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LOC119369038 CRISPRi-FlowFISH-validated HDAC6 regulatory element 1 [ Homo sapiens (human) ]

Gene ID: 119369038, updated on 10-Oct-2023

Summary

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Gene symbol
LOC119369038
Gene description
CRISPRi-FlowFISH-validated HDAC6 regulatory element 1
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 positively-acting cis-regulatory element for the HDAC6 (histone deacetylase 6) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. Another subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. 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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Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (47232664..47233947)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (46642355..46643585)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (47092063..47093285)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ubiquitin like modifier activating enzyme 1 Neighboring gene uncharacterized LOC105373194 Neighboring gene inactivation escape 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29586 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29587 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:47078167-47078806 Neighboring gene cyclin dependent kinase 16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:47087788-47088288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:47088289-47088789 Neighboring gene ubiquitin specific peptidase 11 Neighboring gene small nucleolar RNA U13 Neighboring gene nicolin 2, pseudogene

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. 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
  3. 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 29588
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:47092763-47093346

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_070967.2 

    Range
    101..1384
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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
    47232664..47233947
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    46642355..46643585
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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