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Th2-lcr Th2 cytokine locus control region [ Mus musculus (house mouse) ]

Gene ID: 106099061, updated on 9-Aug-2024

Summary

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Gene symbol
Th2-lcr
Gene description
Th2 cytokine locus control region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, locus_control_region
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Rr366633
Summary
This genomic region represents a locus control region (LCR) that can confer copy number-dependent, position-independent expression on the T helper type 2 (Th2) cytokine locus in transgenic assays. It regulates coordinated expression of the interleukin 4 (Il4), interleukin 13 (Il13) and interleukin 5 (Il5) genes during differentiation of naive CD4+ T cells along the Th2 pathway. The LCR overlaps the 3' end of the Rad50 gene, which is located between the Il13 and Il5 genes. The LCR is characterized by four DNase I hypersensitive sites (RHS4-RHS7), which bind transcription factors necessary for induction of the Il4, Il5 and Il13 genes. The promoters of these genes first undergo looping interactions with each other to form a pre-poised hub, and later in differentiation the LCR participates in the hub, resulting in a poised structure for rapid transcription activation. In addition to participating in long-range intrachromosomal interactions, this Th2 LCR on chromosome 11 can also form interchromosomal interactions with the Th1 interferon gamma (Ifng) promoter on chromosome 10, and also with the interleukin 17A (Il17a) locus on chromosome 1. Deletion of this LCR results in various lung and airway defects in a mouse model of allergic asthma, suggesting that it functions in the pathogenesis of that disease. [provided by RefSeq, Aug 2015]
Orthologs
human all
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Genomic context

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See Th2-lcr in Genome Data Viewer
Location:
11 A5-B1
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (53538416..53563179)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (53647589..53672352)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene origin of replication in Il13 Neighboring gene interleukin 13 Neighboring gene ribosomal protein S2, pseudogene 4 Neighboring gene RAD50 double strand break repair protein Neighboring gene interleukin 5 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:53568511-53568694 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:53576931-53577191 Neighboring gene microRNA 7671

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. Regulation of the Th2 cytokine locus by a locus control region. Lee GR, et al. Immunity, 2003 Jul. PMID 12871646
  2. An updated view on transcription factor GATA3-mediated regulation of Th1 and Th2 cell differentiation. Yagi R, et al. Int Immunol, 2011 Jul. PMID 21632975, Free PMC Article
  3. Demethylation of a specific hypersensitive site in the Th2 locus control region. Kim ST, et al. Proc Natl Acad Sci U S A, 2007 Oct 23. PMID 17940027, Free PMC Article
  4. Murine neonatal CD4+ cells are poised for rapid Th2 effector-like function. Rose S, et al. J Immunol, 2007 Mar 1. PMID 17312108, Free PMC Article
  5. Critical role for the transcription regulator CCCTC-binding factor in the control of Th2 cytokine expression. Ribeiro de Almeida C, et al. J Immunol, 2009 Jan 15. PMID 19124743

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Other Names

  • T helper type 2 cytokine LCR
  • regulatory region 366633

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_042300.1 

    Range
    101..24864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    53538416..53563179
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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