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GH-LCR growth hormone locus control region [ Homo sapiens (human) ]

Gene ID: 106128904, updated on 17-Sep-2024

Summary

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Gene symbol
GH-LCR
Gene description
growth hormone locus control region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer, enhancer_blocking_element, insulator, locus_control_region, promoter, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This element represents a locus control region (LCR) that can confer copy number-dependent, position-independent expression on members of the human growth hormone gene cluster in transgenic assays. It regulates expression of the GH1 (growth hormone 1), CSHL1 (chorionic somatomammotropin hormone-like 1), CSH1 (chorionic somatomammotropin hormone 1 (placental lactogen)), GH2 (growth hormone 2) and CSH2 (chorionic somatomammotropin hormone 2) genes in this cluster. This LCR spans approximately 40 kb upstream of the GH1 gene and is characterized by five major DNase I hypersensitive sites (HSI-HSV). It overlaps the CD79B (CD79b molecule, immunoglobulin-associated beta) gene, and also the 3' end of the SCN4A (sodium channel, voltage gated, type IV alpha subunit) gene. This LCR includes several transcription factor binding sites as well as subregions with enhancer, enhancer-blocking and boundary element activity. Three subregions were shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where all are marked by the H3K4me1 histone modification and one is additionally marked by H3K27ac. A subregion was also validated as a functional repressive element 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 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). This locus also includes seven accessible chromatin subregions, six of which were validated as enhancers and one as a silencer, based on their ability to activate or repress 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. Polymorphisms in this LCR may be associated with isolated growth hormone deficiency (IGHD), affecting serum IGF-I levels and height. [provided by RefSeq, May 2023]
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Genomic context

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See GH-LCR in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (63917193..63958852)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64787952..64829628)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (61994553..62036212)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene chorionic somatomammotropin hormone 1 Neighboring gene IGHD type 1A-1 recombination region Neighboring gene uncharacterized LOC112268204 Neighboring gene IGHD type 1A-2 recombination region Neighboring gene chorionic somatomammotropin hormone like 1 Neighboring gene growth hormone 1 Neighboring gene CD79b molecule Neighboring gene sodium voltage-gated channel alpha subunit 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:62036321-62037320 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:62037321-62038319 Neighboring gene uncharacterized LOC105371858 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:62044651-62044849 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62045661-62046161 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62064225-62064778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62064779-62065330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62075897-62076874 Neighboring gene PRR29 antisense RNA 1 Neighboring gene proline rich 29

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. Histone acetylation beyond promoters: long-range acetylation patterns in the chromatin world. Forsberg EC, et al. Bioessays, 2001 Sep. PMID 11536294
  2. Locus control region transcription plays an active role in long-range gene activation. Ho Y, et al. Mol Cell, 2006 Aug 4. PMID 16885026
  3. Bystander gene activation by a locus control region. Cajiao I, et al. EMBO J, 2004 Oct 1. PMID 15359275, Free PMC Article
  4. A conserved sequence upstream of the B29 (Ig beta, CD79b) gene interacts with YY1. Patrone L, et al. Mol Biol Rep, 2004 Mar. PMID 15040449
  5. Epigenetic modifications at the human growth hormone locus predict distinct roles for histone acetylation and methylation in placental gene activation. Kimura AP, et al. Mol Endocrinol, 2004 Apr. PMID 14715931

See all (53) citations in PubMed

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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 12565
  • ATAC-STARR-seq lymphoblastoid active region 12566
  • ATAC-STARR-seq lymphoblastoid active region 12567
  • ATAC-STARR-seq lymphoblastoid active region 12568
  • ATAC-STARR-seq lymphoblastoid active region 12569
  • ATAC-STARR-seq lymphoblastoid active region 12570
  • ATAC-STARR-seq lymphoblastoid silent region 8835
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:62009671-62010341
  • H3K4me1 hESC enhancer GRCh37_chr17:62026059-62026640
  • H3K4me1 hESC enhancer GRCh37_chr17:62026641-62027220
  • Sharpr-MPRA regulatory region 9471

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_042788.1 

    Range
    101..41760
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    63917193..63958852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    64787952..64829628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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