequences mirrors the vast majority of endogenous initiation patterns and transcription levels. ( A ) Schematic of TSS-MPRA. Transcription activity and location of transcription initiation is determined by 5′ RNA-seq of reporter transcripts initiating within synthetic DNA inserts cloned into reporter plasmids and electroporated into cells. Histograms on the right show cumulative DNA-normalized number of sequence tags aligning to each base position of a 153-bp region surrounding the human HBE1 promoter in K562 cells. Capped reporter transcripts are drawn in purple. RT: reverse transcription primer landing site. BC: barcode sequence. ( B ) Spearman's correlation of DNA-normalized RNA levels of all inserts of two replicate episomal TSS-MPRA experiments. ( C ) Correlation between the transcriptional signal of 250 genomic DNA inserts in epi-short TSS-MPRA and csRNA-seq of the corresponding endogenous loci. TSS-MPRA inserts were chosen randomly from locations exhibiting transcription activity as measured by csRNA-seq. Spearman's correlation of TSS-MPRA and csRNA-seq transcription levels of all regulatory sequences, or of promoters (red) or enhancers (blue, outside of a ± 2-kb window of RefSeq-annotated promoters). Regions were chosen to cover a wide range of transcription levels and initiation patterns. Each dot represents the relative transcript levels observed in each assay as total normalized read counts of all transcripts aligning to each region. TSS-MPRA RNA read counts were normalized by the corresponding plasmid DNA read counts.
Episomal Tss Mpra Plasmid, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cpg+free+promoter+lucia+plasmid/pmc10450201-40-1-13?v=Promega
Average 90 stars, based on 1 article reviews
episomal tss-mpra plasmid - by Bioz Stars, 2026-07
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Image Search Results


GRN expression in human lymphoblast cell lines is inversely correlated to its promoter methylation. ( a ) GRN net secretion was measured by ELISA in LCLs derived from neurologically healthy individuals (LCL #1-13), unaffected relatives of FTLD patients (LCL #14, 15, highlighted in blue) and FTLD-patients (LCL#16, 17, highlighted in red). n = 3, mean ± SEM. ( b ) Scheme of GRN promoter region. Red bars depict PCR-amplicons analyzed for DNA methylation levels by MassARRAY. Blue bars indicate full length and short promoter region that was cloned into the pCpGL vector for luciferase assays (compare Figure ). White circles display CpG units in amplicons A-1 to A-5 and A-DAC quantified by MassARRAY. CpG units that were not analyzed are not shown. Asterisks indicate significant correlation between GRN mRNA expression or GRN secretion and GRN methylation at respective CpG unit (*p < 0.05, linear regression analysis, Benjamini Hochberg multiple testing and FDR correction, compare Additional file : Table S3). ( c ) Average DNA methylation levels in amplicons A-1 to A-5 for individual LCLs are plotted. Mean ± SD. Color code as in (a). ( d ) Correlation between GRN mRNA expression and average DNA methylation at CpG units 1, 2, 6, 8 and 11 is shown. GRN mRNA expression was quantified by qPCR and normalized to PGK1 and GAPDH. Relative mRNA expression levels were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a). ( e ) Correlation between GRN secretion and average DNA methylation at CpG units 1, 2, 6, 8 and 11. GRN secretion was determined by ELISA and relative units (R.U.) were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a).

Journal: Acta Neuropathologica Communications

Article Title: Promoter DNA methylation regulates progranulin expression and is altered in FTLD

doi: 10.1186/2051-5960-1-16

Figure Lengend Snippet: GRN expression in human lymphoblast cell lines is inversely correlated to its promoter methylation. ( a ) GRN net secretion was measured by ELISA in LCLs derived from neurologically healthy individuals (LCL #1-13), unaffected relatives of FTLD patients (LCL #14, 15, highlighted in blue) and FTLD-patients (LCL#16, 17, highlighted in red). n = 3, mean ± SEM. ( b ) Scheme of GRN promoter region. Red bars depict PCR-amplicons analyzed for DNA methylation levels by MassARRAY. Blue bars indicate full length and short promoter region that was cloned into the pCpGL vector for luciferase assays (compare Figure ). White circles display CpG units in amplicons A-1 to A-5 and A-DAC quantified by MassARRAY. CpG units that were not analyzed are not shown. Asterisks indicate significant correlation between GRN mRNA expression or GRN secretion and GRN methylation at respective CpG unit (*p < 0.05, linear regression analysis, Benjamini Hochberg multiple testing and FDR correction, compare Additional file : Table S3). ( c ) Average DNA methylation levels in amplicons A-1 to A-5 for individual LCLs are plotted. Mean ± SD. Color code as in (a). ( d ) Correlation between GRN mRNA expression and average DNA methylation at CpG units 1, 2, 6, 8 and 11 is shown. GRN mRNA expression was quantified by qPCR and normalized to PGK1 and GAPDH. Relative mRNA expression levels were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a). ( e ) Correlation between GRN secretion and average DNA methylation at CpG units 1, 2, 6, 8 and 11. GRN secretion was determined by ELISA and relative units (R.U.) were plotted against average DNA methylation levels. Correlation between parameters was quantified by linear regression analysis, r 2 and p-values are given. Color code as in (a).

Article Snippet: The GRN promoter region (−2423 to +207 bp relative to transcriptional start site, for primers see Additional file : Table S1) was cloned directly into the CpG-free vector pCpGL and in vitro methylated using recombinant DNA methyltransferase M.SssI (New England Biolabs).

Techniques: Expressing, Methylation, Enzyme-linked Immunosorbent Assay, Derivative Assay, DNA Methylation Assay, Clone Assay, Plasmid Preparation, Luciferase

DNA methylation inhibits GRN promoter activity at distinct CpG units. In vitro methylated and unmethylated pCpGL plasmids containing the GRN core promoter region driving expression of firefly luciferase were transiently cotransfected into ( a ) HEK 293FT cells and ( b ) primary rat cortical neurons together with a Renilla luciferase expressing plasmid. The full length GRN promoter pCpGL plasmid, a GRN promoter construct with site specific mutations of the significant CpG units in amplicons A-1 and A-2, and a short GRN promoter construct lacking amplicons A-1 and A-2 were transiently cotransfected into ( c ) HEK 293FT cells and ( d ) primary rat cortical neurons together with a Renilla luciferase expressing plasmid. Luciferase reporter activity was measured 48 h (a + c, HEK 293FT) or 72 h (b + d, neurons) after transfection. Relative luciferase activity was determined by normalizing firefly luciferase against Renilla luciferase activity. The empty vector was used as negative control. Mean ± SEM, n ≥ 3. ***p < 0.001, Student’s t-test, sign . significant.

Journal: Acta Neuropathologica Communications

Article Title: Promoter DNA methylation regulates progranulin expression and is altered in FTLD

doi: 10.1186/2051-5960-1-16

Figure Lengend Snippet: DNA methylation inhibits GRN promoter activity at distinct CpG units. In vitro methylated and unmethylated pCpGL plasmids containing the GRN core promoter region driving expression of firefly luciferase were transiently cotransfected into ( a ) HEK 293FT cells and ( b ) primary rat cortical neurons together with a Renilla luciferase expressing plasmid. The full length GRN promoter pCpGL plasmid, a GRN promoter construct with site specific mutations of the significant CpG units in amplicons A-1 and A-2, and a short GRN promoter construct lacking amplicons A-1 and A-2 were transiently cotransfected into ( c ) HEK 293FT cells and ( d ) primary rat cortical neurons together with a Renilla luciferase expressing plasmid. Luciferase reporter activity was measured 48 h (a + c, HEK 293FT) or 72 h (b + d, neurons) after transfection. Relative luciferase activity was determined by normalizing firefly luciferase against Renilla luciferase activity. The empty vector was used as negative control. Mean ± SEM, n ≥ 3. ***p < 0.001, Student’s t-test, sign . significant.

Article Snippet: The GRN promoter region (−2423 to +207 bp relative to transcriptional start site, for primers see Additional file : Table S1) was cloned directly into the CpG-free vector pCpGL and in vitro methylated using recombinant DNA methyltransferase M.SssI (New England Biolabs).

Techniques: DNA Methylation Assay, Activity Assay, In Vitro, Methylation, Expressing, Luciferase, Plasmid Preparation, Construct, Transfection, Negative Control

Overexpression of DNMT3a alters GRN promoter activity in primary cortical neurons and reduces GRN mRNA expression in LCLs. ( a ) pCpGL plasmid containing the GRN core promoter and a DNMT3a overexpression construct were transiently transfected in HEK 293FT cells (left panel) and in rat primary cortical neurons (right panel). Relative luciferase activity was determined by normalizing firefly luciferase against Renilla luciferase activity. Empty vectors were used as negative control. Firefly luciferase expression was significantly reduced upon DNMT3a overexpression. Mean ± SEM, n ≥ 3. ***p < 0.001, ANOVA with Tukey’s Multiple Comparison test. ( b ) Lentiviral expression of DNMT3a in LCLs #3 and #14. Overexpression was verified by qPCR five days after viral transduction. n = 5, mean ± SEM, *p < 0.05, Student’s t-test. ( c ) GRN mRNA expression levels were significantly reduced in DNMT3a overexpressing LCLs as quantified by qPCR and normalized to PGK1 expression levels. n = 5, mean ± SEM, *p < 0.05, Student’s t-test.

Journal: Acta Neuropathologica Communications

Article Title: Promoter DNA methylation regulates progranulin expression and is altered in FTLD

doi: 10.1186/2051-5960-1-16

Figure Lengend Snippet: Overexpression of DNMT3a alters GRN promoter activity in primary cortical neurons and reduces GRN mRNA expression in LCLs. ( a ) pCpGL plasmid containing the GRN core promoter and a DNMT3a overexpression construct were transiently transfected in HEK 293FT cells (left panel) and in rat primary cortical neurons (right panel). Relative luciferase activity was determined by normalizing firefly luciferase against Renilla luciferase activity. Empty vectors were used as negative control. Firefly luciferase expression was significantly reduced upon DNMT3a overexpression. Mean ± SEM, n ≥ 3. ***p < 0.001, ANOVA with Tukey’s Multiple Comparison test. ( b ) Lentiviral expression of DNMT3a in LCLs #3 and #14. Overexpression was verified by qPCR five days after viral transduction. n = 5, mean ± SEM, *p < 0.05, Student’s t-test. ( c ) GRN mRNA expression levels were significantly reduced in DNMT3a overexpressing LCLs as quantified by qPCR and normalized to PGK1 expression levels. n = 5, mean ± SEM, *p < 0.05, Student’s t-test.

Article Snippet: The GRN promoter region (−2423 to +207 bp relative to transcriptional start site, for primers see Additional file : Table S1) was cloned directly into the CpG-free vector pCpGL and in vitro methylated using recombinant DNA methyltransferase M.SssI (New England Biolabs).

Techniques: Over Expression, Activity Assay, Expressing, Plasmid Preparation, Construct, Transfection, Luciferase, Negative Control, Comparison, Transduction

FIGURE 1 | H2O2 suppresses NF-kB activity in MEC-1 cells. (A–D). Quantification of the luciferase activity in MEC-1 cells transfected with either NF-AT-luciferase (C) or NF-kB-luciferase (D) reporter constructs and then treated for 6 h with H2O2 at the indicated concentrations. Data are expressed as relative luciferase units (RLU). A combination of A23187 and PMA was used as positive control (n independent experiments = 4). A mix of cells transfected with the two constructs and treated as above were used for the flow cytometric analysis of ROS intracellular content in cells stained with 5 mM CM-H2DCFDA (A) and of cell viability, calculated as the percentage of Annexin V-/PI- cells (B) (n independent experiments = 4). Mean ± SD. Anova two-way test, Multiple Comparison. p ≤0.0001, ****; p ≤0.001, ***; p ≤0.01, **; p ≤0.05, *.

Journal: Frontiers in oncology

Article Title: p66Shc Deficiency in Chronic Lymphocytic Leukemia Promotes Chemokine Receptor Expression Through the ROS-Dependent Inhibition of NF-κB.

doi: 10.3389/fonc.2022.877495

Figure Lengend Snippet: FIGURE 1 | H2O2 suppresses NF-kB activity in MEC-1 cells. (A–D). Quantification of the luciferase activity in MEC-1 cells transfected with either NF-AT-luciferase (C) or NF-kB-luciferase (D) reporter constructs and then treated for 6 h with H2O2 at the indicated concentrations. Data are expressed as relative luciferase units (RLU). A combination of A23187 and PMA was used as positive control (n independent experiments = 4). A mix of cells transfected with the two constructs and treated as above were used for the flow cytometric analysis of ROS intracellular content in cells stained with 5 mM CM-H2DCFDA (A) and of cell viability, calculated as the percentage of Annexin V-/PI- cells (B) (n independent experiments = 4). Mean ± SD. Anova two-way test, Multiple Comparison. p ≤0.0001, ****; p ≤0.001, ***; p ≤0.01, **; p ≤0.05, *.

Article Snippet: The transfection efficiency of the NF-kBluciferase reporter and p66Shc-encoding vectors was assessed by qRT-PCR of p66Shc and flow cytometric analysis of the percentage of luciferase+ cells using mouse anti-firefly luciferase antibodies (Novus Biotechnology, #NB600-307ss) (Supplementary Figure 1).

Techniques: Activity Assay, Luciferase, Transfection, Construct, Positive Control, Staining, Comparison

FIGURE 4 | The pro-oxidant activity of p66Shc inhibits NF-kB activity in MEC-1 cells. (A) Immunoblot analysis with anti-Shc antibodies of postnuclear supernatants of MEC-1 cells stably transfected with empty vector (ctr) or with a vector encoding either wild-type (p66) or mutated (p66QQ) p66Shc. The stripped filters were reprobed with anti-actin antibodies. Molecular weights (kDa) are indicated on the left of the panel. The quantification of three independent experiments is shown on the right. (B) Flow cytometric analysis of ROS intracellular content in MEC-1 transfectants stained with CM-H2DCFDA (n independent experiments = 3). (C) Quantification of the luciferase activity in MEC-1 stable transfectants transiently transfected with the NF-kB-luciferase reporter construct and then treated for 6 h with either DMSO, or 100 mM H2O2 or A23187+PMA. Data are expressed as relative luciferase units (RLU) (n independent experiments = 4). (D, E) Immunoblot (D) and flow cytometric (E) analysis of phospho-NF-kB (Ser536) in MEC-1 transfectants, transiently transfected with the NF-kB-luciferase reporter construct and then treated for 30 min as above. The stripped filters were reprobed with anti-actin antibodies. Molecular weights (kDa) are indicated on the left of the panel. [(D) n independent experiments = 3; (E) n independent experiments = 4]. (F) Quantitative RT-PCR analysis of CCR2, CXCR3 and CCR7 mRNA in MEC-1 cells transfected and treated as in (C) The relative gene transcript abundance was determined on triplicate samples using the ddCt method and normalized to HPRT1 (n independent experiments = 4). Mean ± SD. C-F. Anova two-way test, Multiple Comparison. (A, B). Mann Whitney Rank Sum Test. p ≤0.0001, ****; p ≤0.001, ***; p ≤0.01, **; p ≤0.05, *.

Journal: Frontiers in oncology

Article Title: p66Shc Deficiency in Chronic Lymphocytic Leukemia Promotes Chemokine Receptor Expression Through the ROS-Dependent Inhibition of NF-κB.

doi: 10.3389/fonc.2022.877495

Figure Lengend Snippet: FIGURE 4 | The pro-oxidant activity of p66Shc inhibits NF-kB activity in MEC-1 cells. (A) Immunoblot analysis with anti-Shc antibodies of postnuclear supernatants of MEC-1 cells stably transfected with empty vector (ctr) or with a vector encoding either wild-type (p66) or mutated (p66QQ) p66Shc. The stripped filters were reprobed with anti-actin antibodies. Molecular weights (kDa) are indicated on the left of the panel. The quantification of three independent experiments is shown on the right. (B) Flow cytometric analysis of ROS intracellular content in MEC-1 transfectants stained with CM-H2DCFDA (n independent experiments = 3). (C) Quantification of the luciferase activity in MEC-1 stable transfectants transiently transfected with the NF-kB-luciferase reporter construct and then treated for 6 h with either DMSO, or 100 mM H2O2 or A23187+PMA. Data are expressed as relative luciferase units (RLU) (n independent experiments = 4). (D, E) Immunoblot (D) and flow cytometric (E) analysis of phospho-NF-kB (Ser536) in MEC-1 transfectants, transiently transfected with the NF-kB-luciferase reporter construct and then treated for 30 min as above. The stripped filters were reprobed with anti-actin antibodies. Molecular weights (kDa) are indicated on the left of the panel. [(D) n independent experiments = 3; (E) n independent experiments = 4]. (F) Quantitative RT-PCR analysis of CCR2, CXCR3 and CCR7 mRNA in MEC-1 cells transfected and treated as in (C) The relative gene transcript abundance was determined on triplicate samples using the ddCt method and normalized to HPRT1 (n independent experiments = 4). Mean ± SD. C-F. Anova two-way test, Multiple Comparison. (A, B). Mann Whitney Rank Sum Test. p ≤0.0001, ****; p ≤0.001, ***; p ≤0.01, **; p ≤0.05, *.

Article Snippet: The transfection efficiency of the NF-kBluciferase reporter and p66Shc-encoding vectors was assessed by qRT-PCR of p66Shc and flow cytometric analysis of the percentage of luciferase+ cells using mouse anti-firefly luciferase antibodies (Novus Biotechnology, #NB600-307ss) (Supplementary Figure 1).

Techniques: Activity Assay, Western Blot, Stable Transfection, Transfection, Plasmid Preparation, Staining, Luciferase, Construct, Quantitative RT-PCR, Comparison, MANN-WHITNEY

FIGURE 5 | p66Shc normalization inhibits NF-kB activity in CLL cells. (A) Quantitative RT-PCR analysis of CCR2, CXCR3 and CCR7 mRNA in B lymphocytes purified from peripheral blood of CLL patients (CLL; n CLL patients = 5) treated for 24 h with either 1 mM IT-901 or 100 mM H2O2. The relative gene transcript abundance was determined on triplicate samples using the ddCt method and normalized to HPRT1. (B, C) Flow cytometric (B) and immunoblot (C) analysis of phospho-NF-kB (Ser536) in B lymphocytes purified from peripheral blood of CLL patients (CLL) and then treated as above [(B) n CLL patients = 5; (C) n CLL patients = 3). (D)] Quantification of the luciferase activity in B lymphocytes purified from peripheral blood of CLL patients (CLL; n CLL patients = 4) transiently transfected with the NF-kB-luciferase reporter in combination with empty vector (vect) or a vector encoding either wild-type (p66) or mutated (p66QQ) p66Shc. 16 h after transfection cells were treated with either DMSO, or 100 mM H2O2 or A23187+PMA. Data are expressed as relative luciferase units (RLU). (E, F) Immunoblot (E) and flow cytometric (F) analysis of phospho-NF-kB (Ser536) in B lymphocytes purified from peripheral blood of CLL patients (CLL); then transfected as in D and treated for 30 min with either DMSO, or 100 mM H2O2 or A23187+PMA [(E) n CLL patients = 4; (F): n CLL patients = 4]. (G) Quantitative RT-PCR analysis of CCR2, CXCR3 and CCR7 mRNA in B lymphocytes purified from peripheral blood of CLL patients (CLL; n CLL patients = 4), transfected and treated as in (C) The relative gene transcript abundance was determined on triplicate samples using the ddCt method and normalized to HPRT1. Mean ± SD. D-F. Anova two-way test, Multiple Comparison. (A, B). Mann Whitney Rank Sum Test. (C) One-sample Wilcoxon test. p ≤0.0001, ****; p ≤0.001, ***; p ≤0.01, **; p ≤0.05, *.

Journal: Frontiers in oncology

Article Title: p66Shc Deficiency in Chronic Lymphocytic Leukemia Promotes Chemokine Receptor Expression Through the ROS-Dependent Inhibition of NF-κB.

doi: 10.3389/fonc.2022.877495

Figure Lengend Snippet: FIGURE 5 | p66Shc normalization inhibits NF-kB activity in CLL cells. (A) Quantitative RT-PCR analysis of CCR2, CXCR3 and CCR7 mRNA in B lymphocytes purified from peripheral blood of CLL patients (CLL; n CLL patients = 5) treated for 24 h with either 1 mM IT-901 or 100 mM H2O2. The relative gene transcript abundance was determined on triplicate samples using the ddCt method and normalized to HPRT1. (B, C) Flow cytometric (B) and immunoblot (C) analysis of phospho-NF-kB (Ser536) in B lymphocytes purified from peripheral blood of CLL patients (CLL) and then treated as above [(B) n CLL patients = 5; (C) n CLL patients = 3). (D)] Quantification of the luciferase activity in B lymphocytes purified from peripheral blood of CLL patients (CLL; n CLL patients = 4) transiently transfected with the NF-kB-luciferase reporter in combination with empty vector (vect) or a vector encoding either wild-type (p66) or mutated (p66QQ) p66Shc. 16 h after transfection cells were treated with either DMSO, or 100 mM H2O2 or A23187+PMA. Data are expressed as relative luciferase units (RLU). (E, F) Immunoblot (E) and flow cytometric (F) analysis of phospho-NF-kB (Ser536) in B lymphocytes purified from peripheral blood of CLL patients (CLL); then transfected as in D and treated for 30 min with either DMSO, or 100 mM H2O2 or A23187+PMA [(E) n CLL patients = 4; (F): n CLL patients = 4]. (G) Quantitative RT-PCR analysis of CCR2, CXCR3 and CCR7 mRNA in B lymphocytes purified from peripheral blood of CLL patients (CLL; n CLL patients = 4), transfected and treated as in (C) The relative gene transcript abundance was determined on triplicate samples using the ddCt method and normalized to HPRT1. Mean ± SD. D-F. Anova two-way test, Multiple Comparison. (A, B). Mann Whitney Rank Sum Test. (C) One-sample Wilcoxon test. p ≤0.0001, ****; p ≤0.001, ***; p ≤0.01, **; p ≤0.05, *.

Article Snippet: The transfection efficiency of the NF-kBluciferase reporter and p66Shc-encoding vectors was assessed by qRT-PCR of p66Shc and flow cytometric analysis of the percentage of luciferase+ cells using mouse anti-firefly luciferase antibodies (Novus Biotechnology, #NB600-307ss) (Supplementary Figure 1).

Techniques: Activity Assay, Quantitative RT-PCR, Western Blot, Luciferase, Transfection, Plasmid Preparation, Comparison, MANN-WHITNEY

Journal: Cell Reports

Article Title: Restoration of visual function in advanced disease after transplantation of purified human pluripotent stem cell-derived cone photoreceptors

doi: 10.1016/j.celrep.2021.109022

Figure Lengend Snippet:

Article Snippet: Plasmid: L-MYC and LIN28 episonal insert (pCXLE-hUL) , , Addgene plasmid #27080.

Techniques: Virus, Recombinant, Plasmid Preparation, Software

TSS-MPRA of synthetic regulatory sequences mirrors the vast majority of endogenous initiation patterns and transcription levels. ( A ) Schematic of TSS-MPRA. Transcription activity and location of transcription initiation is determined by 5′ RNA-seq of reporter transcripts initiating within synthetic DNA inserts cloned into reporter plasmids and electroporated into cells. Histograms on the right show cumulative DNA-normalized number of sequence tags aligning to each base position of a 153-bp region surrounding the human HBE1 promoter in K562 cells. Capped reporter transcripts are drawn in purple. RT: reverse transcription primer landing site. BC: barcode sequence. ( B ) Spearman's correlation of DNA-normalized RNA levels of all inserts of two replicate episomal TSS-MPRA experiments. ( C ) Correlation between the transcriptional signal of 250 genomic DNA inserts in epi-short TSS-MPRA and csRNA-seq of the corresponding endogenous loci. TSS-MPRA inserts were chosen randomly from locations exhibiting transcription activity as measured by csRNA-seq. Spearman's correlation of TSS-MPRA and csRNA-seq transcription levels of all regulatory sequences, or of promoters (red) or enhancers (blue, outside of a ± 2-kb window of RefSeq-annotated promoters). Regions were chosen to cover a wide range of transcription levels and initiation patterns. Each dot represents the relative transcript levels observed in each assay as total normalized read counts of all transcripts aligning to each region. TSS-MPRA RNA read counts were normalized by the corresponding plasmid DNA read counts.

Journal: Nucleic Acids Research

Article Title: Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

doi: 10.1093/nar/gkad562

Figure Lengend Snippet: TSS-MPRA of synthetic regulatory sequences mirrors the vast majority of endogenous initiation patterns and transcription levels. ( A ) Schematic of TSS-MPRA. Transcription activity and location of transcription initiation is determined by 5′ RNA-seq of reporter transcripts initiating within synthetic DNA inserts cloned into reporter plasmids and electroporated into cells. Histograms on the right show cumulative DNA-normalized number of sequence tags aligning to each base position of a 153-bp region surrounding the human HBE1 promoter in K562 cells. Capped reporter transcripts are drawn in purple. RT: reverse transcription primer landing site. BC: barcode sequence. ( B ) Spearman's correlation of DNA-normalized RNA levels of all inserts of two replicate episomal TSS-MPRA experiments. ( C ) Correlation between the transcriptional signal of 250 genomic DNA inserts in epi-short TSS-MPRA and csRNA-seq of the corresponding endogenous loci. TSS-MPRA inserts were chosen randomly from locations exhibiting transcription activity as measured by csRNA-seq. Spearman's correlation of TSS-MPRA and csRNA-seq transcription levels of all regulatory sequences, or of promoters (red) or enhancers (blue, outside of a ± 2-kb window of RefSeq-annotated promoters). Regions were chosen to cover a wide range of transcription levels and initiation patterns. Each dot represents the relative transcript levels observed in each assay as total normalized read counts of all transcripts aligning to each region. TSS-MPRA RNA read counts were normalized by the corresponding plasmid DNA read counts.

Article Snippet: The episomal TSS-MPRA plasmid is based on the background-reduced pGL4.10 luciferase reporter plasmid (Promega).

Techniques: Activity Assay, RNA Sequencing Assay, Clone Assay, Sequencing, Reverse Transcription, Plasmid Preparation

TSS-MPRA fidelity correlates with genomic TSS pattern width, transcription level, and presence of core promoter elements. ( A ) Schematic of the outlier detection model used to determine whether two TSS distributions are similar or not. Higher WIP scores (see methods for derivation) are indicative of more dissimilar initiation patterns. ( B ) TSS-MPRA preferentially recapitulates focused initiation patterns. Focus ratios (y-axis) of TSS-MPRA initiation patterns that are similar (blue) or dissimilar (red) to the corresponding endogenous initiation patterns as measured by csRNA-seq. Focus ratios of 0 indicate fully dispersed (broad) initiation patterns, while 1 indicates fully focused (sharp) patterns. ( C ) TSS-MPRA better recapitulates initiation patterns of more actively transcribed genomic regions. Endogenous locus transcription levels (csRNA-seq tag counts, y-axis) where TSS-MPRA initiation shape is similar (blue) or dissimilar (red) to the corresponding endogenous initiation pattern. ( D ) Strong transcription in the TSS-MPRA correlates with presence of TATA and Inr core promoter elements. Position-specific nucleotide frequencies (y-axis) (A: blue, C: purple, G: red, and T: orange) relative to each TSS in all TSS-MPRA inserts where: overall TSS-MPRA shapes of the inserts mirror the endogenous initiation patterns (I), or where insert TSS shapes do not mirror endogenous initiation patterns and either the respective TSSs within the overall TSS shape have 3x higher contribution to the overall signal of a given insert in TSS-MPRA data than in csRNA-seq (II), or the respective TSSs have 3× higher contribution to the overall signal of a given insert in csRNA-seq over TSS-MPRA data (III). The x-axis denotes the distance in bp from each TSS (bp 0).

Journal: Nucleic Acids Research

Article Title: Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

doi: 10.1093/nar/gkad562

Figure Lengend Snippet: TSS-MPRA fidelity correlates with genomic TSS pattern width, transcription level, and presence of core promoter elements. ( A ) Schematic of the outlier detection model used to determine whether two TSS distributions are similar or not. Higher WIP scores (see methods for derivation) are indicative of more dissimilar initiation patterns. ( B ) TSS-MPRA preferentially recapitulates focused initiation patterns. Focus ratios (y-axis) of TSS-MPRA initiation patterns that are similar (blue) or dissimilar (red) to the corresponding endogenous initiation patterns as measured by csRNA-seq. Focus ratios of 0 indicate fully dispersed (broad) initiation patterns, while 1 indicates fully focused (sharp) patterns. ( C ) TSS-MPRA better recapitulates initiation patterns of more actively transcribed genomic regions. Endogenous locus transcription levels (csRNA-seq tag counts, y-axis) where TSS-MPRA initiation shape is similar (blue) or dissimilar (red) to the corresponding endogenous initiation pattern. ( D ) Strong transcription in the TSS-MPRA correlates with presence of TATA and Inr core promoter elements. Position-specific nucleotide frequencies (y-axis) (A: blue, C: purple, G: red, and T: orange) relative to each TSS in all TSS-MPRA inserts where: overall TSS-MPRA shapes of the inserts mirror the endogenous initiation patterns (I), or where insert TSS shapes do not mirror endogenous initiation patterns and either the respective TSSs within the overall TSS shape have 3x higher contribution to the overall signal of a given insert in TSS-MPRA data than in csRNA-seq (II), or the respective TSSs have 3× higher contribution to the overall signal of a given insert in csRNA-seq over TSS-MPRA data (III). The x-axis denotes the distance in bp from each TSS (bp 0).

Article Snippet: The episomal TSS-MPRA plasmid is based on the background-reduced pGL4.10 luciferase reporter plasmid (Promega).

Techniques:

Longer inserts initiate transcription at additional non-endogenous TSSs and decrease overall TSS-MPRA transcription initiation fidelity. ( A ) Non-native TSS use in epi-long TSS-MPRA. Frequency of TSS usage between csRNA-seq (top), short TSS-MPRA (middle), and long TSS-MPRA (bottom). The y-axis, TSS usage frequency, is defined as the oligo position-specific cumulative normalized initiation frequencies in TSS-MPRA and csRNA-seq across all native TSS-MPRA inserts and corresponding genomic regions. At the top a schematic representation of the insert-containing oligos: overhang cloning sequence, followed by genomic DNA insert, 11-mer barcode and second overhang cloning sequence. The box and dots in blue marked ‘CORE’ are the positions covered by the 153-bp insert of the epi-short pool. ( B ) Increased insert length increases enhancer but not promoter transcription correlation between TSS-MPRA and csRNA-seq. Spearman's correlation of epi-long TSS-MPRA and csRNA-seq levels between all (purple) 250 regulatory sequences selected to cover a wide range of transcription levels and initiation patterns, or of only enhancers (blue), or only promoters (red). ( C ) Increased correlation of CORE (153-bp region) initiation frequencies within longer inserts of enhancers but not promoters. This analysis is restricted to the 153-bp region marked ‘CORE’ in (A). Color scheme as in (B).

Journal: Nucleic Acids Research

Article Title: Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

doi: 10.1093/nar/gkad562

Figure Lengend Snippet: Longer inserts initiate transcription at additional non-endogenous TSSs and decrease overall TSS-MPRA transcription initiation fidelity. ( A ) Non-native TSS use in epi-long TSS-MPRA. Frequency of TSS usage between csRNA-seq (top), short TSS-MPRA (middle), and long TSS-MPRA (bottom). The y-axis, TSS usage frequency, is defined as the oligo position-specific cumulative normalized initiation frequencies in TSS-MPRA and csRNA-seq across all native TSS-MPRA inserts and corresponding genomic regions. At the top a schematic representation of the insert-containing oligos: overhang cloning sequence, followed by genomic DNA insert, 11-mer barcode and second overhang cloning sequence. The box and dots in blue marked ‘CORE’ are the positions covered by the 153-bp insert of the epi-short pool. ( B ) Increased insert length increases enhancer but not promoter transcription correlation between TSS-MPRA and csRNA-seq. Spearman's correlation of epi-long TSS-MPRA and csRNA-seq levels between all (purple) 250 regulatory sequences selected to cover a wide range of transcription levels and initiation patterns, or of only enhancers (blue), or only promoters (red). ( C ) Increased correlation of CORE (153-bp region) initiation frequencies within longer inserts of enhancers but not promoters. This analysis is restricted to the 153-bp region marked ‘CORE’ in (A). Color scheme as in (B).

Article Snippet: The episomal TSS-MPRA plasmid is based on the background-reduced pGL4.10 luciferase reporter plasmid (Promega).

Techniques: Clone Assay, Sequencing

Reporter chromatinization has negligible effect on transcription initiation patterns and lowers correlation between TSS-MPRA and csRNA-seq transcription levels. ( A ) Schematic of genomic integration of a synthetic insert using lentiviral integration. ( B ) High reproducibility of Lenti-TSS-MPRA. Spearman's correlation of RNA/DNA normalized levels between all the inserts of two replicate lentiviral TSS-MPRA experiments. ( C ) High reproducibility in TSS profile changes between episomal and lentiviral TSS-MPRA experiments. WIP scores between csRNA-seq and lentiviral TSS-MPRA on the y-axis are highly correlated with the WIP scores between csRNA-seq and episomal TSS-MPRA on the x-axis. Dots are colored by how dissimilar insert TSS profiles are between lentiviral and episomal TSS-MPRA experiments. Higher WIP scores represent greater dissimilarity. ( D ) Spearman's correlation of lenti-short Lenti-TSS-MPRA and csRNA-seq levels between all 250 randomly selected regulatory sequences covering a wide range of transcription levels and initiation patterns (purple), only enhancers (blue), or only promoters (red). ( E ) Spearman's correlation of lenti-long Lenti-TSS-MPRA and csRNA-seq levels between all 250 randomly selected regulatory sequences covering a wide range of transcription levels and initiation patterns (purple), only enhancers (blue) or only promoters (red). ( F ) Spearman's correlation of lenti-long Lenti-TSS-MPRA and csRNA-seq levels between all 250 randomly selected regulatory sequences covering a wide range of transcription levels and initiation patterns (purple), only enhancers (blue), or only promoters (red). This analysis is restricted to the 153-bp region marked ‘CORE’ in Figure .

Journal: Nucleic Acids Research

Article Title: Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

doi: 10.1093/nar/gkad562

Figure Lengend Snippet: Reporter chromatinization has negligible effect on transcription initiation patterns and lowers correlation between TSS-MPRA and csRNA-seq transcription levels. ( A ) Schematic of genomic integration of a synthetic insert using lentiviral integration. ( B ) High reproducibility of Lenti-TSS-MPRA. Spearman's correlation of RNA/DNA normalized levels between all the inserts of two replicate lentiviral TSS-MPRA experiments. ( C ) High reproducibility in TSS profile changes between episomal and lentiviral TSS-MPRA experiments. WIP scores between csRNA-seq and lentiviral TSS-MPRA on the y-axis are highly correlated with the WIP scores between csRNA-seq and episomal TSS-MPRA on the x-axis. Dots are colored by how dissimilar insert TSS profiles are between lentiviral and episomal TSS-MPRA experiments. Higher WIP scores represent greater dissimilarity. ( D ) Spearman's correlation of lenti-short Lenti-TSS-MPRA and csRNA-seq levels between all 250 randomly selected regulatory sequences covering a wide range of transcription levels and initiation patterns (purple), only enhancers (blue), or only promoters (red). ( E ) Spearman's correlation of lenti-long Lenti-TSS-MPRA and csRNA-seq levels between all 250 randomly selected regulatory sequences covering a wide range of transcription levels and initiation patterns (purple), only enhancers (blue) or only promoters (red). ( F ) Spearman's correlation of lenti-long Lenti-TSS-MPRA and csRNA-seq levels between all 250 randomly selected regulatory sequences covering a wide range of transcription levels and initiation patterns (purple), only enhancers (blue), or only promoters (red). This analysis is restricted to the 153-bp region marked ‘CORE’ in Figure .

Article Snippet: The episomal TSS-MPRA plasmid is based on the background-reduced pGL4.10 luciferase reporter plasmid (Promega).

Techniques:

TSS-MPRA enables studying the effect of motif mutations on reporter-driven initiation patterns and transcription levels. ( A ) Tracking transcription initiation changes caused by mutations in transcription factor and core promoter element motifs in episomal plasmids. Scatterplot comparing the changes in initiation patterns (WIP score, y-axis) and transcription levels (fold change, x-axis) between control and mutated inserts in episomal plasmids. Red dots signify inserts with significantly changed TSS shapes after mutation. ( B ) TSS shape changes after motif mutation in episomal constructs. The y-axis represents the mean WIP score between all inserts (and their barcode replicates) containing a particular motif and the corresponding insert with the mutated motif. Colors correspond to motif identities. ( C ) Transcription level changes associated with motif mutation in episomal constructs. The y-axis represents the mean fold transcription change of the inserts (and their barcode replicates) containing a particular wild-type or mutated motif (x-axis). ( D ) Tracking transcription initiation changes caused by transcription factor and core promoter element motif mutations after lentiviral integration into the genome. Scatterplot comparing the changes in initiation patterns (WIP score, y-axis) and transcription levels (fold change, x-axis) between control and mutated inserts in lentiviral plasmids. Red dots signify inserts with significantly changed TSS shapes after mutation. ( E ) TSS shape changes after motif mutation in lentiviral constructs. The y-axis represents the mean WIP score between all inserts (and their barcode replicates) containing a particular motif and the corresponding insert with the mutated motif. Colors correspond to motif identities. ( F ) Transcription level changes associated with motif mutation in lentiviral constructs. The y-axis represents the mean fold transcription change of the inserts (and their barcode replicates) containing a particular wild-type or mutated motif (x-axis). ( G ) Example track for the ACTB promoter, showing csRNA-seq (top), TSS-MPRA, and Lenti-TSS-MPRA output without (black) and with (red) TATA-box motif mutation. Blue highlights indicate the positions where motifs were replaced by a constant sequence with no known transcription factor motif. ( H ) Example track for the ENO1 promoter, showing csRNA-seq (top), TSS-MPRA, and Lenti-TSS-MPRA output before (black) and after (red) PU.1 motif mutation. Blue highlights indicate the positions where motifs were replaced.

Journal: Nucleic Acids Research

Article Title: Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

doi: 10.1093/nar/gkad562

Figure Lengend Snippet: TSS-MPRA enables studying the effect of motif mutations on reporter-driven initiation patterns and transcription levels. ( A ) Tracking transcription initiation changes caused by mutations in transcription factor and core promoter element motifs in episomal plasmids. Scatterplot comparing the changes in initiation patterns (WIP score, y-axis) and transcription levels (fold change, x-axis) between control and mutated inserts in episomal plasmids. Red dots signify inserts with significantly changed TSS shapes after mutation. ( B ) TSS shape changes after motif mutation in episomal constructs. The y-axis represents the mean WIP score between all inserts (and their barcode replicates) containing a particular motif and the corresponding insert with the mutated motif. Colors correspond to motif identities. ( C ) Transcription level changes associated with motif mutation in episomal constructs. The y-axis represents the mean fold transcription change of the inserts (and their barcode replicates) containing a particular wild-type or mutated motif (x-axis). ( D ) Tracking transcription initiation changes caused by transcription factor and core promoter element motif mutations after lentiviral integration into the genome. Scatterplot comparing the changes in initiation patterns (WIP score, y-axis) and transcription levels (fold change, x-axis) between control and mutated inserts in lentiviral plasmids. Red dots signify inserts with significantly changed TSS shapes after mutation. ( E ) TSS shape changes after motif mutation in lentiviral constructs. The y-axis represents the mean WIP score between all inserts (and their barcode replicates) containing a particular motif and the corresponding insert with the mutated motif. Colors correspond to motif identities. ( F ) Transcription level changes associated with motif mutation in lentiviral constructs. The y-axis represents the mean fold transcription change of the inserts (and their barcode replicates) containing a particular wild-type or mutated motif (x-axis). ( G ) Example track for the ACTB promoter, showing csRNA-seq (top), TSS-MPRA, and Lenti-TSS-MPRA output without (black) and with (red) TATA-box motif mutation. Blue highlights indicate the positions where motifs were replaced by a constant sequence with no known transcription factor motif. ( H ) Example track for the ENO1 promoter, showing csRNA-seq (top), TSS-MPRA, and Lenti-TSS-MPRA output before (black) and after (red) PU.1 motif mutation. Blue highlights indicate the positions where motifs were replaced.

Article Snippet: The episomal TSS-MPRA plasmid is based on the background-reduced pGL4.10 luciferase reporter plasmid (Promega).

Techniques: Control, Mutagenesis, Construct, Sequencing

Assessing the effects of single nucleotide polymorphisms on reporter-driven initiation patterns and transcription levels. ( A ) Allele-specific transcription initiation differences caused by known GWAS SNPs in episomal plasmids. Scatterplot comparing the changes in initiation patterns (y-axis) and transcription fold change (x-axis) between control and variant inserts in episomal constructs. Red dots signify inserts that had significant changes to their TSS shapes. ( B ) Allele-specific transcription initiation differences caused by known GWAS SNPs in lentiviral constructs. Scatterplot comparing the changes in initiation patterns (y-axis) and transcription fold change (x-axis) between control and variant inserts in lentivirally integrated constructs. Red dots signify inserts that had significant changes to their TSS shapes. ( C ) SNP rs1991401 is associated with TSS shape changes. Track showing csRNA-seq (top), TSS-MPRA, and Lenti-TSS-MPRA output of the T (black) and G (red) allele. A blue ‘^’ symbol indicates the location of the SNP. ( D ) TSS shape differences associated with SNP rs131804. Track showing csRNA-seq (top), TSS-MPRA, and Lenti-TSS-MPRA output of the C (black) and A (red) allele. A blue ‘^’ symbol marks the SNP location.

Journal: Nucleic Acids Research

Article Title: Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

doi: 10.1093/nar/gkad562

Figure Lengend Snippet: Assessing the effects of single nucleotide polymorphisms on reporter-driven initiation patterns and transcription levels. ( A ) Allele-specific transcription initiation differences caused by known GWAS SNPs in episomal plasmids. Scatterplot comparing the changes in initiation patterns (y-axis) and transcription fold change (x-axis) between control and variant inserts in episomal constructs. Red dots signify inserts that had significant changes to their TSS shapes. ( B ) Allele-specific transcription initiation differences caused by known GWAS SNPs in lentiviral constructs. Scatterplot comparing the changes in initiation patterns (y-axis) and transcription fold change (x-axis) between control and variant inserts in lentivirally integrated constructs. Red dots signify inserts that had significant changes to their TSS shapes. ( C ) SNP rs1991401 is associated with TSS shape changes. Track showing csRNA-seq (top), TSS-MPRA, and Lenti-TSS-MPRA output of the T (black) and G (red) allele. A blue ‘^’ symbol indicates the location of the SNP. ( D ) TSS shape differences associated with SNP rs131804. Track showing csRNA-seq (top), TSS-MPRA, and Lenti-TSS-MPRA output of the C (black) and A (red) allele. A blue ‘^’ symbol marks the SNP location.

Article Snippet: The episomal TSS-MPRA plasmid is based on the background-reduced pGL4.10 luciferase reporter plasmid (Promega).

Techniques: Control, Variant Assay, Construct