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LOC119407400 CRISPRi-FlowFISH-validated PLP2 regulatory element 4 [ Homo sapiens (human) ]

Gene ID: 119407400, updated on 10-Oct-2023

Summary

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Gene symbol
LOC119407400
Gene description
CRISPRi-FlowFISH-validated PLP2 regulatory element 4
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. A subregion was validated as a negatively-acting cis-regulatory element for the PLP2 (proteolipid protein 2) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. An overlapping subregion was also 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. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its 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 LOC119407400 in Genome Data Viewer
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (48573617..48575558)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (47982633..47984566)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (48432005..48432990)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20817 Neighboring gene CRISPRi-validated cis-regulatory element chrX.929 Neighboring gene EBP cholestenol delta-isomerase Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48397756-48398256 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48398257-48398757 Neighboring gene TBC1 domain family member 25 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48426332-48426532 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48436957-48437166 Neighboring gene RNA binding motif protein 3 Neighboring gene MRPL32 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29606 Neighboring gene WD repeat domain 13 Neighboring gene Sharpr-MPRA regulatory region 1547

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. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco CP, et al. Nat Genet, 2019 Dec. PMID 31784727, 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. 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

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 29603
  • MED14-independent group 3 enhancer GRCh37_chrX:48432747-48433946

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_070972.2 

    Range
    101..2042
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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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    48573617..48575558
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    47982633..47984566
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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