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OriGene full-length chd8 isoform rg230753

Overview of the targeted DamID followed by sequencing (TaDa-seq) pipeline (A) Plasmids used for TaDa. The top plasmid is a diagram for <t>CHD8</t> TaDa experiments. The middle plasmid is a diagram for Dam-only experiments. The bottom plasmid is a diagram for the in utero electroporation control injected with the CHD8 TaDa or Dam-only plasmids. (B) Schematic and flowchart of TaDa-seq experiments. E13.5 mouse embryos were injected with CHD8 TaDa or Dam-only plasmid and the in utero electroporation control plasmid. Four CHD8 TaDa and three Dam-only brains from the same litter were dissected. Frozen brains were then processed for the pipeline indicated in the gray boxes. (C) Immunohistochemistry showing overlap between green fluorescence ( in utero electroporation control), red fluorescence (mCherry expression upstream of the CHD8 TaDa open reading frame), and DAPI (nuclei) illustrates successful transfection of experimental plasmids. (D) TaDa-seq computational analysis pipeline used in this study. (E) Schematic showing example signal from CHD8 TaDa or Dam-only protein binding at genomic loci.

Full Length Chd8 Isoform Rg230753, supplied by OriGene, 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/full+length+chd8+isoform/cdna+chd8/pmc08551073-301-22-25
Average 90 stars, based on 1 article reviews

full-length chd8 isoform rg230753 - by Bioz Stars, 2026-10

90/100 stars

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1) Product Images from "In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain"

Article Title: In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain

Journal: iScience

doi: 10.1016/j.isci.2021.103234

Overview of the targeted DamID followed by sequencing (TaDa-seq) pipeline (A) Plasmids used for TaDa. The top plasmid is a diagram for CHD8 TaDa experiments. The middle plasmid is a diagram for Dam-only experiments. The bottom plasmid is a diagram for the in utero electroporation control injected with the CHD8 TaDa or Dam-only plasmids. (B) Schematic and flowchart of TaDa-seq experiments. E13.5 mouse embryos were injected with CHD8 TaDa or Dam-only plasmid and the in utero electroporation control plasmid. Four CHD8 TaDa and three Dam-only brains from the same litter were dissected. Frozen brains were then processed for the pipeline indicated in the gray boxes. (C) Immunohistochemistry showing overlap between green fluorescence ( in utero electroporation control), red fluorescence (mCherry expression upstream of the CHD8 TaDa open reading frame), and DAPI (nuclei) illustrates successful transfection of experimental plasmids. (D) TaDa-seq computational analysis pipeline used in this study. (E) Schematic showing example signal from CHD8 TaDa or Dam-only protein binding at genomic loci.

Figure Legend Snippet: Overview of the targeted DamID followed by sequencing (TaDa-seq) pipeline (A) Plasmids used for TaDa. The top plasmid is a diagram for CHD8 TaDa experiments. The middle plasmid is a diagram for Dam-only experiments. The bottom plasmid is a diagram for the in utero electroporation control injected with the CHD8 TaDa or Dam-only plasmids. (B) Schematic and flowchart of TaDa-seq experiments. E13.5 mouse embryos were injected with CHD8 TaDa or Dam-only plasmid and the in utero electroporation control plasmid. Four CHD8 TaDa and three Dam-only brains from the same litter were dissected. Frozen brains were then processed for the pipeline indicated in the gray boxes. (C) Immunohistochemistry showing overlap between green fluorescence ( in utero electroporation control), red fluorescence (mCherry expression upstream of the CHD8 TaDa open reading frame), and DAPI (nuclei) illustrates successful transfection of experimental plasmids. (D) TaDa-seq computational analysis pipeline used in this study. (E) Schematic showing example signal from CHD8 TaDa or Dam-only protein binding at genomic loci.

Techniques Used: Sequencing, Plasmid Preparation, In Utero, Electroporation, Control, Injection, Immunohistochemistry, Fluorescence, Expressing, Transfection, Protein Binding

Recapitulation of CHD8 binding near promoters across the genome (A and B) Data showing CHD8 binding at loci previously identified in CHD8 binding characterization studies, including RNA processing genes, Hnrnpll and Srsf7 in A, Srsf1 and Sf3b1 in B, and a chromatin remodeling gene, Top1 , in (B). Gray boxes highlight CHD8 binding near identified promoters of interest. CHD8 TaDa, Dam-only, or Dam-only-normalized CHD8 TaDa (TaDa Dam Norm.) experiment tracks are in blue (representative biological replicates shown), CHD8 ChIP-seq experiments are in gray, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y axis is scaled to show the peak for each track separately. See also <xref ref-type=

Figure S1 . Embryonic CHD8 ChIP ( Cotney et al. (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al. (2017) ) adult CHD8 ChIP-seq. " title="Recapitulation of CHD8 binding near promoters across the genome (A and ..." property="contentUrl" width="100%" height="100%"/>
Figure Legend Snippet: Recapitulation of CHD8 binding near promoters across the genome (A and B) Data showing CHD8 binding at loci previously identified in CHD8 binding characterization studies, including RNA processing genes, Hnrnpll and Srsf7 in A, Srsf1 and Sf3b1 in B, and a chromatin remodeling gene, Top1 , in (B). Gray boxes highlight CHD8 binding near identified promoters of interest. CHD8 TaDa, Dam-only, or Dam-only-normalized CHD8 TaDa (TaDa Dam Norm.) experiment tracks are in blue (representative biological replicates shown), CHD8 ChIP-seq experiments are in gray, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y axis is scaled to show the peak for each track separately. See also Figure S1 . Embryonic CHD8 ChIP ( Cotney et al. (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al. (2017) ) adult CHD8 ChIP-seq.

Techniques Used: Binding Assay, ChIP-sequencing

Computational comparison of CHD8 binding shows correspondence in signal across TaDa-seq and ChIP-seq experiments (A) Bar plots showing association of peaks with transcription start sites (TSS) using the GREAT online analysis tool. Bins along the x axis represent 5, 50, 500, and greater than 500 kilobases away from the nearest TSS. (B) Venn diagram showing the number of peaks annotated to genes overlapping with CHD8 TaDa, Embryonic CHD8 ChIP-seq, and Adult CHD8 ChIP-seq using stringent CHD8 TaDa-seq peak thresholding with peaks meeting an FDR <0.00001 cutoff in at least three replicates. (C) Genome-wide coverage heatmaps showing enrichment of signal at peaks for each dataset indicated on the left-hand side. Y axes of datasets were matched for visual comparison. Small line plots indicate the average normalized peak enrichment for each dataset with the color for each line next to each dataset name. Each peak is centered along the middle of each plot with a 3-kilobase pair window on each side. The legend indicates normalized enrichment. (D) Genome coverage correlation heatmap showing relationship between representative CHD8 TaDa-seq, Dam-only, CHD8 ChIP-seq, and ENCODE histone mark and chromatin accessibility datasets. Data are hierarchically clustered according to genome-wide similarity as indicated by a dendrogram. Legend indicates the correlation value between datasets. H3K27me3 is a histone mark associated with repressed DNA loci. H3K4me3 is a histone mark associated with actively transcribed promoters. ATAC-seq is sequencing data of open chromatin regions. H3K4me1 and H3K27ac are histone marks associated with putative enhancers. (E) Table showing functional annotations associated with CHD8 TaDa-seq called peaks. Region % refers to the percent of the total peak set annotated to each term. (F) Table showing functional annotations associated with peaks only found in the CHD8 TaDa-seq dataset. Region % refers to the percent of the total peak set annotated to each term. See also . Embryonic CHD8 ChIP ( <xref ref-type=

Cotney et al., (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al., (2017) ) adult CHD8 ChIP-seq. " title="Computational comparison of CHD8 binding shows correspondence in signal across TaDa-seq and ..." property="contentUrl" width="100%" height="100%"/>
Figure Legend Snippet: Computational comparison of CHD8 binding shows correspondence in signal across TaDa-seq and ChIP-seq experiments (A) Bar plots showing association of peaks with transcription start sites (TSS) using the GREAT online analysis tool. Bins along the x axis represent 5, 50, 500, and greater than 500 kilobases away from the nearest TSS. (B) Venn diagram showing the number of peaks annotated to genes overlapping with CHD8 TaDa, Embryonic CHD8 ChIP-seq, and Adult CHD8 ChIP-seq using stringent CHD8 TaDa-seq peak thresholding with peaks meeting an FDR <0.00001 cutoff in at least three replicates. (C) Genome-wide coverage heatmaps showing enrichment of signal at peaks for each dataset indicated on the left-hand side. Y axes of datasets were matched for visual comparison. Small line plots indicate the average normalized peak enrichment for each dataset with the color for each line next to each dataset name. Each peak is centered along the middle of each plot with a 3-kilobase pair window on each side. The legend indicates normalized enrichment. (D) Genome coverage correlation heatmap showing relationship between representative CHD8 TaDa-seq, Dam-only, CHD8 ChIP-seq, and ENCODE histone mark and chromatin accessibility datasets. Data are hierarchically clustered according to genome-wide similarity as indicated by a dendrogram. Legend indicates the correlation value between datasets. H3K27me3 is a histone mark associated with repressed DNA loci. H3K4me3 is a histone mark associated with actively transcribed promoters. ATAC-seq is sequencing data of open chromatin regions. H3K4me1 and H3K27ac are histone marks associated with putative enhancers. (E) Table showing functional annotations associated with CHD8 TaDa-seq called peaks. Region % refers to the percent of the total peak set annotated to each term. (F) Table showing functional annotations associated with peaks only found in the CHD8 TaDa-seq dataset. Region % refers to the percent of the total peak set annotated to each term. See also . Embryonic CHD8 ChIP ( Cotney et al., (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al., (2017) ) adult CHD8 ChIP-seq.

Techniques Used: Comparison, Binding Assay, ChIP-sequencing, Genome Wide, Sequencing, Functional Assay

CHD8 binding is associated with activation of highly expressed genes (A) Box and whisker plots showing change in log fold counts per million of genes according to peak rank in CHD8 TaDa-seq (CHD8 TaDa), both CHD8 TaDa-seq and CHD8 ChIP-seq (TaDa & ChIP), or Dam-Only datasets and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and the top 1,000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. (B) Box and whisker plots showing log fold change of genes according to peak rank in CHD8 TaDa-seq (CHD8 TaDa), both CHD8 TaDa-seq and CHD8 ChIP-seq (TaDa & ChIP), or Dam-Only datasets and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and top 1,000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. C-D (left) Venn diagrams indicating the number of genes overlapping between the CHD8 TaDa-seq and E17.5 Chd8 haploinsufficiency significant (p < 0.05) downregulated and upregulated datasets. (C and D right) Tables showing functional annotations associated with genes having CHD8 binding in downregulated (C) and upregulated (D) genes from the E17.5 Chd8 haploinsufficiency dataset (p < 0.05) using goseq. Enrichment values indicate the percent of genes in the dataset that are differentially expressed and bound by CHD8 via TaDa-seq in relation to the total number of genes associated with each term. See also and .

Figure Legend Snippet: CHD8 binding is associated with activation of highly expressed genes (A) Box and whisker plots showing change in log fold counts per million of genes according to peak rank in CHD8 TaDa-seq (CHD8 TaDa), both CHD8 TaDa-seq and CHD8 ChIP-seq (TaDa & ChIP), or Dam-Only datasets and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and the top 1,000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. (B) Box and whisker plots showing log fold change of genes according to peak rank in CHD8 TaDa-seq (CHD8 TaDa), both CHD8 TaDa-seq and CHD8 ChIP-seq (TaDa & ChIP), or Dam-Only datasets and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and top 1,000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. C-D (left) Venn diagrams indicating the number of genes overlapping between the CHD8 TaDa-seq and E17.5 Chd8 haploinsufficiency significant (p < 0.05) downregulated and upregulated datasets. (C and D right) Tables showing functional annotations associated with genes having CHD8 binding in downregulated (C) and upregulated (D) genes from the E17.5 Chd8 haploinsufficiency dataset (p < 0.05) using goseq. Enrichment values indicate the percent of genes in the dataset that are differentially expressed and bound by CHD8 via TaDa-seq in relation to the total number of genes associated with each term. See also and .

Techniques Used: Binding Assay, Activation Assay, Whisker Assay, ChIP-sequencing, Gene Expression, Sequencing, Functional Assay

TaDa-seq identifies both promoter proximal and promoter distal CHD8 binding (A–C) CHD8 binding near genes important for regulation of neuronal gene expression, Myt1l (A), and synaptic function, Ank3 (B) and Dlg4 (C). Gray boxes highlight CHD8 binding near select promoter and distal regions of interest overlapping with putative enhancer marks (H3K27ac and H3K4me1). CHD8 TaDa-seq experiment tracks are in blue, CHD8 ChIP-seq experiments are in gray, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y axis is scaled to show the peak for each track separately. (D) Table showing functional annotations associated with promoter proximal (<1kb from TSS) (top) and promoter distal (bottom) regions. Rank refers to the rank within the dataset. A rank of 1 would mean the annotation with the smallest FDR value (aka the most significant). Region % refers to the percent of regions captured compared with the total number of peaks. (E) Box and whisker plots showing change in log fold counts per million (left) or log fold change (right) of genes according to peak rank in CHD8 TaDa-seq proximal (top) or distal (bottom) datasets and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and top 1,000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. See also and . Embryonic CHD8 ChIP ( <xref ref-type=

Cotney et al., (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al., (2017) ) adult CHD8 ChIP-seq. " title="TaDa-seq identifies both promoter proximal and promoter distal CHD8 binding (A–C) CHD8 binding near genes important for ..." property="contentUrl" width="100%" height="100%"/>
Figure Legend Snippet: TaDa-seq identifies both promoter proximal and promoter distal CHD8 binding (A–C) CHD8 binding near genes important for regulation of neuronal gene expression, Myt1l (A), and synaptic function, Ank3 (B) and Dlg4 (C). Gray boxes highlight CHD8 binding near select promoter and distal regions of interest overlapping with putative enhancer marks (H3K27ac and H3K4me1). CHD8 TaDa-seq experiment tracks are in blue, CHD8 ChIP-seq experiments are in gray, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y axis is scaled to show the peak for each track separately. (D) Table showing functional annotations associated with promoter proximal (<1kb from TSS) (top) and promoter distal (bottom) regions. Rank refers to the rank within the dataset. A rank of 1 would mean the annotation with the smallest FDR value (aka the most significant). Region % refers to the percent of regions captured compared with the total number of peaks. (E) Box and whisker plots showing change in log fold counts per million (left) or log fold change (right) of genes according to peak rank in CHD8 TaDa-seq proximal (top) or distal (bottom) datasets and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and top 1,000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. See also and . Embryonic CHD8 ChIP ( Cotney et al., (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al., (2017) ) adult CHD8 ChIP-seq.

Techniques Used: Binding Assay, Gene Expression, ChIP-sequencing, Functional Assay, Whisker Assay, Sequencing

Figure Legend Snippet:

Techniques Used: Virus, Recombinant, Purification, Software

Plasmid Preparation:

Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID
Article Snippet: .. To generate the experimental plasmid, pCAG-mCherry-intronDam-CHD8, encoding the Dam methylase fused to the human CHD8 open reading frame (hereafter CHD8 TaDa), a full-length CHD8 isoform (Origene, RG230753) was subcloned by Gibson assembly into pCAG-mCherry-intronDam, C-terminal to the Dam methylase and a myc-tag. ..

Image Search Results

Journal: iScience

Article Title: In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain

doi: 10.1016/j.isci.2021.103234

Figure Lengend Snippet: Overview of the targeted DamID followed by sequencing (TaDa-seq) pipeline (A) Plasmids used for TaDa. The top plasmid is a diagram for CHD8 TaDa experiments. The middle plasmid is a diagram for Dam-only experiments. The bottom plasmid is a diagram for the in utero electroporation control injected with the CHD8 TaDa or Dam-only plasmids. (B) Schematic and flowchart of TaDa-seq experiments. E13.5 mouse embryos were injected with CHD8 TaDa or Dam-only plasmid and the in utero electroporation control plasmid. Four CHD8 TaDa and three Dam-only brains from the same litter were dissected. Frozen brains were then processed for the pipeline indicated in the gray boxes. (C) Immunohistochemistry showing overlap between green fluorescence ( in utero electroporation control), red fluorescence (mCherry expression upstream of the CHD8 TaDa open reading frame), and DAPI (nuclei) illustrates successful transfection of experimental plasmids. (D) TaDa-seq computational analysis pipeline used in this study. (E) Schematic showing example signal from CHD8 TaDa or Dam-only protein binding at genomic loci.

Article Snippet: To generate the experimental plasmid, pCAG-mCherry-intronDam-CHD8, encoding the Dam methylase fused to the human CHD8 open reading frame (hereafter CHD8 TaDa), a full-length CHD8 isoform (Origene, RG230753) was subcloned by Gibson assembly into pCAG-mCherry-intronDam, C-terminal to the Dam methylase and a myc-tag.

Techniques: Sequencing, Plasmid Preparation, In Utero, Electroporation, Control, Injection, Immunohistochemistry, Fluorescence, Expressing, Transfection, Protein Binding

Figure S1 . Embryonic CHD8 ChIP ( Cotney et al. (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al. (2017) ) adult CHD8 ChIP-seq. " width="100%" height="100%">

Journal: iScience

Article Title: In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain

doi: 10.1016/j.isci.2021.103234

Figure Lengend Snippet: Recapitulation of CHD8 binding near promoters across the genome (A and B) Data showing CHD8 binding at loci previously identified in CHD8 binding characterization studies, including RNA processing genes, Hnrnpll and Srsf7 in A, Srsf1 and Sf3b1 in B, and a chromatin remodeling gene, Top1 , in (B). Gray boxes highlight CHD8 binding near identified promoters of interest. CHD8 TaDa, Dam-only, or Dam-only-normalized CHD8 TaDa (TaDa Dam Norm.) experiment tracks are in blue (representative biological replicates shown), CHD8 ChIP-seq experiments are in gray, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y axis is scaled to show the peak for each track separately. See also Figure S1 . Embryonic CHD8 ChIP ( Cotney et al. (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al. (2017) ) adult CHD8 ChIP-seq.

Techniques: Binding Assay, ChIP-sequencing

Cotney et al., (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al., (2017) ) adult CHD8 ChIP-seq. " width="100%" height="100%">

Journal: iScience

Article Title: In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain

doi: 10.1016/j.isci.2021.103234

Figure Lengend Snippet: Computational comparison of CHD8 binding shows correspondence in signal across TaDa-seq and ChIP-seq experiments (A) Bar plots showing association of peaks with transcription start sites (TSS) using the GREAT online analysis tool. Bins along the x axis represent 5, 50, 500, and greater than 500 kilobases away from the nearest TSS. (B) Venn diagram showing the number of peaks annotated to genes overlapping with CHD8 TaDa, Embryonic CHD8 ChIP-seq, and Adult CHD8 ChIP-seq using stringent CHD8 TaDa-seq peak thresholding with peaks meeting an FDR <0.00001 cutoff in at least three replicates. (C) Genome-wide coverage heatmaps showing enrichment of signal at peaks for each dataset indicated on the left-hand side. Y axes of datasets were matched for visual comparison. Small line plots indicate the average normalized peak enrichment for each dataset with the color for each line next to each dataset name. Each peak is centered along the middle of each plot with a 3-kilobase pair window on each side. The legend indicates normalized enrichment. (D) Genome coverage correlation heatmap showing relationship between representative CHD8 TaDa-seq, Dam-only, CHD8 ChIP-seq, and ENCODE histone mark and chromatin accessibility datasets. Data are hierarchically clustered according to genome-wide similarity as indicated by a dendrogram. Legend indicates the correlation value between datasets. H3K27me3 is a histone mark associated with repressed DNA loci. H3K4me3 is a histone mark associated with actively transcribed promoters. ATAC-seq is sequencing data of open chromatin regions. H3K4me1 and H3K27ac are histone marks associated with putative enhancers. (E) Table showing functional annotations associated with CHD8 TaDa-seq called peaks. Region % refers to the percent of the total peak set annotated to each term. (F) Table showing functional annotations associated with peaks only found in the CHD8 TaDa-seq dataset. Region % refers to the percent of the total peak set annotated to each term. See also . Embryonic CHD8 ChIP ( Cotney et al., (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al., (2017) ) adult CHD8 ChIP-seq.

Techniques: Comparison, Binding Assay, ChIP-sequencing, Genome Wide, Sequencing, Functional Assay

Journal: iScience

Article Title: In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain

doi: 10.1016/j.isci.2021.103234

Figure Lengend Snippet: CHD8 binding is associated with activation of highly expressed genes (A) Box and whisker plots showing change in log fold counts per million of genes according to peak rank in CHD8 TaDa-seq (CHD8 TaDa), both CHD8 TaDa-seq and CHD8 ChIP-seq (TaDa & ChIP), or Dam-Only datasets and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and the top 1,000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. (B) Box and whisker plots showing log fold change of genes according to peak rank in CHD8 TaDa-seq (CHD8 TaDa), both CHD8 TaDa-seq and CHD8 ChIP-seq (TaDa & ChIP), or Dam-Only datasets and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and top 1,000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. C-D (left) Venn diagrams indicating the number of genes overlapping between the CHD8 TaDa-seq and E17.5 Chd8 haploinsufficiency significant (p < 0.05) downregulated and upregulated datasets. (C and D right) Tables showing functional annotations associated with genes having CHD8 binding in downregulated (C) and upregulated (D) genes from the E17.5 Chd8 haploinsufficiency dataset (p < 0.05) using goseq. Enrichment values indicate the percent of genes in the dataset that are differentially expressed and bound by CHD8 via TaDa-seq in relation to the total number of genes associated with each term. See also and .

Techniques: Binding Assay, Activation Assay, Whisker Assay, ChIP-sequencing, Gene Expression, Sequencing, Functional Assay

Cotney et al., (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al., (2017) ) adult CHD8 ChIP-seq. " width="100%" height="100%">

Journal: iScience

Article Title: In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain

doi: 10.1016/j.isci.2021.103234

Figure Lengend Snippet: TaDa-seq identifies both promoter proximal and promoter distal CHD8 binding (A–C) CHD8 binding near genes important for regulation of neuronal gene expression, Myt1l (A), and synaptic function, Ank3 (B) and Dlg4 (C). Gray boxes highlight CHD8 binding near select promoter and distal regions of interest overlapping with putative enhancer marks (H3K27ac and H3K4me1). CHD8 TaDa-seq experiment tracks are in blue, CHD8 ChIP-seq experiments are in gray, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y axis is scaled to show the peak for each track separately. (D) Table showing functional annotations associated with promoter proximal (<1kb from TSS) (top) and promoter distal (bottom) regions. Rank refers to the rank within the dataset. A rank of 1 would mean the annotation with the smallest FDR value (aka the most significant). Region % refers to the percent of regions captured compared with the total number of peaks. (E) Box and whisker plots showing change in log fold counts per million (left) or log fold change (right) of genes according to peak rank in CHD8 TaDa-seq proximal (top) or distal (bottom) datasets and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and top 1,000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. See also and . Embryonic CHD8 ChIP ( Cotney et al., (2015) ) embryonic CHD8 ChIP-seq, Adult CHD8 ChIP ( Platt et al., (2017) ) adult CHD8 ChIP-seq.

Techniques: Binding Assay, Gene Expression, ChIP-sequencing, Functional Assay, Whisker Assay, Sequencing

Journal: iScience

Article Title: In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain

doi: 10.1016/j.isci.2021.103234

Figure Lengend Snippet:

Techniques: Virus, Recombinant, Purification, Software

( A ) Plasmids used for TaDa. The top plasmid is a diagram for CHD8 TaDa experiments. The middle plasmid is a diagram for Dam-only experiments. The bottom plasmid is a diagram for the in utero electroporation control injected with the CHD8 TaDa or Dam-only plasmids. ( B ) Schematic and flowchart of TaDa-seq experiments. E13.5 mouse embryos were injected with CHD8 TaDa or Dam-only plasmid and the in utero electroporation control plasmid. Four CHD8 TaDa and three Dam-only brains from the same litter were dissected. Frozen brains were then processed for the pipeline indicated in the grey boxes. ( C ) Immunohistochemistry showing overlap between green fluorescence (in utero electroporation control), red fluorescence (mCherry expression upstream of the CHD8 TaDa open reading frame), and DAPI (nuclei) illustrates successful transfection of experimental plasmids. ( D ) TaDa-seq computational analysis pipeline used in this study. ( E ) Schematic showing example signal from CHD8 TaDa or Dam-only protein binding at genomic loci.

Journal: bioRxiv

Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

doi: 10.1101/2021.01.12.426468

Figure Lengend Snippet: ( A ) Plasmids used for TaDa. The top plasmid is a diagram for CHD8 TaDa experiments. The middle plasmid is a diagram for Dam-only experiments. The bottom plasmid is a diagram for the in utero electroporation control injected with the CHD8 TaDa or Dam-only plasmids. ( B ) Schematic and flowchart of TaDa-seq experiments. E13.5 mouse embryos were injected with CHD8 TaDa or Dam-only plasmid and the in utero electroporation control plasmid. Four CHD8 TaDa and three Dam-only brains from the same litter were dissected. Frozen brains were then processed for the pipeline indicated in the grey boxes. ( C ) Immunohistochemistry showing overlap between green fluorescence (in utero electroporation control), red fluorescence (mCherry expression upstream of the CHD8 TaDa open reading frame), and DAPI (nuclei) illustrates successful transfection of experimental plasmids. ( D ) TaDa-seq computational analysis pipeline used in this study. ( E ) Schematic showing example signal from CHD8 TaDa or Dam-only protein binding at genomic loci.

Techniques: Plasmid Preparation, In Utero, Electroporation, Control, Injection, Immunohistochemistry, Fluorescence, Expressing, Transfection, Protein Binding

Data showing CHD8 binding at loci previously identified in CHD8 binding characterization studies, including RNA processing genes, Hnrnpll and Srsf7 in panel A, Srsf1 and Sf3b1 in panel B, and a chromatin remodeling gene, Top1 , in panel B. Grey boxes highlight CHD8 binding near identified promoters of interest. CHD8 TaDa, Dam-only, or Dam-only normalized CHD8 TaDa (TaDa Dam Norm.) experiment tracks are in blue (representative biological replicates shown), CHD8 ChIP-seq experiments are in grey, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y-axis is scaled to show the peak for each track separately.

Journal: bioRxiv

Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

doi: 10.1101/2021.01.12.426468

Figure Lengend Snippet: Data showing CHD8 binding at loci previously identified in CHD8 binding characterization studies, including RNA processing genes, Hnrnpll and Srsf7 in panel A, Srsf1 and Sf3b1 in panel B, and a chromatin remodeling gene, Top1 , in panel B. Grey boxes highlight CHD8 binding near identified promoters of interest. CHD8 TaDa, Dam-only, or Dam-only normalized CHD8 TaDa (TaDa Dam Norm.) experiment tracks are in blue (representative biological replicates shown), CHD8 ChIP-seq experiments are in grey, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y-axis is scaled to show the peak for each track separately.

Techniques: Binding Assay, ChIP-sequencing

( A ) Bar plots showing association of peaks with transcription start sites (TSS) using the GREAT online analysis tool. Bins along the x-axis represent 5, 50, 500, and greater than 500 kilobases away from the nearest TSS. ( B ) Genome-wide coverage heatmaps showing enrichment of signal at peaks for each dataset indicated on the left-hand side. Y axis of datasets were matched for visual comparison. Small line plots indicate the average normalized peak enrichment for each dataset with the color for each line next to each dataset name. Each peak is centered along the middle of each plot with a 3 kilobase pair window on each side. The legend indicates normalized enrichment. ( C ) Venn diagram showing the number of peaks annotated to genes overlapping with CHD8 TaDa, Embryonic CHD8 ChIP-seq, and Adult CHD8 ChIP-seq using stringent CHD8 TaDa-seq peak thresholding with peaks meeting an FDR < 0.00001 cutoff in at least 3 replicates (Top) or a looser threshold of peaks present in at least 3 replicates (Bottom). ( D ) Genome coverage correlation heatmap showing relationship between representative CHD8 TaDa-seq, Dam-only, CHD8 ChIP-seq, and ENCODE histone mark and chromatin accessibility datasets. Data are hierarchically clustered according to genome-wide similarity as indicated by a dendrogram. Legend indicates the correlation value between datasets. H3K27me3 is a histone mark associated with repressed DNA loci. H3K4me3 is a histone mark associated with actively transcribed promoters. ATAC-seq is sequencing data of open chromatin regions. H3K4me1 and H3K27ac are histone marks associated with putative enhancers. ( E ) Table showing functional annotations associated with CHD8 TaDa-seq called peaks. Region % refers to the percent of the total peak set annotated to each term.

Journal: bioRxiv

Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

doi: 10.1101/2021.01.12.426468

Figure Lengend Snippet: ( A ) Bar plots showing association of peaks with transcription start sites (TSS) using the GREAT online analysis tool. Bins along the x-axis represent 5, 50, 500, and greater than 500 kilobases away from the nearest TSS. ( B ) Genome-wide coverage heatmaps showing enrichment of signal at peaks for each dataset indicated on the left-hand side. Y axis of datasets were matched for visual comparison. Small line plots indicate the average normalized peak enrichment for each dataset with the color for each line next to each dataset name. Each peak is centered along the middle of each plot with a 3 kilobase pair window on each side. The legend indicates normalized enrichment. ( C ) Venn diagram showing the number of peaks annotated to genes overlapping with CHD8 TaDa, Embryonic CHD8 ChIP-seq, and Adult CHD8 ChIP-seq using stringent CHD8 TaDa-seq peak thresholding with peaks meeting an FDR < 0.00001 cutoff in at least 3 replicates (Top) or a looser threshold of peaks present in at least 3 replicates (Bottom). ( D ) Genome coverage correlation heatmap showing relationship between representative CHD8 TaDa-seq, Dam-only, CHD8 ChIP-seq, and ENCODE histone mark and chromatin accessibility datasets. Data are hierarchically clustered according to genome-wide similarity as indicated by a dendrogram. Legend indicates the correlation value between datasets. H3K27me3 is a histone mark associated with repressed DNA loci. H3K4me3 is a histone mark associated with actively transcribed promoters. ATAC-seq is sequencing data of open chromatin regions. H3K4me1 and H3K27ac are histone marks associated with putative enhancers. ( E ) Table showing functional annotations associated with CHD8 TaDa-seq called peaks. Region % refers to the percent of the total peak set annotated to each term.

Techniques: Genome Wide, Comparison, ChIP-sequencing, Sequencing, Functional Assay

HOMER results of the top 30 motifs identified in CHD8 TaDa-seq peaks. Target sequences refer to sequences from CHD8 TaDa-seq peaks used as input. Background sequences refers to random sequence-content matched intervals in the genome.

Journal: bioRxiv

Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

doi: 10.1101/2021.01.12.426468

Figure Lengend Snippet: HOMER results of the top 30 motifs identified in CHD8 TaDa-seq peaks. Target sequences refer to sequences from CHD8 TaDa-seq peaks used as input. Background sequences refers to random sequence-content matched intervals in the genome.

Techniques: Sequencing

Genome coverage correlation heatmap showing relationship between CHD8 TaDa-seq replicates, Chd8 ChIP-seq replicates, and ENCODE histone mark and chromatin accessibility dataset replicates. Data are hierarchically clustered according to similarity as indicated by a dendrogram. Differences in signal intensity between CHD8 TaDa-seq replicates in the correlation heatmaps were due to differences in sequencing depth. The legend indicates the correlation value between datasets. H3K27me3 is a histone mark associated with repressed DNA loci. H3K4me3 is a histone mark associated with actively transcribed promoters. ATAC-seq identifies regions of open chromatin. H3K4me1 and H3K27ac are histone marks associated with putative enhancers. CHD8 TaDa Merge – Merged CHD8 TaDa-seq dataset. Dam-only Merge – Merged Dam-only dataset.

Journal: bioRxiv

Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

doi: 10.1101/2021.01.12.426468

Figure Lengend Snippet: Genome coverage correlation heatmap showing relationship between CHD8 TaDa-seq replicates, Chd8 ChIP-seq replicates, and ENCODE histone mark and chromatin accessibility dataset replicates. Data are hierarchically clustered according to similarity as indicated by a dendrogram. Differences in signal intensity between CHD8 TaDa-seq replicates in the correlation heatmaps were due to differences in sequencing depth. The legend indicates the correlation value between datasets. H3K27me3 is a histone mark associated with repressed DNA loci. H3K4me3 is a histone mark associated with actively transcribed promoters. ATAC-seq identifies regions of open chromatin. H3K4me1 and H3K27ac are histone marks associated with putative enhancers. CHD8 TaDa Merge – Merged CHD8 TaDa-seq dataset. Dam-only Merge – Merged Dam-only dataset.

Techniques: ChIP-sequencing, Sequencing

( A ) Box and whisker plots showing comparison between CHD8 TaDa-seq peak rank and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Change in log fold counts per million of genes according to CHD8 binding (Left). Change in log fold change of genes according to CHD8 binding (Right). Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and the top 1000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. ( B ) Box and whisker plots showing comparison between Dam-only peak rank and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Change in log fold counts per million of genes according to Dam binding (Left). Change in log fold change of genes according to Dam binding (Right). Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and top 1000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. ( C-D left ) Venn diagrams indicating the number of genes overlapping between the CHD8 TaDa-seq and E17.5 Chd8 haploinsufficiency significant (p < 0.05) downregulated and upregulated datasets. ( C-D right ) Tables showing functional annotations associated with genes having CHD8 binding in downregulated (C) and upregulated (D) genes from the E17.5 Chd8 haploinsufficiency dataset (p < 0.05) using goseq. Enrichment values indicate the percent of genes in the dataset that are differentially expressed and bound by CHD8 via TaDa-seq in relation to the total number of genes associated with each term.

Journal: bioRxiv

Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

doi: 10.1101/2021.01.12.426468

Figure Lengend Snippet: ( A ) Box and whisker plots showing comparison between CHD8 TaDa-seq peak rank and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Change in log fold counts per million of genes according to CHD8 binding (Left). Change in log fold change of genes according to CHD8 binding (Right). Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and the top 1000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. ( B ) Box and whisker plots showing comparison between Dam-only peak rank and an E17.5 Chd8 haploinsufficiency differential gene expression dataset. Change in log fold counts per million of genes according to Dam binding (Left). Change in log fold change of genes according to Dam binding (Right). Boxes were plotted according to CHD8 binding affinity bins: all genes meeting at least 0.1 count per million sequencing coverage (Expressed Genes), any genes having CHD8 binding (All Bound Genes), and top 1000 genes near CHD8 peaks (Top 1000 Bound). Notches indicate values within the 95% confidence interval of the median. ( C-D left ) Venn diagrams indicating the number of genes overlapping between the CHD8 TaDa-seq and E17.5 Chd8 haploinsufficiency significant (p < 0.05) downregulated and upregulated datasets. ( C-D right ) Tables showing functional annotations associated with genes having CHD8 binding in downregulated (C) and upregulated (D) genes from the E17.5 Chd8 haploinsufficiency dataset (p < 0.05) using goseq. Enrichment values indicate the percent of genes in the dataset that are differentially expressed and bound by CHD8 via TaDa-seq in relation to the total number of genes associated with each term.

Techniques: Whisker Assay, Comparison, Gene Expression, Binding Assay, Sequencing, Functional Assay

( A-C ) CHD8 binding near genes important for regulation of neuronal gene expression, Myt1l (A), and synaptic function, Ank3 (B) and Dlg4 (C). Grey boxes highlight CHD8 binding near select promoter and distal regions of interest overlapping with putative enhancer marks (H3K27ac and H3K4me1). CHD8 TaDa-seq experiment tracks are in blue, CHD8 ChIP-seq experiments are in grey, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y-axis is scaled to show the peak for each track separately. ( D ) Table showing functional annotations associated with promoter proximal (<1kb from TSS) (Top) and promoter distal (Bottom) regions. Rank refers to the rank within the dataset. A rank of 1 would mean the annotation with the smallest FDR value (aka the most significant). Region hits capture the number of peaks associated with each term. Region % captures the percent of regions captured compared to the total number of peaks.

Journal: bioRxiv

Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

doi: 10.1101/2021.01.12.426468

Figure Lengend Snippet: ( A-C ) CHD8 binding near genes important for regulation of neuronal gene expression, Myt1l (A), and synaptic function, Ank3 (B) and Dlg4 (C). Grey boxes highlight CHD8 binding near select promoter and distal regions of interest overlapping with putative enhancer marks (H3K27ac and H3K4me1). CHD8 TaDa-seq experiment tracks are in blue, CHD8 ChIP-seq experiments are in grey, and datasets of histone and chromatin accessibility signatures from the ENCODE consortium are in black. Linear representations of genes from the mouse mm10 genome are shown below coverage tracks. Height of the y-axis is scaled to show the peak for each track separately. ( D ) Table showing functional annotations associated with promoter proximal (<1kb from TSS) (Top) and promoter distal (Bottom) regions. Rank refers to the rank within the dataset. A rank of 1 would mean the annotation with the smallest FDR value (aka the most significant). Region hits capture the number of peaks associated with each term. Region % captures the percent of regions captured compared to the total number of peaks.

Techniques: Binding Assay, Gene Expression, ChIP-sequencing, Functional Assay

Table showing functional annotations associated with peaks in CHD8 ChIP-seq datasets. Region hits capture the number of peaks associated with each term. Region % captures the percent of regions captured compared to the total number of peaks.

Journal: bioRxiv

Article Title: Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID

doi: 10.1101/2021.01.12.426468

Figure Lengend Snippet: Table showing functional annotations associated with peaks in CHD8 ChIP-seq datasets. Region hits capture the number of peaks associated with each term. Region % captures the percent of regions captured compared to the total number of peaks.

Techniques: Functional Assay, ChIP-sequencing

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full-length chd8 isoform rg230753 (OriGene)

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