SUPT16H SPT16 homolog, facilitates chromatin remodeling subunit [Homo sapiens (human)] - Gene

Summary

Official Symbol: SUPT16Hprovided by HGNC
Official Full Name: SPT16 homolog, facilitates chromatin remodeling subunitprovided by HGNC
Primary source: HGNC:HGNC:11465
See related: Ensembl:ENSG00000092201 MIM:605012; AllianceGenome:HGNC:11465
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: CDC68; SPT16; NEDDFAC; FACTP140; SPT16/CDC68
Summary: Transcription of protein-coding genes can be reconstituted on naked DNA with only the general transcription factors and RNA polymerase II. However, this minimal system cannot transcribe DNA packaged into chromatin, indicating that accessory factors may facilitate access to DNA. One such factor, FACT (facilitates chromatin transcription), interacts specifically with histones H2A/H2B to effect nucleosome disassembly and transcription elongation. FACT is composed of an 80 kDa subunit and a 140 kDa subunit; this gene encodes the 140 kDa subunit. [provided by RefSeq, Feb 2009]
Expression: Ubiquitous expression in testis (RPKM 30.8), lymph node (RPKM 27.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q11.2

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (21351476..21384019, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (15548935..15581495, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (21819635..21852178, complement)

Chromosome 14 - NC_000014.9 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 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 Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The fly homolog of SUPT16H, a gene associated with neurodevelopmental disorders, is required in a cell-autonomous fashion for cell survival.
Title: The fly homolog of SUPT16H, a gene associated with neurodevelopmental disorders, is required in a cell-autonomous fashion for cell survival.
Structural basis for H2A-H2B recognitions by human Spt16.
Title: Structural basis for H2A-H2B recognitions by human Spt16.
Supt16 Haploinsufficiency Impairs PI3K/AKT/mTOR/Autophagy Pathway in Human Pluripotent Stem Cells Derived Neural Stem Cells.
Title: Supt16 Haploinsufficiency Impairs PI3K/AKT/mTOR/Autophagy Pathway in Human Pluripotent Stem Cells Derived Neural Stem Cells.
Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes.
Title: Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes.
FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling.
Title: FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling.
De novo variants in SUPT16H cause neurodevelopmental disorders associated with corpus callosum abnormalities.
Title: De novo variants in SUPT16H cause neurodevelopmental disorders associated with corpus callosum abnormalities.
Neurodevelopmental phenotype associated with CHD8-SUPT16H duplication.
Title: Neurodevelopmental phenotype associated with CHD8-SUPT16H duplication.
Proteasomal Regulation of Mammalian SPT16 in Controlling Transcription.
Title: Proteasomal Regulation of Mammalian SPT16 in Controlling Transcription.
suggest a compelling mechanism for how FACT maintains chromatin integrity during polymerase passage, by facilitating removal of the H2A-H2B dimer, stabilizing intermediate subnucleosomal states and promoting nucleosome reassembly
Title: FACT caught in the act of manipulating the nucleosome.
FACT subunit Spt16 controls UVSSA recruitment to lesion-stalled RNA Pol II and stimulates transcription-coupled nucleotide excision repair.
Title: FACT subunit Spt16 controls UVSSA recruitment to lesion-stalled RNA Pol II and stimulates TC-NER.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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
Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum MedGen: C5551361 OMIM: 619480 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2012-05-09) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2012-05-09) ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
shRNA knockdown of SUPT16H increases HIV-1 LTR-driven gene expression in HEK293 cells transduced with VSV-G pseudo-typed HIV-1 NL4-3-Luc construct; i.e. HIV-1 is restricted by SUPT16H	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	HIV-1 Rev interacting protein, suppressor of Ty 16 homolog (SUPT16H), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with SUPT16H is increased by RRE	PubMed
Tat	tat	The heterodimeric complex FACT proteins SPT16 and SSRP1 are recognized to interact with HIV-1 in Jurkat cell	PubMed
	tat	HIV-1 Tat activated transcription facilitates removal of histones H2A and H2B at the LTR, and that the FACT complex, at least consisting of SPT16 and SSRP1, may be responsible for their removal	PubMed

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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

WI-20203 (e-PCR)
- UniSTS:29445

G29214 (e-PCR)
- UniSTS:6927

WI-20832 (e-PCR)
- UniSTS:6943

D14S1321 (e-PCR)
- UniSTS:65859

RH48778 (e-PCR)
- UniSTS:40313

WI-14045 (e-PCR)
- UniSTS:39614

G20455 (e-PCR)
- UniSTS:12256

A005R45 (e-PCR)
- UniSTS:12257

A004V16 (e-PCR)
- UniSTS:61411

G35908 (e-PCR)
- UniSTS:24053

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables nucleosome binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in nucleosome assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in nucleosome disassembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription, elongation	TAS Traceable Author Statement more info	PubMed
involved_in transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed
involved_in transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of FACT complex	IBA Inferred from Biological aspect of Ancestor more info
part_of FACT complex	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: FACT complex subunit SPT16

Names: FACT 140 kDa subunit; chromatin-specific transcription elongation factor 140 kDa subunit; facilitates chromatin remodeling 140 kDa subunit; facilitates chromatin transcription complex subunit SPT16; hSPT16; suppressor of Ty 16 homolog

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.