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LOC126862289 BRD4-independent group 4 enhancer GRCh37_chr16:11944561-11945760 [ Homo sapiens (human) ]

Gene ID: 126862289, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862289
Gene description
BRD4-independent group 4 enhancer GRCh37_chr16:11944561-11945760
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. In HCT116 colorectal carcinoma cells, a subregion was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. Another subregion was also validated as an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (11850704..11852210)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (11886755..11888261)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10457 Neighboring gene zinc finger CCCH-type containing 7A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7209 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:11890813-11891350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11915504-11916004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11916005-11916505 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11932294-11932479 Neighboring gene breast cancer anti-estrogen resistance 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11946068-11946601 Neighboring gene ribosomal L1 domain containing 1 Neighboring gene G1 to S phase transition 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7212 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:12009257-12010194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:12011253-12011753 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 1 Neighboring gene nuclear pore complex interacting protein family member B2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10462 Neighboring gene TNF receptor superfamily member 17

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

GeneRIFs: Gene References Into Functions

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

General gene information

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Other Names

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11945533-11946067
  • ReSE screen-validated silencer GRCh37_chr16:11945329-11945515

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

  1. NG_086787.2 

    Range
    101..1607
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    11850704..11852210
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    11886755..11888261
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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