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LOC111501791 BRD4-independent group 4 enhancer GRCh37_chr5:42950525-42951724 [ Homo sapiens (human) ]

Gene ID: 111501791, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111501791
Gene description
BRD4-independent group 4 enhancer GRCh37_chr5:42950525-42951724
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer, transcriptional_cis_regulatory_region
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 was predicted to be a cell type-specific enhancer based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. The major subregion includes an enhancer that was validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in HCT116 colorectal carcinoma cells, where it 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. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. Another subregion also had enhancer activity 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 DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). An overlapping fragment also had enhancer activity by high-throughput massively parallel reporter assays (MPRAs) in both HepG2 cells and K562 cells, where that fragment contains a motif for the NFE2L2 activator, and mutation of the motif results in reduced enhancer activity. This locus also includes three accessible chromatin subregions, two of which were validated as enhancers and one as a silencer based on their ability to activate or 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]
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Genomic context

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Location:
5p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (42950423..42951852)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (43203351..43204777)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (42950769..42951063)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PRELI domain containing 3B pseudogene 6 Neighboring gene uncharacterized LOC124900971 Neighboring gene uncharacterized LOC105374745 Neighboring gene PRELI domain containing 3B pseudogene 7 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:42980851-42981676 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:42981677-42982502 Neighboring gene uncharacterized LOC643977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22516 Neighboring gene uncharacterized LOC105374746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22518 Neighboring gene Sharpr-MPRA regulatory region 2050

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 dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Kheradpour P, et al. Genome Res, 2013 May. PMID 23512712, Free PMC Article
  2. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, et al. Nature, 2011 May 5. PMID 21441907, Free PMC Article
  3. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  4. 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
  5. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article

See all (6) citations in PubMed

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

  • ATAC-STARR-seq lymphoblastoid active region 22514
  • ATAC-STARR-seq lymphoblastoid active region 22515
  • ATAC-STARR-seq lymphoblastoid silent region 15987
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:42950861-42951383
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:42951384-42951905
  • NFE2L2 activator MPRA enhancer 35
  • NFE2L2 motif-containing MPRA enhancer 35
  • Sharpr-MPRA regulatory region 1008
  • massively parallel reporter assay enhancer 35

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_055947.5 

    Range
    101..1530
    Download
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    42950423..42951852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    43203351..43204777
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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