LOC108281177 SOX2 5' regulatory region [Homo sapiens (human)] - Gene

Summary

Gene symbol: LOC108281177
Gene description: SOX2 5' regulatory region
Gene type: biological region
Feature type(s): protein_bind
regulatory: enhancer, promoter, silencer
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SRR1
Summary: This region encompasses the 5' regulatory region of SOX2 (SRY-box 2) and includes the proximal promoter and SOX2 regulatory region 1 (SRR1), which is a conserved enhancer. This sequence is positively regulated by binding of high mobility group AT-hook 1 and 2 and NK6 homeobox 3, and may be suppressed by msh homeobox 2, Y-box binding protein 1, and the polycomb complex. This promoter may be methylated and silenced in tumor cells. Four subregions were validated as active enhancers by ChIP-STARR-seq in human embryonic stem cells, where three are associated with the OCT4 and/or NANOG transcription factors, and three are marked by the H3K27ac and H3K4me1 histone modifications. A subregion of the SRR1 sequence was also validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
Orthologs: mouse all
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Genomic context

Location:: 3q

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (181707848..181712914)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (184512421..184517490)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (181425650..181429974)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SOX2 enhancers SRR1 and SRR2 are each differentially methylated and acetylated, on a temporal basis, contributing to the generation of neuron- and astrocyte-specific epigenomes from a common progenitor cell.
Title: Epigenetic modifications of SOX2 enhancers, SRR1 and SRR2, correlate with in vitro neural differentiation.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

ATAC-STARR-seq lymphoblastoid silent region 14929
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:181428142-181428995
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:181428996-181429848
OCT4-NANOG hESC enhancer GRCh37_chr3:181425636-181426633
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:181429849-181430702
SOX2 gene-proximal regulation region
SOX2 regulatory region 1
Sharpr-MPRA regulatory region 720

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.