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(A) Venn diagram showing overlap between ATAC-seq summits and H3K27Ac peaks (±500 nt), used to define 134,520 active enhancers in PHHs. (B) Genomic classification of <t>hepatocyte</t> enhancers relative to position of protein-coding genes (GENCODE v43). (C) Heatmaps of PRO-seq (left), H3K27Ac ChIP-seq (center), and ATAC-seq (right) signal at active enhancers, centered on ATAC-seq summits (± 1,500 nt). Color scale represents normalized read coverage (RPM) per 10 nt bin. Signal above the dashed line corresponds to the 96,169 enhancers exhibiting detectable transcriptional activity, defined as >0.02 PRO-seq reads per million (RPM). (D) Histogram of PRO-seq signal intensities (RPM) for the top 10,000 paRNA– and eRNA-producing regions. PRO-seq signal was measured within a 1 kb window centered on ATAC-seq peak summits. Reads mapped to the plus and minus strands were quantified separately. For enhancers (not overlapping promoters), PRO-seq signal was measured within ±500 nt of ATAC-seq peak summits. For intragenic enhancers, only antisense signal relative to the direction of transcription of the corresponding host gene was quantified. PRO-seq signals for paRNAs were similarly quantified within ±500 nt of ATAC-seq peak summits located within ±1 kb of annotated TSSs using only antisense signal relative to gene transcription. Mean and median values are indicated. (E) Histogram showing PRO-seq read distribution for 13,979 paRNA– and 68,052 eRNA-producing loci. PRO-seq signals were calculated as in (D). Intragenic enhancers with only sense PRO-seq signal relative to the host gene transcription were excluded. Mean and median values are indicated.
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(A) Venn diagram showing overlap between ATAC-seq summits and H3K27Ac peaks (±500 nt), used to define 134,520 active enhancers in PHHs. (B) Genomic classification of <t>hepatocyte</t> enhancers relative to position of protein-coding genes (GENCODE v43). (C) Heatmaps of PRO-seq (left), H3K27Ac ChIP-seq (center), and ATAC-seq (right) signal at active enhancers, centered on ATAC-seq summits (± 1,500 nt). Color scale represents normalized read coverage (RPM) per 10 nt bin. Signal above the dashed line corresponds to the 96,169 enhancers exhibiting detectable transcriptional activity, defined as >0.02 PRO-seq reads per million (RPM). (D) Histogram of PRO-seq signal intensities (RPM) for the top 10,000 paRNA– and eRNA-producing regions. PRO-seq signal was measured within a 1 kb window centered on ATAC-seq peak summits. Reads mapped to the plus and minus strands were quantified separately. For enhancers (not overlapping promoters), PRO-seq signal was measured within ±500 nt of ATAC-seq peak summits. For intragenic enhancers, only antisense signal relative to the direction of transcription of the corresponding host gene was quantified. PRO-seq signals for paRNAs were similarly quantified within ±500 nt of ATAC-seq peak summits located within ±1 kb of annotated TSSs using only antisense signal relative to gene transcription. Mean and median values are indicated. (E) Histogram showing PRO-seq read distribution for 13,979 paRNA– and 68,052 eRNA-producing loci. PRO-seq signals were calculated as in (D). Intragenic enhancers with only sense PRO-seq signal relative to the host gene transcription were excluded. Mean and median values are indicated.
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(A) Venn diagram showing overlap between ATAC-seq summits and H3K27Ac peaks (±500 nt), used to define 134,520 active enhancers in PHHs. (B) Genomic classification of <t>hepatocyte</t> enhancers relative to position of protein-coding genes (GENCODE v43). (C) Heatmaps of PRO-seq (left), H3K27Ac ChIP-seq (center), and ATAC-seq (right) signal at active enhancers, centered on ATAC-seq summits (± 1,500 nt). Color scale represents normalized read coverage (RPM) per 10 nt bin. Signal above the dashed line corresponds to the 96,169 enhancers exhibiting detectable transcriptional activity, defined as >0.02 PRO-seq reads per million (RPM). (D) Histogram of PRO-seq signal intensities (RPM) for the top 10,000 paRNA– and eRNA-producing regions. PRO-seq signal was measured within a 1 kb window centered on ATAC-seq peak summits. Reads mapped to the plus and minus strands were quantified separately. For enhancers (not overlapping promoters), PRO-seq signal was measured within ±500 nt of ATAC-seq peak summits. For intragenic enhancers, only antisense signal relative to the direction of transcription of the corresponding host gene was quantified. PRO-seq signals for paRNAs were similarly quantified within ±500 nt of ATAC-seq peak summits located within ±1 kb of annotated TSSs using only antisense signal relative to gene transcription. Mean and median values are indicated. (E) Histogram showing PRO-seq read distribution for 13,979 paRNA– and 68,052 eRNA-producing loci. PRO-seq signals were calculated as in (D). Intragenic enhancers with only sense PRO-seq signal relative to the host gene transcription were excluded. Mean and median values are indicated.
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(A) Venn diagram showing overlap between ATAC-seq summits and H3K27Ac peaks (±500 nt), used to define 134,520 active enhancers in PHHs. (B) Genomic classification of <t>hepatocyte</t> enhancers relative to position of protein-coding genes (GENCODE v43). (C) Heatmaps of PRO-seq (left), H3K27Ac ChIP-seq (center), and ATAC-seq (right) signal at active enhancers, centered on ATAC-seq summits (± 1,500 nt). Color scale represents normalized read coverage (RPM) per 10 nt bin. Signal above the dashed line corresponds to the 96,169 enhancers exhibiting detectable transcriptional activity, defined as >0.02 PRO-seq reads per million (RPM). (D) Histogram of PRO-seq signal intensities (RPM) for the top 10,000 paRNA– and eRNA-producing regions. PRO-seq signal was measured within a 1 kb window centered on ATAC-seq peak summits. Reads mapped to the plus and minus strands were quantified separately. For enhancers (not overlapping promoters), PRO-seq signal was measured within ±500 nt of ATAC-seq peak summits. For intragenic enhancers, only antisense signal relative to the direction of transcription of the corresponding host gene was quantified. PRO-seq signals for paRNAs were similarly quantified within ±500 nt of ATAC-seq peak summits located within ±1 kb of annotated TSSs using only antisense signal relative to gene transcription. Mean and median values are indicated. (E) Histogram showing PRO-seq read distribution for 13,979 paRNA– and 68,052 eRNA-producing loci. PRO-seq signals were calculated as in (D). Intragenic enhancers with only sense PRO-seq signal relative to the host gene transcription were excluded. Mean and median values are indicated.
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(A) Venn diagram showing overlap between ATAC-seq summits and H3K27Ac peaks (±500 nt), used to define 134,520 active enhancers in PHHs. (B) Genomic classification of <t>hepatocyte</t> enhancers relative to position of protein-coding genes (GENCODE v43). (C) Heatmaps of PRO-seq (left), H3K27Ac ChIP-seq (center), and ATAC-seq (right) signal at active enhancers, centered on ATAC-seq summits (± 1,500 nt). Color scale represents normalized read coverage (RPM) per 10 nt bin. Signal above the dashed line corresponds to the 96,169 enhancers exhibiting detectable transcriptional activity, defined as >0.02 PRO-seq reads per million (RPM). (D) Histogram of PRO-seq signal intensities (RPM) for the top 10,000 paRNA– and eRNA-producing regions. PRO-seq signal was measured within a 1 kb window centered on ATAC-seq peak summits. Reads mapped to the plus and minus strands were quantified separately. For enhancers (not overlapping promoters), PRO-seq signal was measured within ±500 nt of ATAC-seq peak summits. For intragenic enhancers, only antisense signal relative to the direction of transcription of the corresponding host gene was quantified. PRO-seq signals for paRNAs were similarly quantified within ±500 nt of ATAC-seq peak summits located within ±1 kb of annotated TSSs using only antisense signal relative to gene transcription. Mean and median values are indicated. (E) Histogram showing PRO-seq read distribution for 13,979 paRNA– and 68,052 eRNA-producing loci. PRO-seq signals were calculated as in (D). Intragenic enhancers with only sense PRO-seq signal relative to the host gene transcription were excluded. Mean and median values are indicated.
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(A) Venn diagram showing overlap between ATAC-seq summits and H3K27Ac peaks (±500 nt), used to define 134,520 active enhancers in PHHs. (B) Genomic classification of hepatocyte enhancers relative to position of protein-coding genes (GENCODE v43). (C) Heatmaps of PRO-seq (left), H3K27Ac ChIP-seq (center), and ATAC-seq (right) signal at active enhancers, centered on ATAC-seq summits (± 1,500 nt). Color scale represents normalized read coverage (RPM) per 10 nt bin. Signal above the dashed line corresponds to the 96,169 enhancers exhibiting detectable transcriptional activity, defined as >0.02 PRO-seq reads per million (RPM). (D) Histogram of PRO-seq signal intensities (RPM) for the top 10,000 paRNA– and eRNA-producing regions. PRO-seq signal was measured within a 1 kb window centered on ATAC-seq peak summits. Reads mapped to the plus and minus strands were quantified separately. For enhancers (not overlapping promoters), PRO-seq signal was measured within ±500 nt of ATAC-seq peak summits. For intragenic enhancers, only antisense signal relative to the direction of transcription of the corresponding host gene was quantified. PRO-seq signals for paRNAs were similarly quantified within ±500 nt of ATAC-seq peak summits located within ±1 kb of annotated TSSs using only antisense signal relative to gene transcription. Mean and median values are indicated. (E) Histogram showing PRO-seq read distribution for 13,979 paRNA– and 68,052 eRNA-producing loci. PRO-seq signals were calculated as in (D). Intragenic enhancers with only sense PRO-seq signal relative to the host gene transcription were excluded. Mean and median values are indicated.

Journal: bioRxiv

Article Title: Profiling and Targeting of Regulatory RNAs to Upregulate Gene Expression

doi: 10.64898/2026.04.21.719874

Figure Lengend Snippet: (A) Venn diagram showing overlap between ATAC-seq summits and H3K27Ac peaks (±500 nt), used to define 134,520 active enhancers in PHHs. (B) Genomic classification of hepatocyte enhancers relative to position of protein-coding genes (GENCODE v43). (C) Heatmaps of PRO-seq (left), H3K27Ac ChIP-seq (center), and ATAC-seq (right) signal at active enhancers, centered on ATAC-seq summits (± 1,500 nt). Color scale represents normalized read coverage (RPM) per 10 nt bin. Signal above the dashed line corresponds to the 96,169 enhancers exhibiting detectable transcriptional activity, defined as >0.02 PRO-seq reads per million (RPM). (D) Histogram of PRO-seq signal intensities (RPM) for the top 10,000 paRNA– and eRNA-producing regions. PRO-seq signal was measured within a 1 kb window centered on ATAC-seq peak summits. Reads mapped to the plus and minus strands were quantified separately. For enhancers (not overlapping promoters), PRO-seq signal was measured within ±500 nt of ATAC-seq peak summits. For intragenic enhancers, only antisense signal relative to the direction of transcription of the corresponding host gene was quantified. PRO-seq signals for paRNAs were similarly quantified within ±500 nt of ATAC-seq peak summits located within ±1 kb of annotated TSSs using only antisense signal relative to gene transcription. Mean and median values are indicated. (E) Histogram showing PRO-seq read distribution for 13,979 paRNA– and 68,052 eRNA-producing loci. PRO-seq signals were calculated as in (D). Intragenic enhancers with only sense PRO-seq signal relative to the host gene transcription were excluded. Mean and median values are indicated.

Article Snippet: At 4 hours post-plating, cells were treated with 5 μM ASO via gymnosis in Cellartis Power Primary Hepatocyte Medium.

Techniques: ChIP-sequencing, Activity Assay