smarca4a SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: smarca4aprovided by ZNC
Official Full Name: SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030605-1
See related: Ensembl:ENSDARG00000077226 AllianceGenome:ZFIN:ZDB-GENE-030605-1
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: brg1; smarca2; smarca4; wu:fb51a08
Summary: Predicted to enable DNA binding activity; chromatin binding activity; and nucleosome array spacer activity. Acts upstream of or within several processes, including camera-type eye development; heart development; and nervous system development. Predicted to be located in chromatin. Predicted to be part of SWI/SNF complex. Predicted to be active in nucleus. Is expressed in several structures, including hematopoietic multipotent progenitor cell; mesoderm; nervous system; pectoral fin; and presumptive neural retina. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 4; hepatocellular carcinoma; lung non-small cell carcinoma; and rhabdoid cancer. Orthologous to human SMARCA4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 3

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	3	NC_007114.7 (19245806..19281878)
105	previous assembly	GRCz10 (GCF_000002035.5)	3	NC_007114.6 (19099291..19131507)

Chromosome 3 - NC_007114.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The chromatin remodeler Brg1 is required for formation and maintenance of hematopoietic stem cells.
Title: The chromatin remodeler Brg1 is required for formation and maintenance of hematopoietic stem cells.
promotes heart regeneration by repressing cyclin-dependent kinase inhibitors partly through Dnmt3ab-dependent DNA methylation
Title: Chromatin-remodelling factor Brg1 regulates myocardial proliferation and regeneration in zebrafish.
Transplantation experiments demonstrated that med14 and brg1 are required directly in neural crest cells. Analysis of med14; brg1 double mutant embryos suggested the existence of strong genetic interaction between members of Mediator and BAF complexes.
Title: Med14 cooperates with brg1 in the differentiation of skeletogenic neural crest.
The purpose of this study was to develop a framework for analyzing retinal pigment epithelium (RPE) expression profiles from zebrafish smarca4 mutants.
Title: Expression profiling of the RPE in zebrafish smarca4 mutant revealed altered signals that potentially affect RPE and retinal differentiation.
These observations suggest a different regulatory mechanism on bhlhe22 expression by smarca4 and irx7.
Title: Irx7, a Smarca4-regulated gene for retinal differentiation, regulates other genes controlled by Smarca4 in zebrafish retinas.
Cellular expression of Smarca4 (Brg1)-regulated genes in zebrafish retinas
Title: Cellular expression of Smarca4 (Brg1)-regulated genes in zebrafish retinas.
Disrupting the balance between Brg1 and disease-causing cardiac transcription factors, including Tbx5, Tbx20 and Nkx2-5, causes severe cardiac anomalies.
Title: Chromatin remodelling complex dosage modulates transcription factor function in heart development.
Results implicate ATP-dependent chromatin remodelers such as Brg1 in myogenic microRNA gene regulation.
Title: Myogenic microRNA expression requires ATP-dependent chromatin remodeling enzyme function.
Results suggest that Brg1 is involved in neural crest induction, which is critical for the development of neurons, glia, pigment cells, and craniofacial structures.
Title: Critical role of Brg1 member of the SWI/SNF chromatin remodeling complex during neurogenesis and neural crest induction in zebrafish.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

fc81g12.y1 (e-PCR)
- UniSTS:194590

fc27d06.x1 (e-PCR)
- UniSTS:193355

fb30b02.x1 (e-PCR)
- UniSTS:190379

fb51a08.x1 (e-PCR)
- UniSTS:190647

fc78d10.y1 (e-PCR)
- UniSTS:194518

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables nucleosome array spacer activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cardiac muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell migration involved in heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within central nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic camera-type eye morphogenesis	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within embryonic retina morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hematopoietic progenitor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neural crest cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural retina development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within optic nerve formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of MAPK cascade	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within positive regulation of nitric oxide mediated signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within retina layer formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retinal pigment epithelium development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of SWI/SNF complex	IEA Inferred from Electronic Annotation more info
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4a; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4a

Names: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4; brahma protein-like protein 1; brahma-related gene 1; yng; young

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_181603.1 → NP_853634.1 SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4a

See identical proteins and their annotated locations for NP_853634.1

Status: PROVISIONAL

Source sequence(s)

AY205256

UniProtKB/TrEMBL

A0A286Y8V2, F6NKY0, Q7ZSY3

Related

ENSDARP00000143385.1, ENSDART00000174668.2

Conserved Domains (8) summary

cd05516
Location:1440 → 1545

Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...

smart00573
Location:478 → 550

HSA; domain in helicases and associated with SANT domains

pfam07533
Location:630 → 670

BRK; BRK domain

pfam08880
Location:198 → 231

QLQ; QLQ

pfam09606
Location:65 → 378

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam14619
Location:1301 → 1368

SnAC; Snf2-ATP coupling, chromatin remodelling complex

cl25732
Location:388 → 595

SMC_N; RecF/RecN/SMC N terminal domain

cl26465
Location:762 → 1244

SNF2_N; SNF2 family N-terminal domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007114.7 Reference GRCz11 Primary Assembly

Range

19245806..19281878

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021469728.2 → XP_021325403.1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4a isoform X1

UniProtKB/TrEMBL

A0A286Y8V2, F6NKY0, Q7ZSY3

Related

ENSDARP00000120295.1, ENSDART00000134514.2

Conserved Domains (8) summary

cd05516
Location:1440 → 1545

Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...

smart00573
Location:478 → 550

HSA; domain in helicases and associated with SANT domains

pfam07533
Location:630 → 670

BRK; BRK domain

pfam08880
Location:198 → 231

QLQ; QLQ

pfam09606
Location:65 → 378

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam14619
Location:1301 → 1368

SnAC; Snf2-ATP coupling, chromatin remodelling complex

cl25732
Location:388 → 595

SMC_N; RecF/RecN/SMC N terminal domain

cl26465
Location:762 → 1244

SNF2_N; SNF2 family N-terminal domain