H4C3
H4 clustered histone 3 | H4/g, dJ221C16.1, H4FG, HIST1H4C

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H4 family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015]

Member of: DE-6 DE-6.13
Biological processes 31 terms
DNA binding (GO:0003677)DNA binding (GO:0003677)RNA binding (GO:0003723)chromatin organization (GO:0006325)chromosome (GO:0005694)chromosome, telomeric region (GO:0000781)extracellular exosome (GO:0070062)extracellular exosome (GO:0070062)extracellular region (GO:0005576)membrane (GO:0016020)negative regulation of megakaryocyte differentiation (GO:0045653)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleosome (GO:0000786)nucleosome (GO:0000786)nucleosome (GO:0000786)nucleosome assembly (GO:0006334)nucleosome assembly (GO:0006334)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)protein heterodimerization activity (GO:0046982)protein localization to CENP-A containing chromatin (GO:0061644)protein-containing complex (GO:0032991)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)telomere organization (GO:0032200)
Expression (TPM)
H4C3 — as a Regulated Gene

TFs regulating H4C3 0 TFs

Transcription factors with Perturb-seq knockdown data for H4C3. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = H4C3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to H4C3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of H4C3, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr6:25,882,032–25,882,516 221.6 kb Distal (>10kb) Multiome 165
chr6:25,992,391–25,993,479 111.2 kb Distal (>10kb) Multiome 1012
chr6:26,020,104–26,022,401 83.6 kb Distal (>10kb) Multiome 920
chr6:26,025,866–26,027,859 77.6 kb Distal (>10kb) Multiome 1194
chr6:26,031,341–26,032,990 71.8 kb Distal (>10kb) Multiome 1083
chr6:26,033,113–26,034,309 70.3 kb Distal (>10kb) Multiome 800
chr6:26,054,926–26,057,287 48.6 kb Distal (>10kb) Multiome 1174
chr6:26,087,383–26,088,017 16.3 kb Distal (>10kb) Multiome 572
chr6:26,097,401–26,097,584 6.3 kb Proximal (<10kb) 186
chr6:26,103,452–26,105,109 2 bp At TSS Multiome 1169
chr6:26,122,481–26,124,909 19.0 kb Distal (>10kb) Multiome 1216
chr6:26,125,788–26,126,592 22.3 kb Distal (>10kb) Multiome 670
chr6:26,156,184–26,158,744 54.1 kb Distal (>10kb) Multiome 1310
chr6:26,171,798–26,172,499 68.1 kb Distal (>10kb) Multiome 580
chr6:26,183,128–26,184,377 79.8 kb Distal (>10kb) Multiome 311
chr6:26,187,874–26,189,538 85.2 kb Distal (>10kb) Multiome 1053
chr6:26,196,695–26,197,676 93.4 kb Distal (>10kb) Multiome 842
chr6:26,198,203–26,200,197 95.5 kb Distal (>10kb) Multiome 939
chr6:26,203,791–26,205,119 100.5 kb Distal (>10kb) Multiome 1071
chr6:26,214,872–26,218,468 112.9 kb Distal (>10kb) Multiome 1096
chr6:26,223,716–26,224,480 120.1 kb Distal (>10kb) Multiome 507
chr6:26,224,856–26,226,566 121.3 kb Distal (>10kb) Multiome 451
chr6:26,239,944–26,240,920 136.4 kb Distal (>10kb) Multiome 375
chr6:26,249,682–26,251,138 146.4 kb Distal (>10kb) Multiome 731
chr6:26,251,339–26,252,079 147.8 kb Distal (>10kb) Multiome 445
chr6:26,270,815–26,273,967 169.0 kb Distal (>10kb) Multiome 742
chr6:26,285,011–26,286,121 181.6 kb Distal (>10kb) Multiome 1121
chr6:26,304,972–26,305,585 201.5 kb Distal (>10kb) Multiome 586
chr6:26,312,505–26,313,475 209.1 kb Distal (>10kb) Multiome 896
chr6:26,322,092–26,323,232 218.7 kb Distal (>10kb) Multiome 811
chr6:26,327,476–26,328,318 224.2 kb Distal (>10kb) Multiome 716
chr6:26,341,545–26,342,139 237.8 kb Distal (>10kb) Multiome 716
chr6:26,365,073–26,365,647 261.4 kb Distal (>10kb) Multiome 587
chr6:26,382,957–26,383,951 279.2 kb Distal (>10kb) Multiome 448
chr6:27,145,480–27,148,111 1043.1 kb Distal (>10kb) Multiome HiCAR 951

Genome Browser

Genomic view of the H4C3 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr6:25,872,032 – 27,158,111
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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