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LOC111828508 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:46364456-46365655 [ Homo sapiens (human) ]

Gene ID: 111828508, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111828508
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:46364456-46365655
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells, where it was defined as a group 1 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on P300/CBP. A subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). Another subregion was shown to be an enhancer by ChIP-STARR-seq in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Dec 2022]
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Genomic context

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See LOC111828508 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (45968576..45969775)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (46453186..46454385)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (46364989..46365283)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ataxin 10 Neighboring gene origin of replication for ATXN10 repeat region Neighboring gene ataxin 10 repeat instability region Neighboring gene TRNT1 pseudogene 2 Neighboring gene VISTA enhancer hs1559 Neighboring gene uncharacterized LOC105373071 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46263223-46263797 Neighboring gene uncharacterized LOC107985535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46275792-46276707 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46276708-46277622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46291489-46292372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46292373-46293254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46331075-46331575 Neighboring gene Wnt family member 7B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46358809-46359309 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46362863-46363759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46382740-46383240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46383241-46383741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46388443-46388942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46391059-46391977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46392941-46393610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46402157-46403148 Neighboring gene uncharacterized LOC124905134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13893 Neighboring gene dynein heavy chain -like pseudogene

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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46364475-46365378
  • Sharpr-MPRA regulatory region 1865

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_056236.2 

    Range
    101..1300
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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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    45968576..45969775
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    46453186..46454385
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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