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LOC117038776 CRISPRi-FlowFISH-validated NFE2 regulatory element 2 [ Homo sapiens (human) ]

Gene ID: 117038776, updated on 10-Oct-2023

Summary

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Gene symbol
LOC117038776
Gene description
CRISPRi-FlowFISH-validated NFE2 regulatory element 2
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. The major subregion was validated as a negatively-acting cis-regulatory element for the NFE2 (nuclear factor, erythroid 2) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. Two subregions were shown to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both are marked by the H3K27ac histone modification, with one being additionally marked by H3K4me1 and associated with the NANOG transcription factor. 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (54279485..54282005)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (54246062..54248582)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54673305..54675605)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene chromobox 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:54650247-54650908 Neighboring gene RNA, 7SL, cytoplasmic 390, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6436 Neighboring gene S-phase cancer associated transcript 2 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 regulatory element Neighboring gene CRISPRi-FlowFISH-validated COPZ1 and HNRNPA1 regulatory element Neighboring gene nuclear factor, erythroid 2 Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 and NFE2 regulatory element 1 Neighboring gene CRISPRi-FlowFISH-validated COPZ1, HNRNPA1 and NFE2 regulatory element Neighboring gene CRISPRi-FlowFISH-validated HNRNPA1 and NFE2 regulatory element 2 Neighboring gene RNA, U6 small nuclear 950, 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 6437
  • ATAC-STARR-seq lymphoblastoid active region 6438
  • ATAC-STARR-seq lymphoblastoid active region 6439
  • ATAC-STARR-seq lymphoblastoid active region 6440
  • H3K27ac hESC enhancer GRCh37_chr12:54673511-54674270
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54675031-54675789

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_068103.3 

    Range
    101..2621
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    54279485..54282005
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    54246062..54248582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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