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Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing

Sachin Pundhir1, Tine Dahlbæk Hannibal2, Claus Heiner Bang-Berthelsen3

  • 1Center for Non-coding RNA in Technology and Health, University of Copenhagen, Grønnegå̊rdsvej 3, 1870 Frederiksberg C, Denmark; IKVH, University of Copenhagen, Grønnegå̊rdsvej 3, 1870 Frederiksberg C, Denmark.

Gene
|May 7, 2014
PubMed
Summary

Researchers identified regulatory elements and a long non-coding RNA in the Cd247 gene, crucial for T cell function and linked to Type 1 Diabetes (T1D) risk.

Keywords:
CD247ENCODEUCSC genome browsercis-regulatory sequencehigh-throughput sequencinglncRNA

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Area of Science:

  • Immunology
  • Genetics
  • Molecular Biology

Background:

  • The Cd247 gene is vital for T cell receptor/CD3 complex expression and assembly.
  • CD247 down-regulation is implicated in systemic autoimmunity and Type 1 Diabetes (T1D).

Purpose of the Study:

  • To identify spatially conserved regulatory elements within the Cd247 gene in human and mouse.
  • To characterize a novel long non-coding RNA within the Cd247 gene.
  • To investigate the association of T1D-associated SNPs with the Cd247 gene locus.

Main Methods:

  • Utilized ENCODE project high-throughput sequencing data.
  • Analyzed histone modifications and ChIP-seq data.
  • Performed qRT-PCR for gene expression analysis in mouse models.
  • Integrated GENCODE manual annotations.

Main Results:

  • Identified two transcription factor binding sites with enhancer and promoter features within the Cd247 gene.
  • Discovered a putative long non-coding RNA in the first intron of Cd247.
  • Found 17 of 23 known T1D-associated SNPs within the mouse long non-coding RNA region.

Conclusions:

  • The identified regulatory elements and lncRNA provide new insights into Cd247 gene regulation.
  • These findings may enhance understanding of Cd247's role in autoimmune diabetes.
  • The study highlights the potential of non-coding RNAs in T1D pathogenesis.