DES-LCR desmin locus control region [Homo sapiens (human)] - Gene

Summary

Gene symbol: DES-LCR
Gene description: desmin locus control region
Gene type: biological region
Feature type(s): protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer, locus_control_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
Summary: This region represents a locus control region (LCR) that regulates expression of the DES (desmin) gene, whereby it can confer copy number-dependent and position of integration-independent muscle-specific developmental expression on this gene. It is also thought, though not yet demonstrated, that this LCR may control expression of the preferentially muscle-expressed SPEG (SPEG complex locus) gene that exists downstream of the DES gene. This LCR is characterized by the presence of five major DNase I hypersensitive sites (HSs), which bind factors that mediate developmental expression of the DES gene. This region also includes a promoter-proximal enhancer that can drive DES gene expression in skeletal but not cardiac muscle. This LCR and enhancer region can drive expression of other muscle-specific genes, and it is a potential regulatory element for use in muscle-specific gene therapy vectors. A subregion was also shown to be an enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. 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]
Orthologs: mouse all
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Genomic context

Location:: 2q35

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (219399709..219418452)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (219884504..219903246)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (220264431..220283174)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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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

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General gene information

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Other Names

ATAC-STARR-seq lymphoblastoid active region 17152
H3K4me1 hESC enhancer GRCh37_chr2:220273128-220273628
desmin upstream regulatory region

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.