SMARCE1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCE1provided by HGNC
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1provided by HGNC
Primary source: HGNC:HGNC:11109
See related: Ensembl:ENSG00000073584 MIM:603111; Vega:OTTHUMG00000133367
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CSS5; BAF57
Summary: The protein encoded by this gene is part of the large ATP-dependent chromatin remodeling complex SWI/SNF, which is required for transcriptional activation of genes normally repressed by chromatin. The encoded protein, either alone or when in the SWI/SNF complex, can bind to 4-way junction DNA, which is thought to mimic the topology of DNA as it enters or exits the nucleosome. The protein contains a DNA-binding HMG domain, but disruption of this domain does not abolish the DNA-binding or nucleosome-displacement activities of the SWI/SNF complex. Unlike most of the SWI/SNF complex proteins, this protein has no yeast counterpart. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in endometrium (RPKM 61.3), ovary (RPKM 41.8) and 25 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 17q21.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	17	NC_000017.11 (40627720..40647851, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (38781214..38805658, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

High SMARCE1 expression is associated with eventual relapse and metastasis in breast cancer.
Title: SMARCE1 is required for the invasive progression of in situ cancers.
miR-29a promotes hepatitis B virus (HBV) replication and expression through regulating SMARCE1 in HBV-infected HepG2.2.15 cells.
Title: miR-29a promotes hepatitis B virus replication and expression by targeting SMARCE1 in hepatoma carcinoma.
the malignancy risk in schwannomatosis is not well defined but may include an increased risk of malignant peripheral nerve sheath tumor in SMARCB1 Imaging protocols are also proposed for SMARCB1 and LZTR1 schwannomatosis and SMARCE1-related meningioma predisposition.
Title: Cancer and Central Nervous System Tumor Surveillance in Pediatric Neurofibromatosis 2 and Related Disorders.
BAF57, BAF60a and SNF5 might act as novel pro-senescence factors in both normal and tumor human skin cells
Title: Cellular senescence regulated by SWI/SNF complex subunits through p53/p21 and p16/pRB pathway.
We report here three additional individuals with clinical features consistent with CSS and alterations in SMARCE1, one of which is novel. The probands all exhibited dysmorphic facial features, moderate developmental and cognitive delay, poor growth, and hypoplastic digital nails/phalanges, including digits not typically affected in the other genes associated with CSS.
Title: SMARCE1, a rare cause of Coffin-Siris Syndrome: Clinical description of three additional cases.
SMARCE1 mutational hits, including novel SMARCE1 mutations, were found in six of eight tested patients with clear cell meningioma
Title: SMARCE1 mutation screening in classification of clear cell meningiomas.
SMARCE1 plays an essential role in breast cancer metastasis by protecting cells against anoikis through the HIF1A/PTK2 pathway.
Title: SMARCE1 regulates metastatic potential of breast cancer cells through the HIF1A/PTK2 pathway.
An exhaustive analysis of the BAF57 molecular and biochemical properties, cellular functions, loss-of-function phenotypes in living organisms and pathological manifestations in cases of human mutations. [review]
Title: The developmental and pathogenic roles of BAF57, a special subunit of the BAF chromatin-remodeling complex.
a family with a pediatric CCM patient and an adult CCM patient and several asymptomatic relatives carrying a germline SMARCE1 mutation.
Title: A heritable form of SMARCE1-related meningiomas with important implications for follow-up and family screening.
Addition of the EGFR inhibitor gefitinib restores the sensitivity of SMARCE1-knockdown cells to MET and ALK inhibitors in NSCLCs. Our findings link SMARCE1 to EGFR oncogenic signaling and suggest targeted treatment options for SMARCE1-deficient tumors.
Title: SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer.

Submit: New GeneRIF Correction See all GeneRIFs (25)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Coffin-Siris syndrome 5 MedGen: C4310788 OMIM: 616938 GeneReviews: Not available	Compare labs
Meningioma, familial MedGen: C1333989 OMIM: 607174 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from BioSystems

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Androgen receptor signaling pathway, organism-specific biosystem (from WikiPathways)
Androgen receptor signaling pathway, organism-specific biosystemAndrogens, mainly testosterone and 5alpha-dihydrotestosterone (DHT) play significant role in the growth and development of the male reproductive organs. These steroid hormones bring about their biolo...
Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
Chromatin organization, organism-specific biosystem (from REACTOME)
Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...
RMTs methylate histone arginines, organism-specific biosystem (from REACTOME)
RMTs methylate histone arginines, organism-specific biosystemArginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways...
Regulation of Androgen receptor activity, organism-specific biosystem (from Pathway Interaction Database)
Regulation of Androgen receptor activity, organism-specific biosystem
Regulation of Androgen receptor activity

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-AA035420 (e-PCR)
- UniSTS:22083

A002R45 (e-PCR)
- UniSTS:27721

D17S1237 (e-PCR)
- UniSTS:149850

SMARCE1_2145 (e-PCR)
- UniSTS:281023

RH103157 (e-PCR)
- UniSTS:97491

Homology

Homologs of the SMARCE1 gene: The SMARCE1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, mosquito, C.elegans, and frog.
Orthologs from Annotation Pipeline: 246 organisms have orthologs with human gene SMARCE1
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
N-acetyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
RNA binding	IEA Inferred from Electronic Annotation more info
contributes_to RNA polymerase II distal enhancer sequence-specific DNA binding	HDA more info	PubMed
contributes_to RNA polymerase II proximal promoter sequence-specific DNA binding	HDA more info	PubMed
chromatin binding	TAS Traceable Author Statement more info	PubMed
nuclear receptor binding	IPI Inferred from Physical Interaction more info	PubMed
contributes_to nucleosomal DNA binding	HDA more info	PubMed
protein N-terminus binding	IPI Inferred from Physical Interaction more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
transcription coactivator activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
ATP-dependent chromatin remodeling	HDA more info	PubMed
chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
negative regulation of transcription, DNA-templated	IDA Inferred from Direct Assay more info	PubMed
neurogenesis	IEA Inferred from Electronic Annotation more info
nucleosome disassembly	IDA Inferred from Direct Assay more info	PubMed
positive regulation of nucleic acid-templated transcription	IEA Inferred from Electronic Annotation more info
regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
SWI/SNF complex	IDA Inferred from Direct Assay more info	PubMed
nBAF complex	ISS Inferred from Sequence or Structural Similarity more info
npBAF complex	ISS Inferred from Sequence or Structural Similarity more info
nuclear chromatin	HDA more info	PubMed
nuclear chromosome	TAS Traceable Author Statement more info	PubMed
nucleoplasm	IDA Inferred from Direct Assay more info
nucleus	IDA Inferred from Direct Assay more info
protein-containing complex	HDA more info	PubMed

General protein information

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Preferred Names: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1

Names: BRG1-associated factor 57; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin e1; chromatin remodeling complex BRG1-associated factor 57

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.

Genomic

NG_032163.1 RefSeqGene

Range

5001..25132

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_003079.4 → NP_003070.3 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1

See identical proteins and their annotated locations for NP_003070.3

Status: REVIEWED

Source sequence(s)

AK095047, BC063700, BQ707908

Consensus CDS

CCDS11370.1

UniProtKB/Swiss-Prot

Q969G3

UniProtKB/TrEMBL

A0A024R1S7

Related

ENSP00000323967.6, OTTHUMP00000164519, ENST00000348513.11, OTTHUMT00000257203

Conserved Domains (3) summary

cd01390
Location:70 → 131

HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...

cl25732
Location:220 → 328

SMC_N; RecF/RecN/SMC N terminal domain

cl26511
Location:110 → 411

Neuromodulin_N; Gap junction protein N-terminal region