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

Sachin Pundhir, Tine Dahlbaek Hannibal, Claus Heiner Bang-Berthelsen, Anne-Marie Karin Wegener, Flemming Pociot, Dan Holmberg, Jan Gorodkin

Research output: Contribution to journalJournal articleResearchpeer-review


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. (C) 2014 Elsevier B.V. All rights reserved.
Original languageEnglish
Issue number1
Pages (from-to)80-87
Number of pages8
Publication statusPublished - 2014
Externally publishedYes


  • Genetics
  • Medicine (all)
  • CD247
  • Cis-regulatory sequence
  • High-throughput sequencing
  • LncRNA
  • UCSC genome browser
  • Cd247 protein
  • histone
  • long untranslated RNA
  • membrane protein
  • transcription factor
  • unclassified drug
  • CD3 antigen
  • CD3 antigen, zeta chain
  • animal cell
  • animal experiment
  • animal tissue
  • article
  • binding site
  • controlled study
  • down regulation
  • enhancer region
  • female
  • gene expression
  • high throughput sequencing
  • intron
  • male
  • mouse
  • nonhuman
  • priority journal
  • promoter region
  • reverse transcription polymerase chain reaction
  • single nucleotide polymorphism
  • animal
  • C57BL mouse
  • DNA microarray
  • gene expression regulation
  • genetics
  • human
  • metabolism
  • molecular evolution
  • nonobese diabetic mouse
  • nucleotide sequence
  • regulatory sequence
  • Mus
  • Animals
  • Antigens, CD3
  • Base Sequence
  • Binding Sites
  • Conserved Sequence
  • Evolution, Molecular
  • Female
  • Gene Expression Regulation
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Mice, Inbred NOD
  • Oligonucleotide Array Sequence Analysis
  • Polymorphism, Single Nucleotide
  • Regulatory Sequences, Nucleic Acid
  • RNA, Long Noncoding
  • Transcription Factors
  • SEQ
  • cis-regulatory sequence
  • IncRNA
  • high-throughput sequencing
  • lncRNA
  • Diabetes Mellitus, Insulin-Dependent
  • Genetics - General
  • Genetics - Animal
  • Genetics - Human
  • Biochemistry studies - Proteins, peptides and amino acids
  • Metabolism - General metabolism and metabolic pathways
  • Metabolism - Metabolic disorders
  • Endocrine - General
  • Endocrine - Pancreas
  • Immunology - General and methods
  • Immunology - Immunopathology, tissue immunology
  • Animals, Chordates, Mammals, Nonhuman Vertebrates, Nonhuman Mammals, Rodents, Vertebrates


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