MACROH2A1

macroH2A.1 histone | macroH2A1.2, H2AFY

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent histone that is a member of the histone H2A family. It replaces conventional H2A histones in a subset of nucleosomes where it represses transcription and participates in stable X chromosome inactivation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]

Member of: DE-1 DE-1.25 Developmental clusters: GC6

Biological processes 80 terms

ADP-D-ribose binding (GO:0072570)ADP-D-ribose modification-dependent protein binding (GO:0160002)ADP-D-ribose modification-dependent protein binding (GO:0160002)Barr body (GO:0001740)Barr body (GO:0001740)DNA binding (GO:0003677)DNA binding (GO:0003677)DNA repair (GO:0006281)RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)chromatin (GO:0000785)chromatin (GO:0000785)chromatin DNA binding (GO:0031490)chromatin DNA binding (GO:0031490)chromatin binding (GO:0003682)chromosome (GO:0005694)chromosome, telomeric region (GO:0000781)condensed chromosome (GO:0000793)dosage compensation by inactivation of X chromosome (GO:0009048)dosage compensation by inactivation of X chromosome (GO:0009048)double-stranded methylated DNA binding (GO:0010385)enzyme binding (GO:0019899)epigenetic regulation of gene expression (GO:0040029)establishment of protein localization to chromatin (GO:0071169)establishment of protein localization to chromatin (GO:0071169)extracellular exosome (GO:0070062)heterochromatin formation (GO:0031507)negative regulation of cell cycle G2/M phase transition (GO:1902750)negative regulation of gene expression, epigenetic (GO:0045814)negative regulation of protein localization to chromosome, telomeric region (GO:1904815)negative regulation of response to oxidative stress (GO:1902883)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription of nucleolar large rRNA by RNA polymerase I (GO:1901837)negative regulation of transcription of nucleolar large rRNA by RNA polymerase I (GO:1901837)negative regulation of transcription of nucleolar large rRNA by RNA polymerase I (GO:1901837)negative regulation of transcription of nucleolar large rRNA by RNA polymerase I (GO:1901837)nuclear chromosome (GO:0000228)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleosomal DNA binding (GO:0031492)nucleosomal DNA binding (GO:0031492)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)pericentric heterochromatin (GO:0005721)poly-ADP-D-ribose modification-dependent protein binding (GO:0160004)positive regulation of endodermal cell differentiation (GO:1903226)positive regulation of keratinocyte differentiation (GO:0045618)positive regulation of keratinocyte differentiation (GO:0045618)positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)positive regulation of response to oxidative stress (GO:1902884)promoter-specific chromatin binding (GO:1990841)promoter-specific chromatin binding (GO:1990841)protein binding (GO:0005515)protein heterodimerization activity (GO:0046982)protein kinase binding (GO:0019901)protein serine/threonine kinase inhibitor activity (GO:0030291)rDNA binding (GO:0000182)regulation of NAD metabolic process (GO:1902688)regulation of NAD metabolic process (GO:1902688)regulation of lipid metabolic process (GO:0019216)regulation of oxidative phosphorylation (GO:0002082)regulation of oxidative phosphorylation (GO:0002082)regulation of rDNA heterochromatin formation (GO:0061187)regulation of response to oxidative stress (GO:1902882)regulation of response to oxidative stress (GO:1902882)sex chromatin (GO:0001739)site of DNA damage (GO:0090734)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)transcription cis-regulatory region binding (GO:0000976)transcription initiation-coupled chromatin remodeling (GO:0045815)

Expression (TPM)

TFs regulating MACROH2A1 0 TFs

Transcription factors with Perturb-seq knockdown data for MACROH2A1. 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 = MACROH2A1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to MACROH2A1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of MACROH2A1, 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.

Element	Dist. to TSS	Link type	TFs
chr5:135,149,740–135,150,607	249.1 kb	Distal (>10kb) Multiome	86
chr5:135,191,031–135,191,899	207.7 kb	Distal (>10kb) Multiome	728
chr5:135,307,347–135,308,154	91.5 kb	Distal (>10kb) Multiome	124
chr5:135,395,361–135,395,782	3.4 kb	Proximal (<10kb)	44
chr5:135,398,125–135,400,713	782 bp	At TSS Multiome	973
chr5:135,403,574–135,403,776	4.3 kb	Proximal (<10kb)	21
chr5:135,465,814–135,467,333	67.1 kb	Distal (>10kb) Multiome	341
chr5:135,478,683–135,479,412	79.9 kb	Distal (>10kb) Multiome	177
chr5:135,488,761–135,489,592	89.8 kb	Distal (>10kb) Multiome	472
chr5:135,491,551–135,492,281	92.6 kb	Distal (>10kb) Multiome	397
chr5:135,534,725–135,536,450	136.9 kb	Distal (>10kb) Multiome	424
chr5:135,578,670–135,579,411	179.8 kb	Distal (>10kb) Multiome	193

Genome Browser

Genomic view of the MACROH2A1 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.