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Bethyl nipbl
Nipbl, supplied by Bethyl, used in various techniques. Bioz Stars score: 94/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/nipbl/pm41826481-316-37-39?v=Bethyl
Average 94 stars, based on 62 article reviews

nipbl - by Bioz Stars, 2026-06

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A – D Quantification of MAU2 and NIPBL transcript levels by qPCR. In all panels, data from four unrelated healthy controls are represented in gray, samples harboring the frameshift variant p.(Gln135Argfs*32) are shown in red, and Individual 1 with the in-frame variant known to disrupt NIPBL interaction (p.(Gln310_Ala316del)) is shown in blue. Six independent experiments were performed, with two technical replicates for each of the three RNA preparations. Technical replicates were averaged to yield one value per biological replicate, which was used for statistical comparisons (two-sided Mann–Whitney U test followed by Bonferroni Correction for multiple comparisons, * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001). P -values are indicated above the corresponding box plot. Box plot elements are defined as follows: center line: median; box limits: upper and lower quartiles; whiskers: 1.5× interquartile range. (A) MAU2 transcript levels normalized to NADH . B MAU2 transcript levels normalized to SNAPIN . C NIPBL transcript levels normalized to NADH . D NIPBL transcript levels normalized to SNAPIN . E Assessment of MAU2 and NIPBL protein levels by Western Blot. Protein levels were assessed in two healthy controls (Ctrl 1 and Ctrl 2), Individual 14 and her father ( MAU2 frameshift variant), and in Individual 1 ( MAU2 in-frame deletion). The membranes were cut to allow all three proteins (NIPBL, MAU2, and the loading control Actinin) to be visualized from a single blot. This blot is representative of three independent experiments with similar results. Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: Pathogenic variants in the cohesin loader subunit MAU2 underlie a distinct Cornelia de Lange Syndrome subtype

doi: 10.1038/s41467-026-71177-6

Figure Lengend Snippet: A – D Quantification of MAU2 and NIPBL transcript levels by qPCR. In all panels, data from four unrelated healthy controls are represented in gray, samples harboring the frameshift variant p.(Gln135Argfs*32) are shown in red, and Individual 1 with the in-frame variant known to disrupt NIPBL interaction (p.(Gln310_Ala316del)) is shown in blue. Six independent experiments were performed, with two technical replicates for each of the three RNA preparations. Technical replicates were averaged to yield one value per biological replicate, which was used for statistical comparisons (two-sided Mann–Whitney U test followed by Bonferroni Correction for multiple comparisons, * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001). P -values are indicated above the corresponding box plot. Box plot elements are defined as follows: center line: median; box limits: upper and lower quartiles; whiskers: 1.5× interquartile range. (A) MAU2 transcript levels normalized to NADH . B MAU2 transcript levels normalized to SNAPIN . C NIPBL transcript levels normalized to NADH . D NIPBL transcript levels normalized to SNAPIN . E Assessment of MAU2 and NIPBL protein levels by Western Blot. Protein levels were assessed in two healthy controls (Ctrl 1 and Ctrl 2), Individual 14 and her father ( MAU2 frameshift variant), and in Individual 1 ( MAU2 in-frame deletion). The membranes were cut to allow all three proteins (NIPBL, MAU2, and the loading control Actinin) to be visualized from a single blot. This blot is representative of three independent experiments with similar results. Source data are provided as a Source Data file.

Article Snippet: The following TaqMan gene expression assays were used for the analysis: Hs01062386_m1 (for the MAU2 transcript) and Hs00209846_m1 (for the NIPBL transcript) (Thermo Fisher Scientific).

Techniques: Variant Assay, MANN-WHITNEY, Western Blot, Control

a Heatmaps showing changes induced after NIPBL knockdown (KD) for RAD21 and NIPBL at downregulated RAD21 peaks. These peaks are divided into four distinct classes, which are promoters (TSS), enhancers (Enh), CTCF sites at loop anchors (CL), and CTCF sites outside loop anchors (CnL, Supplementary Fig. ) from top to bottom. ChIP-Seq signals within ±1 kb region surrounding transcription start sites (TSSs) or peak summits are plotted. RPMPB: reads per million per 50 bp bin. Ctrl: control hESCs transfected with negative control siRNA; si-N: hESCs transfected with siRNA targeting NIPBL. b Average profiles of ChIP-seq signals for RAD21, NIPBL, CTCF, H3K27ac, centered on the same set of genomic anchors as in ( a ). Anchors are categorized into three classes: transcription start sites (TSS), enhancers (Enh), and CTCF sites at chromatin loop anchors (CL). Meta-analysis quantifying changes in cohesin subunits SA1 and SA2 after NIPBL KD. For SA1 and A2, analysis was focused on TSS, Enh, and CL sites, which were first ranked by their baseline SA2 ChIP-seq signal intensity in control cells. The plots display the change in SA1 and SA2 levels specifically for the top quintile (20%) of sites with the highest initial SA2 binding. Lines and shaded regions represent the mean signal and the 95% confidence interval, respectively. c Example of SIP loops lost, stable, and gained in si-NIPBL with respect to Ctrl hESCs. Blue squares: lost loops; green: gained; black: stable. Green arrows point to the smaller loop located between a pair of tandem CTCF sites, which is lost when RAD21 and SA1 levels are maintained at anchors. Blue arrows indicate the larger loop located between a pair of convergent CTCF sites in the same region, which is also lost upon NIPBL KD. Blue and yellow shading is used to highlight loop anchors formed by forward and reverse pairs of CTCF motifs, respectively. The distribution of input normalized ChIP-Seq signals of several proteins in the same region in both cells is shown. Above the CTCF ChIP-seq track, red and green arrowheads indicate the orientation of individual CTCF motifs. On the NIPBL ChIP-seq track, black and blue arrows mark stable and gained NIPBL binding events, respectively. On the WAPL ChIP-seq track, black and gold asterisks denote stable and decreased WAPL occupancy, respectively. Reference genome: hg38. d Aggregate peak analysis (APA) of Hi-C data obtained in ctrl and si-NIPBL hESCs at lost, stable, and gained SIP loops. Each square represents the aggregate of the signals present in all corner dots corresponding to loops detected by SIP in either condition (see “Methods”) and the surrounding 100 kb regions up- and down-stream. Top row: lost loops, middle row: stable loops, bottom row: gained loops. Subtraction of APA metaplots of si-NIPBL minus Ctrl is shown in the last column of each row. e APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at SIP loops containing promoters or enhancers at neither, one, or both anchors. E enhancers, P promoters. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), NIPBL ChIP-seq ( n = 3), ChIP-seq for other proteins ( n = 2).

Journal: Communications Biology

Article Title: Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse

doi: 10.1038/s42003-026-09838-x

Figure Lengend Snippet: a Heatmaps showing changes induced after NIPBL knockdown (KD) for RAD21 and NIPBL at downregulated RAD21 peaks. These peaks are divided into four distinct classes, which are promoters (TSS), enhancers (Enh), CTCF sites at loop anchors (CL), and CTCF sites outside loop anchors (CnL, Supplementary Fig. ) from top to bottom. ChIP-Seq signals within ±1 kb region surrounding transcription start sites (TSSs) or peak summits are plotted. RPMPB: reads per million per 50 bp bin. Ctrl: control hESCs transfected with negative control siRNA; si-N: hESCs transfected with siRNA targeting NIPBL. b Average profiles of ChIP-seq signals for RAD21, NIPBL, CTCF, H3K27ac, centered on the same set of genomic anchors as in ( a ). Anchors are categorized into three classes: transcription start sites (TSS), enhancers (Enh), and CTCF sites at chromatin loop anchors (CL). Meta-analysis quantifying changes in cohesin subunits SA1 and SA2 after NIPBL KD. For SA1 and A2, analysis was focused on TSS, Enh, and CL sites, which were first ranked by their baseline SA2 ChIP-seq signal intensity in control cells. The plots display the change in SA1 and SA2 levels specifically for the top quintile (20%) of sites with the highest initial SA2 binding. Lines and shaded regions represent the mean signal and the 95% confidence interval, respectively. c Example of SIP loops lost, stable, and gained in si-NIPBL with respect to Ctrl hESCs. Blue squares: lost loops; green: gained; black: stable. Green arrows point to the smaller loop located between a pair of tandem CTCF sites, which is lost when RAD21 and SA1 levels are maintained at anchors. Blue arrows indicate the larger loop located between a pair of convergent CTCF sites in the same region, which is also lost upon NIPBL KD. Blue and yellow shading is used to highlight loop anchors formed by forward and reverse pairs of CTCF motifs, respectively. The distribution of input normalized ChIP-Seq signals of several proteins in the same region in both cells is shown. Above the CTCF ChIP-seq track, red and green arrowheads indicate the orientation of individual CTCF motifs. On the NIPBL ChIP-seq track, black and blue arrows mark stable and gained NIPBL binding events, respectively. On the WAPL ChIP-seq track, black and gold asterisks denote stable and decreased WAPL occupancy, respectively. Reference genome: hg38. d Aggregate peak analysis (APA) of Hi-C data obtained in ctrl and si-NIPBL hESCs at lost, stable, and gained SIP loops. Each square represents the aggregate of the signals present in all corner dots corresponding to loops detected by SIP in either condition (see “Methods”) and the surrounding 100 kb regions up- and down-stream. Top row: lost loops, middle row: stable loops, bottom row: gained loops. Subtraction of APA metaplots of si-NIPBL minus Ctrl is shown in the last column of each row. e APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at SIP loops containing promoters or enhancers at neither, one, or both anchors. E enhancers, P promoters. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), NIPBL ChIP-seq ( n = 3), ChIP-seq for other proteins ( n = 2).

Article Snippet: For hESCs undergoing NIPBL transfection, 10 mM UNC3866 (MedChemExpress, HY-100832) is added to the culture medium the day before transfection to achieve a final working concentration of 40 μM.

Techniques: Knockdown, ChIP-sequencing, Control, Transfection, Negative Control, Binding Assay, Hi-C

a Diagram showing distinct enhancer-promoter (E-P) loops containing CTCF at neither, one or both anchors. APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at these loops. Subtraction of APA metaplots is listed in the last column of each row. b Average profiles of ChIP-seq signals of RAD21, SA1, and H3K27ac at the scaled regions ± 50% of their sizes between loop anchors in ( a ). E enhancers, P promoters. Left column: E/P loops containing CTCF at both anchors; right column: E/P loops lacking CTCF at both anchors. c , d Diagrams showing promoter (P-P) loops ( c ) and enhancer (E-E) loops ( d ) containing stable levels of RAD21 at both anchors after NIPBL KD. APA metaplots of Hi-C and RAD21 HiChIP data obtained in ctrl and si-NIPBL hESCs at these P-P loops ( c ) and E-E loops ( d ). Subtraction of APA metaplots is listed in the last column of each row. e Average profiles of ChIP-seq signals of CTCF, RAD21, H3K27ac, RNF2, and H3K27me3 at the scaled regions ± 50% of their sizes between loop anchors in ( c ) and ( d ). Lines and shaded regions represent the mean signal and the 95% confidence interval, respectively. f , g APA metaplots of Pol II and H3K4me1 HiChIP data obtained in ctrl and si-NIPBL hESCs at these P-P loops ( f ) and E-E loops ( g ). Subtraction of APA metaplots is listed in the last column of each row. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), HiChIP ( n = 2), ChIP-seq ( n = 2).

Journal: Communications Biology

Article Title: Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse

doi: 10.1038/s42003-026-09838-x

Figure Lengend Snippet: a Diagram showing distinct enhancer-promoter (E-P) loops containing CTCF at neither, one or both anchors. APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at these loops. Subtraction of APA metaplots is listed in the last column of each row. b Average profiles of ChIP-seq signals of RAD21, SA1, and H3K27ac at the scaled regions ± 50% of their sizes between loop anchors in ( a ). E enhancers, P promoters. Left column: E/P loops containing CTCF at both anchors; right column: E/P loops lacking CTCF at both anchors. c , d Diagrams showing promoter (P-P) loops ( c ) and enhancer (E-E) loops ( d ) containing stable levels of RAD21 at both anchors after NIPBL KD. APA metaplots of Hi-C and RAD21 HiChIP data obtained in ctrl and si-NIPBL hESCs at these P-P loops ( c ) and E-E loops ( d ). Subtraction of APA metaplots is listed in the last column of each row. e Average profiles of ChIP-seq signals of CTCF, RAD21, H3K27ac, RNF2, and H3K27me3 at the scaled regions ± 50% of their sizes between loop anchors in ( c ) and ( d ). Lines and shaded regions represent the mean signal and the 95% confidence interval, respectively. f , g APA metaplots of Pol II and H3K4me1 HiChIP data obtained in ctrl and si-NIPBL hESCs at these P-P loops ( f ) and E-E loops ( g ). Subtraction of APA metaplots is listed in the last column of each row. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), HiChIP ( n = 2), ChIP-seq ( n = 2).

Techniques: Hi-C, ChIP-sequencing, HiChIP

a Diagram describing CTCF loops at different sizes. APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at SIP loops of distinct sizes. Subtraction of APA metaplots is listed in the last row of each column. b Diagram depicting CTCF loops anchoring at lost and stable RAD21 peaks upon NIPBL KD. APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at these CTCF loops. Subtraction of APA metaplots is listed in the last row of each column. c Average profiles of ChIP-seq signals of CTCF, SA1, RAD21 and RNF2 at the scaled regions ± 50% of their sizes between loop anchors containing stable RAD21 peaks in ( b ) and lost RAD21 peaks in ( b ). Lines and shaded regions represent the mean signal and the 95% confidence interval, respectively. RPMPB: reads per million per 50 bp bin. d APA metaplots of RAD21 and CTCF HiChIP data obtained in ctrl and si-NIPBL hESCs at CTCF loops containing stable RAD21 peaks at both anchors upon NIPBL KD. Subtraction of APA metaplots is listed in the last row of each column. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), HiChIP ( n = 2), ChIP-seq ( n = 2).

Journal: Communications Biology

Article Title: Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse

doi: 10.1038/s42003-026-09838-x

Figure Lengend Snippet: a Diagram describing CTCF loops at different sizes. APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at SIP loops of distinct sizes. Subtraction of APA metaplots is listed in the last row of each column. b Diagram depicting CTCF loops anchoring at lost and stable RAD21 peaks upon NIPBL KD. APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at these CTCF loops. Subtraction of APA metaplots is listed in the last row of each column. c Average profiles of ChIP-seq signals of CTCF, SA1, RAD21 and RNF2 at the scaled regions ± 50% of their sizes between loop anchors containing stable RAD21 peaks in ( b ) and lost RAD21 peaks in ( b ). Lines and shaded regions represent the mean signal and the 95% confidence interval, respectively. RPMPB: reads per million per 50 bp bin. d APA metaplots of RAD21 and CTCF HiChIP data obtained in ctrl and si-NIPBL hESCs at CTCF loops containing stable RAD21 peaks at both anchors upon NIPBL KD. Subtraction of APA metaplots is listed in the last row of each column. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), HiChIP ( n = 2), ChIP-seq ( n = 2).

Techniques: Hi-C, ChIP-sequencing, HiChIP

a Heatmaps are presented with protein-specific genomic windows: ±5 kb for RAD21, ±1 kb for NIPBL, and ±50 kb for RNF2, optimized to best visualize the distribution of each factor (see “Methods”). These peaks within PRC domains (PDs) are divided into four distinct classes, which are promoters (P_PD), enhancers (E_PD), CTCF sites at loop anchors (CL_PD), and CTCF sites outside loop anchors (CnL_PD) from top to bottom. RPMPB: reads per million per 50 bp bin. b Average profiles of ChIP-seq signals of CTCF, SA1, WAPL, SA2, and H3K27ac on the same anchors as ( a ). Lines and shaded regions indicate the mean value and 95% confidence interval, respectively. TSSs transcription start sites, Enh enhancers, CL CTCF sites at loop anchors, PD PRC domains. c Example of interactions between PRC domains in si- NIPBL with respect to Ctrl hESCs. Black circles in Hi-C heatmaps highlight the interactions between three adjacent PRC domains, including HOXD gene cluster on chr2. The virtual 4C signals originating from the HOXD cluster derived by converting Hi-C data and the distribution of several proteins in the same region in both cells are also shown. Arcs represent the SIP loops. Blue shading: HOXD gene cluster as the viewpoint of virtual 4C; yellow shading: two adjacent PRC domains. Reference genome: hg38. d Diagram describing the enhanced contacts between PDs upon NIPBL KD. APA metaplots of Hi-C, RAD21, and RNF2 Hi-ChIP data obtained in ctrl and si-NIPBL hESCs among PDs. Sample sizes: Hi-C ( n = 3 biologically independent experiments), HiChIP ( n = 2). PD: PRC domains. Subtraction of APA metaplots is listed in the last column of each row. e Immunofluorescence microscopy of hESCs of Ctrl, si-NIPBL, and si-NIPBL treated with UNC3866 stained with antibodies to RNF2 (green). 4′,6-diamidino-2-phenylindole (DAPI) is indicated in blue. Red dashed circles highlighted cells are enlarged for better view on the right side of each row. White scale bars: 20 µm. Violin plots and boxplots show the mean intensities and number of PcG bodies within each nucleus for the three groups of hESCs. Boxplots within violin: median (center line), 25th–75th percentiles (box), and 1.5 × interquartile range (whiskers). P values are calculated by Wilcoxon rank-sum test. Sample sizes: Immunofluorescence ( n = 3 biologically independent experiments). f Diagram describing the promoter (P_PD), enhancer (E_PD), and CTCF (CL_PD) loops located within PDs. APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at these loops. Sample sizes: Hi-C ( n = 3 biologically independent experiments). TSSs transcription start sites, Enh enhancers, CL CTCF sites at loop anchors, PD PRC domains. Subtraction of APA metaplots is listed in the last column of each row. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), HiChIP ( n = 2), NIPBL ChIP-seq ( n = 3), ChIP-seq for other proteins ( n = 2), Immunofluorescence ( n = 3).

Journal: Communications Biology

Article Title: Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse

doi: 10.1038/s42003-026-09838-x

Figure Lengend Snippet: a Heatmaps are presented with protein-specific genomic windows: ±5 kb for RAD21, ±1 kb for NIPBL, and ±50 kb for RNF2, optimized to best visualize the distribution of each factor (see “Methods”). These peaks within PRC domains (PDs) are divided into four distinct classes, which are promoters (P_PD), enhancers (E_PD), CTCF sites at loop anchors (CL_PD), and CTCF sites outside loop anchors (CnL_PD) from top to bottom. RPMPB: reads per million per 50 bp bin. b Average profiles of ChIP-seq signals of CTCF, SA1, WAPL, SA2, and H3K27ac on the same anchors as ( a ). Lines and shaded regions indicate the mean value and 95% confidence interval, respectively. TSSs transcription start sites, Enh enhancers, CL CTCF sites at loop anchors, PD PRC domains. c Example of interactions between PRC domains in si- NIPBL with respect to Ctrl hESCs. Black circles in Hi-C heatmaps highlight the interactions between three adjacent PRC domains, including HOXD gene cluster on chr2. The virtual 4C signals originating from the HOXD cluster derived by converting Hi-C data and the distribution of several proteins in the same region in both cells are also shown. Arcs represent the SIP loops. Blue shading: HOXD gene cluster as the viewpoint of virtual 4C; yellow shading: two adjacent PRC domains. Reference genome: hg38. d Diagram describing the enhanced contacts between PDs upon NIPBL KD. APA metaplots of Hi-C, RAD21, and RNF2 Hi-ChIP data obtained in ctrl and si-NIPBL hESCs among PDs. Sample sizes: Hi-C ( n = 3 biologically independent experiments), HiChIP ( n = 2). PD: PRC domains. Subtraction of APA metaplots is listed in the last column of each row. e Immunofluorescence microscopy of hESCs of Ctrl, si-NIPBL, and si-NIPBL treated with UNC3866 stained with antibodies to RNF2 (green). 4′,6-diamidino-2-phenylindole (DAPI) is indicated in blue. Red dashed circles highlighted cells are enlarged for better view on the right side of each row. White scale bars: 20 µm. Violin plots and boxplots show the mean intensities and number of PcG bodies within each nucleus for the three groups of hESCs. Boxplots within violin: median (center line), 25th–75th percentiles (box), and 1.5 × interquartile range (whiskers). P values are calculated by Wilcoxon rank-sum test. Sample sizes: Immunofluorescence ( n = 3 biologically independent experiments). f Diagram describing the promoter (P_PD), enhancer (E_PD), and CTCF (CL_PD) loops located within PDs. APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at these loops. Sample sizes: Hi-C ( n = 3 biologically independent experiments). TSSs transcription start sites, Enh enhancers, CL CTCF sites at loop anchors, PD PRC domains. Subtraction of APA metaplots is listed in the last column of each row. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), HiChIP ( n = 2), NIPBL ChIP-seq ( n = 3), ChIP-seq for other proteins ( n = 2), Immunofluorescence ( n = 3).

Techniques: ChIP-sequencing, Hi-C, Derivative Assay, HiChIP, Immunofluorescence, Microscopy, Staining

a Heatmaps showing changes induced after NIPBL knockdown for ChIP-Seq signals of RAD21, NIPBL, and H3K27ac at lost RAD21 peaks within super enhancers (SEs) (see “Methods”). These peaks within SEs are divided into four distinct classes, which are promoters (P_SE), enhancers (E_SE), CTCF sites at loop anchors (CL_SE), and CTCF sites outside loop anchors (CnL_SE). RPMPB: reads per million per 50 bp bin. b Average profiles of ChIP-seq signals of CTCF, SA1, WAPL, SA2, and H3K27ac on the same anchors as ( a ). Lines and shaded regions indicate the mean values and 95% confidence interval, respectively. c Example of interactions between SEs in si-NIPBL with respect to Ctrl hESCs as shown in the Hi-C heatmaps. The virtual 4C signals originating from two viewpoints of SEs highlighted in blue rectangles derived by converting Hi-C data and the distribution of H3K27ac and RAD21 in the same region in both cells are also shown. The yellow rectangles highlight the SEs whose interactions are not increased upon NIPBL KD. Reference genome: hg38. d Diagrams showing contacts between SEs that are down and upregulated upon NIPBL KD. Violin and boxplots showing the distances between SEs of these two classes. Boxplots within violin: median (center line), 25th–75th percentiles (box), and 1.5 × interquartile range (whiskers). P values are calculated by Wilcoxon rank-sum test. Sample sizes: Hi-C ( n = 3 biologically independent experiments). APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at enhanced and weakened interactions between SEs upon NIPBL KD. SD: SE domain. Subtraction of APA metaplots is listed in the last row of each column. e Diagrams depicting SIP loops containing SEs at one or both anchors. Violin and boxplots showing sizes of loops of these two classes. Boxplots within violin: median (center line), 25th–75th percentiles (box), and 1.5 × interquartile range (whiskers). P values are calculated by Wilcoxon rank-sum test. Sample sizes: Hi-C ( n = 3 biologically independent experiments). APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at these two loops. Subtraction of APA metaplots is listed in the last column of each row. f Diagrams describing the changes of RAD21 at loop anchors within SDs upon NIPBL KD. Cumulative curves comparing sizes of loops containing no, stable, up, and downregulated levels of RAD21 at SEs of loop anchors. P values are calculated by Welch’s t -test. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. APA histograms of Hi-C data obtained in ctrl and si-NIPBL hESCs at these SE loops containing different levels of RAD21. Median values of APA scores are labeled as dashed black lines on histograms. non/stable/up/downR SE: SEs containing non, stable, up, and downregulated levels of RAD21. nonE/stableE/upE/downE: SEs containing non, stable, up, and downregulated levels of RAD21. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), NIPBL ChIP-seq ( n = 3), ChIP-seq for other proteins ( n = 2).

Journal: Communications Biology

Article Title: Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse

doi: 10.1038/s42003-026-09838-x

Figure Lengend Snippet: a Heatmaps showing changes induced after NIPBL knockdown for ChIP-Seq signals of RAD21, NIPBL, and H3K27ac at lost RAD21 peaks within super enhancers (SEs) (see “Methods”). These peaks within SEs are divided into four distinct classes, which are promoters (P_SE), enhancers (E_SE), CTCF sites at loop anchors (CL_SE), and CTCF sites outside loop anchors (CnL_SE). RPMPB: reads per million per 50 bp bin. b Average profiles of ChIP-seq signals of CTCF, SA1, WAPL, SA2, and H3K27ac on the same anchors as ( a ). Lines and shaded regions indicate the mean values and 95% confidence interval, respectively. c Example of interactions between SEs in si-NIPBL with respect to Ctrl hESCs as shown in the Hi-C heatmaps. The virtual 4C signals originating from two viewpoints of SEs highlighted in blue rectangles derived by converting Hi-C data and the distribution of H3K27ac and RAD21 in the same region in both cells are also shown. The yellow rectangles highlight the SEs whose interactions are not increased upon NIPBL KD. Reference genome: hg38. d Diagrams showing contacts between SEs that are down and upregulated upon NIPBL KD. Violin and boxplots showing the distances between SEs of these two classes. Boxplots within violin: median (center line), 25th–75th percentiles (box), and 1.5 × interquartile range (whiskers). P values are calculated by Wilcoxon rank-sum test. Sample sizes: Hi-C ( n = 3 biologically independent experiments). APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at enhanced and weakened interactions between SEs upon NIPBL KD. SD: SE domain. Subtraction of APA metaplots is listed in the last row of each column. e Diagrams depicting SIP loops containing SEs at one or both anchors. Violin and boxplots showing sizes of loops of these two classes. Boxplots within violin: median (center line), 25th–75th percentiles (box), and 1.5 × interquartile range (whiskers). P values are calculated by Wilcoxon rank-sum test. Sample sizes: Hi-C ( n = 3 biologically independent experiments). APA metaplots of Hi-C data obtained in ctrl and si-NIPBL hESCs at these two loops. Subtraction of APA metaplots is listed in the last column of each row. f Diagrams describing the changes of RAD21 at loop anchors within SDs upon NIPBL KD. Cumulative curves comparing sizes of loops containing no, stable, up, and downregulated levels of RAD21 at SEs of loop anchors. P values are calculated by Welch’s t -test. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. APA histograms of Hi-C data obtained in ctrl and si-NIPBL hESCs at these SE loops containing different levels of RAD21. Median values of APA scores are labeled as dashed black lines on histograms. non/stable/up/downR SE: SEs containing non, stable, up, and downregulated levels of RAD21. nonE/stableE/upE/downE: SEs containing non, stable, up, and downregulated levels of RAD21. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), NIPBL ChIP-seq ( n = 3), ChIP-seq for other proteins ( n = 2).

Techniques: Knockdown, ChIP-sequencing, Hi-C, Derivative Assay, Labeling

a Heatmaps showing changes in transcription levels of up and downregulated genes in different hESCs based on RNA-seq data. b Bubble plots showing expression of marker genes of pluripotency and three germ layers in different hESCs based on RNA-seq data. Log2FC: log2 fold change over Ctrl. Ctrl control, si-N si-NIPBL, UNC UNC3866. c Metaplot analysis of interactions between CTCF loop anchors and between enhancers and promoters located within the loop anchors. The top diagram indicates the specific scenario in which the CTCF loops encompass E-P interactions analyzed here. Changes in interactions between E-P pairs are analyzed in the context of changes of the CTCF loops inside which they are contained. The bottom panel shows median heatmaps of Hi-C interactions in Ctrl and si-NIPBL hESCs for CTCF loops that contain pairs of downregulated genes and their enhancers. The subtraction of heatmaps from both cells is also shown. Decreases of these loops in si-NIPBL hESCs (black arrowheads indicating decreased interactions at the CTCF loop anchors) correlates with decreased E-P interactions inside the loops (orange arrowheads). d Comparison of the number and sizes of lost versus gained loops upon NIPBL KD. p values of lost and gained versus stable are labeled on top-right and top-left corner respectively. e Metaplot analysis of interactions between CTCF loop anchors that are shortened following the KD of NIPBL. The top diagram illustrates the primary scenario in which Ctrl-specific CTCF loops (green arcs) are shortened by the loss of one of their old anchors (green arrowheads) after NIPBL KD, and smaller loops (purple arcs) are maintained between newly formed anchors (purple arrowheads) and the remaining old anchors. The bottom panel shows the median heatmaps of Hi-C data in both cells on the left side and a subtraction heatmap of Hi-C data comparing both cell types on the right side. f One example showing the loss of NIPBL loading site within lost CTCF loops upon NIPBL KD at SOX2 gene locus. The top panel shows the Hi-C heatmaps. The bottom panel shows the distribution of NIPBL and other proteins at this site. Green and red arrowheads indicate orientation of the CTCF motifs at this site. Black arrowheads show the location of NIPBL sites present in Ctrl but not in si-NIPBL hESCs, which contain high levels of H3K27ac. Reference genome: hg38. g Distribution of NIPBL and several other proteins at loop anchors and loading sites of CTCF loops identified from Hi-C data present in Ctrl cells but not si-NIPBL hESCs. Black arrowheads show the enrichment of NIPBL and RAD21 at cohesin loading sites, which contain high levels of H3K27ac, between CTCF loops present in Ctrl but not in si-NIPBL hESCs. RPMPB: reads per million per 50 bp bin. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), RNA-seq ( n = 2), NIPBL ChIP-seq ( n = 3), ChIP-seq for other proteins ( n = 2).

Journal: Communications Biology

Article Title: Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse

doi: 10.1038/s42003-026-09838-x

Figure Lengend Snippet: a Heatmaps showing changes in transcription levels of up and downregulated genes in different hESCs based on RNA-seq data. b Bubble plots showing expression of marker genes of pluripotency and three germ layers in different hESCs based on RNA-seq data. Log2FC: log2 fold change over Ctrl. Ctrl control, si-N si-NIPBL, UNC UNC3866. c Metaplot analysis of interactions between CTCF loop anchors and between enhancers and promoters located within the loop anchors. The top diagram indicates the specific scenario in which the CTCF loops encompass E-P interactions analyzed here. Changes in interactions between E-P pairs are analyzed in the context of changes of the CTCF loops inside which they are contained. The bottom panel shows median heatmaps of Hi-C interactions in Ctrl and si-NIPBL hESCs for CTCF loops that contain pairs of downregulated genes and their enhancers. The subtraction of heatmaps from both cells is also shown. Decreases of these loops in si-NIPBL hESCs (black arrowheads indicating decreased interactions at the CTCF loop anchors) correlates with decreased E-P interactions inside the loops (orange arrowheads). d Comparison of the number and sizes of lost versus gained loops upon NIPBL KD. p values of lost and gained versus stable are labeled on top-right and top-left corner respectively. e Metaplot analysis of interactions between CTCF loop anchors that are shortened following the KD of NIPBL. The top diagram illustrates the primary scenario in which Ctrl-specific CTCF loops (green arcs) are shortened by the loss of one of their old anchors (green arrowheads) after NIPBL KD, and smaller loops (purple arcs) are maintained between newly formed anchors (purple arrowheads) and the remaining old anchors. The bottom panel shows the median heatmaps of Hi-C data in both cells on the left side and a subtraction heatmap of Hi-C data comparing both cell types on the right side. f One example showing the loss of NIPBL loading site within lost CTCF loops upon NIPBL KD at SOX2 gene locus. The top panel shows the Hi-C heatmaps. The bottom panel shows the distribution of NIPBL and other proteins at this site. Green and red arrowheads indicate orientation of the CTCF motifs at this site. Black arrowheads show the location of NIPBL sites present in Ctrl but not in si-NIPBL hESCs, which contain high levels of H3K27ac. Reference genome: hg38. g Distribution of NIPBL and several other proteins at loop anchors and loading sites of CTCF loops identified from Hi-C data present in Ctrl cells but not si-NIPBL hESCs. Black arrowheads show the enrichment of NIPBL and RAD21 at cohesin loading sites, which contain high levels of H3K27ac, between CTCF loops present in Ctrl but not in si-NIPBL hESCs. RPMPB: reads per million per 50 bp bin. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), RNA-seq ( n = 2), NIPBL ChIP-seq ( n = 3), ChIP-seq for other proteins ( n = 2).

Techniques: RNA Sequencing, Expressing, Marker, Control, Hi-C, Comparison, Labeling, ChIP-sequencing

a Heatmaps showing changes in transcription levels of up and downregulated genes during pancreatic differentiation in Ctrl and si-NIPBL derived PP cells. Up and downregulated genes at PP stage in Ctrl but not in si-NIPBL cells are clustered as dependent DEGs. b Heatmaps showing the ATAC-TF signals of hESCs and differentiated derivatives of Ctrl and si-NIBPL at ATAC-TF peaks gained at DE stage and PGT stage. RPMPB: reads per million per 50 bp bin. c Changes in the enrichment of transcription factor motifs found at the summits of ATAC-TF peaks specific to DE and PGT stages in Ctrl and si-NIPBL-derived differentiated cells. d APA metaplots of Hi-C data obtained from both control and si-NIPBL differentiation at the PP stage focusing on the loops that are gained at this specific stage. e Comparison of the number and size of stable versus gained loops formed at PP stage during pancreatic cell differentiation in both control and NIPBL KD conditions. Diagram depicting different processes by which CTCF loops change during differentiation by moving the location of one or both loop anchors. Subtraction values of ratios representing different processes occurring in both control and si-NIPBL differentiation at the PP stage are labeled. f Metaplot analysis of interactions between CTCF loop anchors and between enhancers and promoters located within the loop anchors. Differentiated PP cells in both Ctrl and NIPBL KD conditions are compared with undifferentiated hESCs. The bottom left diagram indicates the specific scenario in which the CTCF loops encompass E-P interactions analyzed here. Changes in interactions between E-P pairs in two different stages are analyzed in the context of changes of the CTCF loops inside which they are contained. The top panel shows median heatmaps of Hi-C interactions in Ctrl and si-NIPBL PP cells for CTCF loops that contain pairs of upregulated genes and their enhancers. The subtraction heatmaps from both cells are also shown. Increases of these loops at PP stage (black arrowheads indicating increased interactions at the CTCF loop anchors) correlates with increased E-P interactions inside the loops (orange arrowheads) in Ctrl condition. Less increases of both interactions are found at the same PP stage in NIPBL KD condition. g Metaplot analysis of interactions between CTCF loop anchors that are extended at PP stage. The bottom-left diagram illustrates the primary scenario in which hESCs-specific CTCF loops (purple arcs) are extended by replacing both of their old anchors (purple arrowheads) with new anchors (green arrowheads) to form longer loops (green arcs) during differentiation in Ctrl condition. The left panel shows the median heatmaps of Hi-C data and the subtraction heatmaps during pancreatic differentiation in both Ctrl and NIPBL KD conditions. The bottom-right diagram illustrates the primary scenario in which hESCs-specific CTCF loops are extended by replacing one of their old anchors. The right panel shows the meta-analysis of Hi-C data in this scenario. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), RNA-seq ( n = 2), ATAC-seq ( n = 2).

Journal: Communications Biology

Article Title: Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse

doi: 10.1038/s42003-026-09838-x

Figure Lengend Snippet: a Heatmaps showing changes in transcription levels of up and downregulated genes during pancreatic differentiation in Ctrl and si-NIPBL derived PP cells. Up and downregulated genes at PP stage in Ctrl but not in si-NIPBL cells are clustered as dependent DEGs. b Heatmaps showing the ATAC-TF signals of hESCs and differentiated derivatives of Ctrl and si-NIBPL at ATAC-TF peaks gained at DE stage and PGT stage. RPMPB: reads per million per 50 bp bin. c Changes in the enrichment of transcription factor motifs found at the summits of ATAC-TF peaks specific to DE and PGT stages in Ctrl and si-NIPBL-derived differentiated cells. d APA metaplots of Hi-C data obtained from both control and si-NIPBL differentiation at the PP stage focusing on the loops that are gained at this specific stage. e Comparison of the number and size of stable versus gained loops formed at PP stage during pancreatic cell differentiation in both control and NIPBL KD conditions. Diagram depicting different processes by which CTCF loops change during differentiation by moving the location of one or both loop anchors. Subtraction values of ratios representing different processes occurring in both control and si-NIPBL differentiation at the PP stage are labeled. f Metaplot analysis of interactions between CTCF loop anchors and between enhancers and promoters located within the loop anchors. Differentiated PP cells in both Ctrl and NIPBL KD conditions are compared with undifferentiated hESCs. The bottom left diagram indicates the specific scenario in which the CTCF loops encompass E-P interactions analyzed here. Changes in interactions between E-P pairs in two different stages are analyzed in the context of changes of the CTCF loops inside which they are contained. The top panel shows median heatmaps of Hi-C interactions in Ctrl and si-NIPBL PP cells for CTCF loops that contain pairs of upregulated genes and their enhancers. The subtraction heatmaps from both cells are also shown. Increases of these loops at PP stage (black arrowheads indicating increased interactions at the CTCF loop anchors) correlates with increased E-P interactions inside the loops (orange arrowheads) in Ctrl condition. Less increases of both interactions are found at the same PP stage in NIPBL KD condition. g Metaplot analysis of interactions between CTCF loop anchors that are extended at PP stage. The bottom-left diagram illustrates the primary scenario in which hESCs-specific CTCF loops (purple arcs) are extended by replacing both of their old anchors (purple arrowheads) with new anchors (green arrowheads) to form longer loops (green arcs) during differentiation in Ctrl condition. The left panel shows the median heatmaps of Hi-C data and the subtraction heatmaps during pancreatic differentiation in both Ctrl and NIPBL KD conditions. The bottom-right diagram illustrates the primary scenario in which hESCs-specific CTCF loops are extended by replacing one of their old anchors. The right panel shows the meta-analysis of Hi-C data in this scenario. Higher in: the signed difference (treatment−Ctrl) of distance-normalized Hi-C signals. Sample sizes: Hi-C ( n = 3 biologically independent experiments), RNA-seq ( n = 2), ATAC-seq ( n = 2).

Techniques: Derivative Assay, Hi-C, Control, Comparison, Cell Differentiation, Labeling, RNA Sequencing

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