title: Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells.
abstract: Due to poor correlation between steady state mRNA levels and protein product, purely transcriptomic profiling methods may miss genes posttranscriptionally regulated by RNA binding proteins (RBPs) and microRNAs (miRNAs). RNA immunoprecipitation (RIP) methods developed to identify in vivo targets of RBPs have greatly elucidated those mRNAs which may be regulated via transcript stability and translation. The RBP HuR (ELAVL1) and family members are major stabilizers of mRNA. Many labs have identified HuR mRNA targets; however, many of these analyses have been performed in cell lines and oftentimes are not independent biological replicates. Little is known about how HuR target mRNAs behave in conditional knock-out models. In the present work, we performed HuR RIP-Seq and RNA-Seq to investigate HuR direct and indirect targets using a novel conditional knock-out model of HuR genetic ablation during CD4+ T activation and Th2 differentiation. Using independent biological replicates, we generated a high coverage RIP-Seq data set (>160 million reads) that was analyzed using bioinformatics methods specifically designed to find direct mRNA targets in RIP-Seq data. Simultaneously, another set of independent biological replicates were sequenced by RNA-Seq (>425 million reads) to identify indirect HuR targets. These direct and indirect targets were combined to determine canonical pathways in CD4+ T cell activation and differentiation for which HuR plays an important role. We show that HuR may regulate genes in multiple canonical pathways involved in T cell activation especially the CD28 family signaling pathway. These data provide insights into potential HuR-regulated genes during T cell activation and immune mechanisms.
authors.affiliation: Department of Surgery, University of Missouri, Columbia, Missouri, United States of America; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Patsharaporn
authors.initials: P
authors.lastname: Techasintana
authors.affiliation: Department of Biostatistics, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: J Wade
authors.initials: JW
authors.lastname: Davis
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
authors.forename: Matthew M
authors.initials: MM
authors.lastname: Gubin
authors.affiliation: Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Magee
authors.affiliation: Department of Surgery, University of Missouri, Columbia, Missouri, United States of America; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Ulus
authors.initials: U
authors.lastname: Atasoy
mesh_terms: D000818:Animals; D018106:CD28 Antigens / Q000235:genetics / Q000276:immunology; D015496:CD4-Positive T-Lymphocytes / Q000166:cytology / Q000276:immunology* / Q000378:metabolism; D002454:Cell Differentiation; D002478:Cells, Cultured; D000067780:ELAV-Like Protein 1 / Q000235:genetics / Q000276:immunology*; D005786:Gene Expression Regulation; D006801:Humans; D008213:Lymphocyte Activation; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D012333:RNA, Messenger / Q000235:genetics / Q000276:immunology*; D018418:Th2 Cells / Q000166:cytology / Q000276:immunology / Q000378:metabolism; D059467:Transcriptome
chemical_list: D018106:CD28 Antigens; D000067780:ELAV-Like Protein 1; D012333:RNA, Messenger