Macroh2a1 macroH2A.1 histone [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Macroh2a1provided by MGI
Official Full Name: macroH2A.1 histoneprovided by MGI
Primary source: MGI:MGI:1349392
See related: Ensembl:ENSMUSG00000015937 AllianceGenome:MGI:1349392
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: H2afy; mH2a1; H2AF12M
Summary: 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, Nov 2015]
Expression: Ubiquitous expression in thymus adult (RPKM 36.0), CNS E11.5 (RPKM 35.6) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13 B1; 13 30.06 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (56221435..56283439, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (56073622..56135626, complement)

Chromosome 13 - NC_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Histone variant macroH2A1 regulates synchronous firing of replication origins in the inactive X chromosome.
Title: Histone variant macroH2A1 regulates synchronous firing of replication origins in the inactive X chromosome.
Deficiency of histone variant macroH2A1.1 is associated with sexually dimorphic obesity in mice.
Title: Deficiency of histone variant macroH2A1.1 is associated with sexually dimorphic obesity in mice.
MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping.
Title: MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping.
Histone macroH2A1 is a stronger regulator of hippocampal transcription and memory than macroH2A2 in mice.
Title: Histone macroH2A1 is a stronger regulator of hippocampal transcription and memory than macroH2A2 in mice.
Mutant U2AF1-induced alternative splicing of H2afy (macroH2A1) regulates B-lymphopoiesis in mice.
Title: Mutant U2AF1-induced alternative splicing of H2afy (macroH2A1) regulates B-lymphopoiesis in mice.
The Histone Variant MacroH2A1 Regulates Key Genes for Myogenic Cell Fusion in a Splice-Isoform Dependent Manner.
Title: The Histone Variant MacroH2A1 Regulates Key Genes for Myogenic Cell Fusion in a Splice-Isoform Dependent Manner.
LSH mediates gene repression through macroH2A deposition.
Title: LSH mediates gene repression through macroH2A deposition.
Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability.
Title: Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability.
Data report for the first time that loss of macroH2A1.1 expression in mice led to the dysregulation of myeloid differentiation. Thus, macroH2A1.1 delineates its function in hematopoietic stem cell homeostasis and differentiation in mice.
Title: Deficiency and haploinsufficiency of histone macroH2A1.1 in mice recapitulate hematopoietic defects of human myelodysplastic syndrome.
These data indicate that macroH2A1.1-containing chromatin regulates mitochondrial respiration by limiting nuclear NAD(+) consumption and establishing a buffer of NAD(+) precursors in differentiated cells.
Title: MacroH2A1.1 regulates mitochondrial respiration by limiting nuclear NAD(+) consumption.

Submit: New GeneRIF Correction See all GeneRIFs (32)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2) 1 citation
Targeted (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

H2afy (e-PCR), detects polymorphism
- UniSTS:547234

D13Mit113 (e-PCR), detects polymorphism
- UniSTS:126939

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ADP-D-ribose binding	IDA Inferred from Direct Assay more info	PubMed
enables ADP-D-ribose binding	ISO Inferred from Sequence Orthology more info
enables ADP-D-ribose modification-dependent protein binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded methylated DNA binding	IEA Inferred from Electronic Annotation more info
enables double-stranded methylated DNA binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables nucleosomal DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleosomal DNA binding	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein kinase binding	IEA Inferred from Electronic Annotation more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein serine/threonine kinase inhibitor activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase inhibitor activity	ISO Inferred from Sequence Orthology more info
enables rDNA binding	IEA Inferred from Electronic Annotation more info
enables rDNA binding	ISO Inferred from Sequence Orthology more info
enables structural constituent of chromatin	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of chromatin	IEA Inferred from Electronic Annotation more info
enables structural constituent of chromatin	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in epigenetic regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in establishment of protein localization to chromatin	IEA Inferred from Electronic Annotation more info
involved_in establishment of protein localization to chromatin	ISO Inferred from Sequence Orthology more info
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of cell cycle G2/M phase transition	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell cycle G2/M phase transition	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression, epigenetic	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression, epigenetic	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein localization to chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein localization to chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein serine/threonine kinase activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of response to oxidative stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of response to oxidative stress	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription of nucleolar large rRNA by RNA polymerase I	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription of nucleolar large rRNA by RNA polymerase I	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription of nucleolar large rRNA by RNA polymerase I	ISO Inferred from Sequence Orthology more info
involved_in nucleosome assembly	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of endodermal cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of endodermal cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of keratinocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of keratinocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of maintenance of mitotic sister chromatid cohesion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of maintenance of mitotic sister chromatid cohesion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of response to oxidative stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of response to oxidative stress	ISO Inferred from Sequence Orthology more info
involved_in regulation of NAD metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of lipid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of oxidative phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of response to oxidative stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of response to oxidative stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sex-chromosome dosage compensation	ISO Inferred from Sequence Orthology more info
involved_in transcription initiation-coupled chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in transcription initiation-coupled chromatin remodeling	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Barr body	ISO Inferred from Sequence Orthology more info	PubMed
located_in centrosome	TAS Traceable Author Statement more info	PubMed
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in condensed chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear chromosome	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
part_of nucleosome	IBA Inferred from Biological aspect of Ancestor more info
part_of nucleosome	IEA Inferred from Electronic Annotation more info
part_of nucleosome	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in pericentric heterochromatin	IEA Inferred from Electronic Annotation more info
located_in pericentric heterochromatin	ISO Inferred from Sequence Orthology more info
located_in site of DNA damage	IEA Inferred from Electronic Annotation more info
is_active_in site of DNA damage	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: core histone macro-H2A.1

Names: H2A histone family, member Y; H2A.y; H2A/y; MACROH2A1.2; histone macroH2A1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001159513.1 → NP_001152985.1 core histone macro-H2A.1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (2) lacks one internal residue, compared to isoform 1.

Source sequence(s)

AB071988, AK003531, BB633156, BE988321, CJ095488, CV561613

UniProtKB/Swiss-Prot

Q9QZQ8

UniProtKB/TrEMBL

Q9CTH9

Conserved Domains (3) summary

cd00074
Location:5 → 117

H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...

cd02904
Location:177 → 363

Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...

pfam06959
Location:130 → 172

RecQ5; RecQ helicase protein-like 5 (RecQ5)
NM_001159514.1 → NP_001152986.1 core histone macro-H2A.1 isoform 3

See identical proteins and their annotated locations for NP_001152986.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate exon in the central coding region, compared to variant 1. The resulting isoform (3) differs in one internal segment, compared to isoform 1.

Source sequence(s)

AB071988, AK003531, AW990415, BB633156, BE988321, CJ095488

Consensus CDS

CCDS49278.1

UniProtKB/Swiss-Prot

Q91VZ2, Q9QZQ7, Q9QZQ8

Related

ENSMUSP00000038221.8, ENSMUST00000045788.9

Conserved Domains (2) summary

cd00074
Location:5 → 117

H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...

cd02904
Location:178 → 361

Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
NM_001159515.1 → NP_001152987.1 core histone macro-H2A.1 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate in-frame splice site and an alternate exon in the central coding region, compared to variant 1. The resulting isoform (4) lacks an internal residue and differs in an internal segment, compared to isoform 1.

Source sequence(s)

AB071988, AK003531, BB633156, BE988321, CB574813, CJ095488

UniProtKB/Swiss-Prot

Q9QZQ8

UniProtKB/TrEMBL

Q9CTH9

Conserved Domains (3) summary

cd00074
Location:5 → 117

H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...

cd02904
Location:177 → 360

Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...

pfam06959
Location:130 → 172

RecQ5; RecQ helicase protein-like 5 (RecQ5)
NM_012015.2 → NP_036145.1 core histone macro-H2A.1 isoform 1

See identical proteins and their annotated locations for NP_036145.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AB071988, AK003531, BB633156, BE988321, CJ095488

Consensus CDS

CCDS26557.1

UniProtKB/Swiss-Prot

Q9QZQ8

UniProtKB/TrEMBL

Q9CTH9

Related

ENSMUSP00000016081.7, ENSMUST00000016081.13

Conserved Domains (2) summary

cd00074
Location:5 → 117

H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...

cd02904
Location:178 → 364

Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000079.7 Reference GRCm39 C57BL/6J

Range

56221435..56283439 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006517258.3 → XP_006517321.1 core histone macro-H2A.1 isoform X2

See identical proteins and their annotated locations for XP_006517321.1

UniProtKB/TrEMBL

Q8CA90

Conserved Domains (3) summary

cd00074
Location:5 → 117

H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...

pfam06959
Location:130 → 172

RecQ5; RecQ helicase protein-like 5 (RecQ5)

cl00019
Location:177 → 195

Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...
XM_006517257.3 → XP_006517320.1 core histone macro-H2A.1 isoform X1

Conserved Domains (1) summary

cd00074
Location:5 → 117

H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...