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LOC121627846 CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:2168563-2169762 [ Homo sapiens (human) ]

Gene ID: 121627846, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121627846
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:2168563-2169762
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. The major subregion was validated as an active enhancer 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 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. Two subregions marked by the H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells. 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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). 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. This locus also includes four accessible chromatin subregions that were validated as enhancers based on their ability to activate 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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See LOC121627846 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2168069..2169855)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2141316..2143102)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2168068..2169854)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2096431-2096958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2096959-2097484 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2104508-2104680 Neighboring gene IZUMO family member 4 Neighboring gene adaptor related protein complex 3 subunit delta 1 Neighboring gene MPRA-validated peak3230 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2141381-2141538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2144918-2145541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2145542-2146164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13657 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2150717-2150878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13658 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2151574-2152011 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9771 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2165242-2165623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2171045-2171639 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2171640-2172234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2173473-2173991 Neighboring gene DOT1 like histone lysine methyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2180689-2181272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2195534-2196062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2196063-2196591 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2200246-2201219 Neighboring gene DOT1L antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2225862-2226368 Neighboring gene pleckstrin homology domain containing J1 Neighboring gene microRNA 1227

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. 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
  4. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article
  5. 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

  • ATAC-STARR-seq lymphoblastoid active region 13659
  • ATAC-STARR-seq lymphoblastoid active region 13660
  • ATAC-STARR-seq lymphoblastoid active region 13661
  • ATAC-STARR-seq lymphoblastoid active region 13662
  • H3K4me1 hESC enhancer GRCh37_chr19:2168068-2168663
  • H3K4me1 hESC enhancer GRCh37_chr19:2169259-2169854
  • ReSE screen-validated silencer GRCh37_chr19:2169096-2169336
  • Sharpr-MPRA regulatory region 14448

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_075037.3 

    Range
    101..1887
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    2168069..2169855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    2141316..2143102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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