Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation.
Although intergenic long noncoding RNAs (lincRNAs) have been linked to gene regulation in various tissues, little is known about lincRNA transcriptomes in the T cell lineages. Here we identified 1,524 lincRNA clusters in 42 T cell samples, from early T cell progenitors to terminally differentiated helper T cell subsets. Our analysis revealed highly dynamic and cell-specific expression patterns for lincRNAs during T cell differentiation. These lincRNAs were located in genomic regions enriched for genes that encode proteins with immunoregulatory functions. Many were bound and regulated by the key transcription factors T-bet, GATA-3, STAT4 and STAT6. We found that the lincRNA LincR-Ccr2-5'AS, together with GATA-3, was an essential component of a regulatory circuit in gene expression specific to the TH2 subset of helper T cells and was important for the migration of TH2 cells.
1] Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA. [2].
Gangqing
G
Hu
Qingsong
Q
Tang
Suveena
S
Sharma
Fang
F
Yu
Thelma M
TM
Escobar
Stefan A
SA
Muljo
Jinfang
J
Zhu
Keji
K
Zhao
D000818:Animals; D002454:Cell Differentiation; D002465:Cell Movement; D050990:GATA3 Transcription Factor / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D005786:Gene Expression Regulation / Q000276:immunology*; D056426:Genetic Loci; D051379:Mice; D008810:Mice, Inbred C57BL; D058977:Molecular Sequence Annotation; D054504:Precursor Cells, T-Lymphoid / Q000166:cytology / Q000276:immunology / Q000378:metabolism*; D011485:Protein Binding; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000276:immunology; D050797:STAT4 Transcription Factor / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D050800:STAT6 Transcription Factor / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D015398:Signal Transduction; D020825:T-Box Domain Proteins / Q000235:genetics / Q000276:immunology / Q000378:metabolism; D018417:Th1 Cells / Q000166:cytology / Q000276:immunology / Q000378:metabolism*; D058504:Th17 Cells / Q000166:cytology / Q000276:immunology / Q000378:metabolism*; D018418:Th2 Cells / Q000166:cytology / Q000276:immunology / Q000378:metabolism*; D059467:Transcriptome / Q000276:immunology; D000098815:T-bet Transcription Factor
D050990:GATA3 Transcription Factor; C494748:Gata3 protein, mouse; D062085:RNA, Long Noncoding; D050797:STAT4 Transcription Factor; D050800:STAT6 Transcription Factor; C494091:Stat4 protein, mouse; D020825:T-Box Domain Proteins; D000098815:T-bet Transcription Factor