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LOC121740659 MED14-independent group 3 enhancer GRCh37_chr6:99872987-99874186 [ Homo sapiens (human) ]

Gene ID: 121740659, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740659
Gene description
MED14-independent group 3 enhancer GRCh37_chr6:99872987-99874186
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. A 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 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. Three subregions were also shown to be enhancers by ChIP-STARR-seq in human embryonic stem cells, where they associate with the NANOG transcription factor and are marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as an 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 DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). 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 HepG2 cells. This locus also includes three 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, Jun 2023]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (99424609..99426310)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (100598953..100600654)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (99873749..99874043)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene failed axon connections homolog, metaxin like GST domain containing Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:99793932-99794432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:99794433-99794933 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:99795824-99796388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17416 Neighboring gene MPRA-validated peak5980 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:99841327-99841966 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:99849871-99851070 Neighboring gene coenzyme Q3, methyltransferase Neighboring gene PNN interacting serine and arginine rich protein Neighboring gene PNISR antisense RNA 1 Neighboring gene thiosulfate sulfurtransferase like domain containing 3 Neighboring gene NANOG hESC enhancer GRCh37_chr6:99904596-99905315 Neighboring gene ubiquitin specific peptidase 45 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17417 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:99962307-99963214 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:99963215-99964120 Neighboring gene uncharacterized LOC124901365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24859

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 24854
  • ATAC-STARR-seq lymphoblastoid active region 24855
  • ATAC-STARR-seq lymphoblastoid active region 24856
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:99872485-99873005
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:99873006-99873525
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:99873526-99874046
  • ReSE screen-validated silencer GRCh37_chr6:99872662-99872842
  • Sharpr-MPRA regulatory region 16

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_075721.3 

    Range
    101..1802
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    99424609..99426310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    100598953..100600654
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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