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LOC120807613 H3K27me3-DHS negatively-acting regulatory element H4 [ Homo sapiens (human) ]

Gene ID: 120807613, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120807613
Gene description
H3K27me3-DHS negatively-acting regulatory element H4
Gene type
biological region
Feature type(s)
regulatory: 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 gene regulatory element based on the presence of histone H3 lysine 27 tri-methylation overlapping a DNase I hypersensitive site (H3K27me3-DHS). It was experimentally validated as a negatively-acting cis element that reduces activity of an enhancer-driven reporter gene in K562 erythroleukemia cells. [provided by RefSeq, Mar 2021]
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Genomic context

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See LOC120807613 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (33695862..33696480)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (32077645..32078263)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (35068167..35068785)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:34960679-34961178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18382 Neighboring gene DNA replication fork stabilization factor DONSON Neighboring gene crystallin zeta like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18383 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13263 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13265 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:35029077-35029576 Neighboring gene intersectin 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:35063898-35064424 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:35064425-35064951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35069053-35069554 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:35114498-35114600 Neighboring gene NANOG hESC enhancer GRCh37_chr21:35173966-35174467 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:35229825-35230518 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:35257366-35258565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35267187-35267773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35267774-35268359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:35274085-35274680 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:35285966-35287165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18384 Neighboring gene RNA, 7SL, cytoplasmic 740, pseudogene Neighboring gene ATP synthase peripheral stalk subunit OSCP

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. Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs. Muñoa-Hoyos I, et al. Clin Epigenetics, 2020 Nov 9. PMID 33168052, Free PMC Article
  2. EZH2 inhibitory protein (EZHIP/Cxorf67) expression correlates strongly with H3K27me3 loss in posterior fossa ependymomas and is mutually exclusive with H3K27M mutations. Nambirajan A, et al. Brain Tumor Pathol, 2021 Jan. PMID 33130928
  3. Reduced H3K27me3 levels in diffuse gliomas: association with 1p/19q codeletion and difference from H3K27me3 loss in malignant peripheral nerve sheath tumors. Kitahama K, et al. Brain Tumor Pathol, 2021 Jan. PMID 32989606
  4. Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression. Huang D, et al. Genome Res, 2019 Apr. PMID 30886051, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs.
    Title: Morphine leads to global genome changes in H3K27me3 levels via a Polycomb Repressive Complex 2 (PRC2) self-regulatory mechanism in mESCs.
  2. Reduced H3K27me3 levels in diffuse gliomas: association with 1p/19q codeletion and difference from H3K27me3 loss in malignant peripheral nerve sheath tumors.
    Title: Reduced H3K27me3 levels in diffuse gliomas: association with 1p/19q codeletion and difference from H3K27me3 loss in malignant peripheral nerve sheath tumors.
  3. EZH2 inhibitory protein (EZHIP/Cxorf67) expression correlates strongly with H3K27me3 loss in posterior fossa ependymomas and is mutually exclusive with H3K27M mutations.
    Title: EZH2 inhibitory protein (EZHIP/Cxorf67) expression correlates strongly with H3K27me3 loss in posterior fossa ependymomas and is mutually exclusive with H3K27M mutations.
Submit: New GeneRIF Correction

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)

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_073739.1 

    Range
    101..719
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    33695862..33696480
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    32077645..32078263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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