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Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project.

Pundhir, Sachin; Hannibal, Tine LU ; Bang-Berthelsen, Claus Heiner; Wegener, Anne-Marie Karin; Pociot, Flemming; Holmberg, Dan LU and Gorodkin, Jan (2014) In Gene 545(1). p.80-87
Abstract
The Cd247 gene encodes for a transmembrane protein important for the expression and assembly of TCR/CD3 complex on the surface of T lymphocytes. Down-regulation of CD247 has functional consequences in systemic autoimmunity and has been shown to be associated with Type 1 Diabetes in NOD mouse. In this study, we have utilized the wealth of high-throughput sequencing data produced during the Encyclopedia of DNA Elements (ENCODE) project to identify spatially conserved regulatory elements within the Cd247 gene from human and mouse. We show the presence of two transcription factor binding sites, supported by histone marks and ChIP-seq data, that specifically have features of an enhancer and a promoter, respectively. We also identified a... (More)
The Cd247 gene encodes for a transmembrane protein important for the expression and assembly of TCR/CD3 complex on the surface of T lymphocytes. Down-regulation of CD247 has functional consequences in systemic autoimmunity and has been shown to be associated with Type 1 Diabetes in NOD mouse. In this study, we have utilized the wealth of high-throughput sequencing data produced during the Encyclopedia of DNA Elements (ENCODE) project to identify spatially conserved regulatory elements within the Cd247 gene from human and mouse. We show the presence of two transcription factor binding sites, supported by histone marks and ChIP-seq data, that specifically have features of an enhancer and a promoter, respectively. We also identified a putative long non-coding RNA from the characteristically long first intron of the Cd247 gene. The long non-coding RNA annotation is supported by manual annotations from the GENCODE project in human and our expression quantification analysis performed in NOD and B6 mice using qRT-PCR. Furthermore, 17 of the 23 SNPs already known to be implicated with T1D were observed within the long non-coding RNA region in mouse. The spatially conserved regulatory elements identified in this study have the potential to enrich our understanding of the role of Cd247 gene in autoimmune diabetes. (Less)
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author
organization
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type
Contribution to journal
publication status
published
subject
in
Gene
volume
545
issue
1
pages
80 - 87
publisher
Elsevier
external identifiers
  • pmid:24797614
  • wos:000337774500011
  • scopus:84901198797
ISSN
1879-0038
DOI
10.1016/j.gene.2014.05.004
language
English
LU publication?
yes
id
241d7b77-e3ed-4db0-bbe2-41d2d787c2ef (old id 4455818)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/24797614?dopt=Abstract
date added to LUP
2014-06-03 19:51:17
date last changed
2017-04-09 03:20:11
@article{241d7b77-e3ed-4db0-bbe2-41d2d787c2ef,
  abstract     = {The Cd247 gene encodes for a transmembrane protein important for the expression and assembly of TCR/CD3 complex on the surface of T lymphocytes. Down-regulation of CD247 has functional consequences in systemic autoimmunity and has been shown to be associated with Type 1 Diabetes in NOD mouse. In this study, we have utilized the wealth of high-throughput sequencing data produced during the Encyclopedia of DNA Elements (ENCODE) project to identify spatially conserved regulatory elements within the Cd247 gene from human and mouse. We show the presence of two transcription factor binding sites, supported by histone marks and ChIP-seq data, that specifically have features of an enhancer and a promoter, respectively. We also identified a putative long non-coding RNA from the characteristically long first intron of the Cd247 gene. The long non-coding RNA annotation is supported by manual annotations from the GENCODE project in human and our expression quantification analysis performed in NOD and B6 mice using qRT-PCR. Furthermore, 17 of the 23 SNPs already known to be implicated with T1D were observed within the long non-coding RNA region in mouse. The spatially conserved regulatory elements identified in this study have the potential to enrich our understanding of the role of Cd247 gene in autoimmune diabetes.},
  author       = {Pundhir, Sachin and Hannibal, Tine and Bang-Berthelsen, Claus Heiner and Wegener, Anne-Marie Karin and Pociot, Flemming and Holmberg, Dan and Gorodkin, Jan},
  issn         = {1879-0038},
  language     = {eng},
  number       = {1},
  pages        = {80--87},
  publisher    = {Elsevier},
  series       = {Gene},
  title        = {Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project.},
  url          = {http://dx.doi.org/10.1016/j.gene.2014.05.004},
  volume       = {545},
  year         = {2014},
}