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HBB-LCR beta-globin locus control region [ Homo sapiens (human) ]

Gene ID: 109580095, updated on 10-Oct-2023

Summary

Gene symbol
HBB-LCR
Gene description
beta-globin locus control region
Primary source
MIM:152424
Gene type
biological region
Feature type(s)
misc_structure
mobile_element
protein_bind
regulatory: CAAT_signal, DNase_I_hypersensitive_site, TATA_box, enhancer, enhancer_blocking_element, insulator, locus_control_region, matrix_attachment_region, promoter, silencer, 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
Also known as
LCRB; LCR-beta; beta-DCR; beta-LAR
Summary
This genomic sequence, which spans 34 kb upstream of the hemoglobin subunit epsilon 1 (HBE1) gene, represents the 5' regulatory region of the human beta-globin gene cluster on chromosome 11. It includes a locus control region (LCR), which can confer developmentally regulated, position-independent and copy number-dependent expression on linked beta-globin genes in transgenic mice. The LCR is the major element controlling expression of the downstream beta-globin genes (epsilon, G-gamma, A-gamma, delta and beta, or HBE1, HBG2, HBG1, HBD and HBB, respectively), which are organized on the chromosome in their order of developmental expression. This region includes several DNase I hypersensitive sites (HSs; 5'HS1-5'HS7 in the entire region, 5'HS1-5'HS5 in the LCR), some of which possess enhancer activity in erythroid cells and/or function in synergy (e.g., the 5'HS2 and 5'HS3 enhancers). The HSs bind to erythroid transcription factors and are associated with regulatory complexes involved in beta-globin gene expression and the organization of local chromatin domain structure. This region also includes matrix attachment regions (MARs), silencers, an enhancer-blocking element (at 5'HS5), a DNA-RNA triplex-forming region (at 5'HS2) that reduces beta-globin gene expression, and a retroviral element (ERV-9) with enhancer activity in erythrocytes. Chromosome conformation capture assays show that the LCR is an integral part of the beta-globin active chromatin hub in erythroid cells, where it undergoes looping interactions with distal 5' and 3' HSs (HS-111 and 3'HS1) and the active beta-globin gene promoters. A larger region that includes 5'HS2-5'HS5 of the LCR plus an additional 27 kb may regulate replication initiation at a replication origin (IR) in the vicinity of the adult beta-globin (HBB) gene. Mutations in this LCR result in beta-thalassemias and beta-hemoglobinopathies. A large naturally-occurring deletion, which includes the sequence spanning 5'HS2-5'HS7, results in Hispanic gamma-delta-beta thalassemia and a closed chromatin conformation across the beta-globin locus. [provided by RefSeq, Dec 2019]
Orthologs
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Genomic context

See HBB-LCR in Genome Data Viewer
Location:
11p15.4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (5269925..5304186)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (5329290..5363538)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (5291155..5325416)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene A-gamma-globin 3' regulatory region Neighboring gene HBG1 recombination region Neighboring gene HBG2 recombination region Neighboring gene hemoglobin subunit gamma 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:5278491-5279106 Neighboring gene hemoglobin subunit gamma 2 Neighboring gene beta-globin hypersensitive site-embryonic 1 Neighboring gene hemoglobin subunit epsilon 1 Neighboring gene olfactory receptor family 51 subfamily AB member 1 pseudogene Neighboring gene olfactory receptor family 51 subfamily B member 4 Neighboring gene olfactory receptor family 51 subfamily B member 3 pseudogene Neighboring gene olfactory receptor family 51 subfamily B member 2

Genomic regions, transcripts, and products

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information

Other Names

  • CRISPR perturbation-validated HBE1, HBG1, HBG2, HBBP1, HBD and HBB cis-regulatory elements
  • beta Glb-LCR
  • beta-globin 5' regulatory region
  • beta-globin LCR
  • beta-globin dominant control region
  • beta-globin locus activation region
  • beta-globin locus-activating region
  • locus control region, beta

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_052895.1 

    Range
    101..34362
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    5269925..5304186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    5329290..5363538
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)