H3C6
H3 clustered histone 6 | H3.1, H3/d, H3FD, HIST1H3E

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 H3 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]

Biological processes 31 terms
DNA binding (GO:0003677)cadherin binding (GO:0045296)chromatin organization (GO:0006325)chromosome (GO:0005694)epigenetic regulation of gene expression (GO:0040029)extracellular exosome (GO:0070062)extracellular exosome (GO:0070062)extracellular region (GO:0005576)heterochromatin formation (GO:0031507)membrane (GO:0016020)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleosomal DNA binding (GO:0031492)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 binding (GO:0005515)protein heterodimerization activity (GO:0046982)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)
H3C6 — as a Regulated Gene

TFs regulating H3C6 0 TFs

Transcription factors with Perturb-seq knockdown data for H3C6. 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 = H3C6 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 H3C6

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of H3C6, 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
chr6:25,992,391–25,993,479 231.5 kb Distal (>10kb) Multiome 1012
chr6:26,020,104–26,022,401 203.8 kb Distal (>10kb) Multiome 920
chr6:26,025,866–26,027,859 197.9 kb Distal (>10kb) Multiome 1194
chr6:26,031,341–26,032,990 192.0 kb Distal (>10kb) Multiome 1083
chr6:26,033,113–26,034,309 190.5 kb Distal (>10kb) Multiome 800
chr6:26,054,926–26,057,287 168.9 kb Distal (>10kb) Multiome 1174
chr6:26,087,383–26,088,017 136.5 kb Distal (>10kb) Multiome 572
chr6:26,103,452–26,105,109 120.3 kb Distal (>10kb) Multiome 1169
chr6:26,122,481–26,124,909 101.2 kb Distal (>10kb) Multiome 1216
chr6:26,125,788–26,126,592 98.0 kb Distal (>10kb) Multiome 670
chr6:26,156,184–26,158,744 66.1 kb Distal (>10kb) Multiome 1310
chr6:26,171,798–26,172,499 52.2 kb Distal (>10kb) Multiome 580
chr6:26,183,128–26,184,377 40.5 kb Distal (>10kb) Multiome 311
chr6:26,187,874–26,189,538 35.1 kb Distal (>10kb) Multiome 1053
chr6:26,196,695–26,197,676 26.9 kb Distal (>10kb) Multiome 842
chr6:26,198,203–26,200,197 24.8 kb Distal (>10kb) Multiome 939
chr6:26,203,791–26,205,119 19.7 kb Distal (>10kb) Multiome 1071
chr6:26,214,872–26,218,468 7.3 kb Proximal (<10kb) Multiome 1096
chr6:26,223,716–26,224,480 167 bp At TSS Multiome 507
chr6:26,224,856–26,226,566 1.0 kb Proximal (<10kb) Multiome 451
chr6:26,233,127–26,233,590 8.9 kb Proximal (<10kb) 253
chr6:26,233,599–26,233,863 9.4 kb Proximal (<10kb) 400
chr6:26,233,967–26,234,352 9.8 kb Proximal (<10kb) 415
chr6:26,239,944–26,240,920 16.2 kb Distal (>10kb) Multiome 375
chr6:26,249,682–26,251,138 26.1 kb Distal (>10kb) Multiome 731
chr6:26,251,339–26,252,079 27.5 kb Distal (>10kb) Multiome 445
chr6:26,270,815–26,273,967 48.7 kb Distal (>10kb) Multiome 742
chr6:26,285,011–26,286,121 61.4 kb Distal (>10kb) Multiome 1121
chr6:26,304,972–26,305,585 81.2 kb Distal (>10kb) Multiome 586
chr6:26,312,505–26,313,475 88.8 kb Distal (>10kb) Multiome 896
chr6:26,322,092–26,323,232 98.5 kb Distal (>10kb) Multiome 811
chr6:26,327,476–26,328,318 104.0 kb Distal (>10kb) Multiome 716
chr6:26,341,545–26,342,139 117.6 kb Distal (>10kb) Multiome 716
chr6:26,365,073–26,365,647 141.1 kb Distal (>10kb) Multiome 587
chr6:26,382,957–26,383,951 159.0 kb Distal (>10kb) Multiome 448
chr6:26,421,258–26,421,866 197.2 kb Distal (>10kb) Multiome 473
chr6:26,457,390–26,458,395 233.7 kb Distal (>10kb) Multiome 525
chr6:26,473,842–26,474,357 249.9 kb Distal (>10kb) Multiome 487
chr6:26,520,324–26,522,398 296.7 kb Distal (>10kb) Multiome 1082
chr6:27,131,467–27,132,107 907.5 kb Distal (>10kb) Multiome HiCAR 580
chr6:27,132,200–27,134,276 908.7 kb Distal (>10kb) Multiome HiCAR 975
chr6:27,139,091–27,140,128 915.2 kb Distal (>10kb) Multiome HiCAR 662
chr6:27,145,480–27,148,111 922.8 kb Distal (>10kb) Multiome HiCAR 951
chr6:27,791,916–27,792,609 1568.2 kb Distal (>10kb) Multiome HiCAR 728
chr6:27,806,645–27,808,975 1583.8 kb Distal (>10kb) Multiome HiCAR 963
chr6:27,809,816–27,810,576 1585.9 kb Distal (>10kb) Multiome HiCAR 914
chr6:27,813,688–27,816,146 1590.8 kb Distal (>10kb) Multiome HiCAR 564
chr6:27,836,792–27,839,128 1614.2 kb Distal (>10kb) Multiome HiCAR 1131
chr6:27,865,093–27,868,152 1643.4 kb Distal (>10kb) Multiome HiCAR 744
chr6:27,870,957–27,872,527 1648.1 kb Distal (>10kb) Multiome HiCAR 426
chr6:27,872,808–27,873,995 1649.4 kb Distal (>10kb) Multiome HiCAR 372
chr6:27,889,436–27,895,972 1669.1 kb Distal (>10kb) Multiome HiCAR 1215

Genome Browser

Genomic view of the H3C6 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.

chr6:25,982,391 – 27,905,972
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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