title: Determining the Function of Long Noncoding RNA in Innate Immunity.
abstract: The advent of deep sequencing technologies has provided us with an unprecedented view of the human genome. Over 85 % of the genome is actively transcribed, yet we do not know the function of the vast majority of these RNA transcripts. Long noncoding RNAs (lncRNA) represent the largest group of RNA genes transcribed in the cell and currently there is limited experimental data supporting the functions of a very small proportion of these transcripts. lncRNA are expressed in a highly cell type specific manner and our interests involve understanding the role they play in innate immune signaling networks. In this chapter I will outline the approach we took to attempt to uncover the role for lncRNA in innate immune cells. Two of the main techniques required to study lncRNA are RNA-seq and loss of function analysis. This allows us to first identify all lncRNA in a cell type of choice and then try to determine the functional significance of these transcripts. This approach has been successful for us to date in identifying lincRNA-Cox2 as a highly inflammatory inducible lncRNA that is responsible for activation and repression of distinct immune genes.
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High St, MailStop: 225 Sinsheimer Labs, Santa Cruz, CA, 95064, USA. sucarpen@ucsc.edu.
authors.forename: Susan
authors.initials: S
authors.lastname: Carpenter
mesh_terms: D000818:Animals; D002460:Cell Line; D003001:Cloning, Molecular; D015870:Gene Expression; D005786:Gene Expression Regulation; D015723:Gene Library; D006801:Humans; D007113:Immunity, Innate / Q000235:genetics*; D051379:Mice; D034622:RNA Interference; D062085:RNA, Long Noncoding / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D014162:Transfection
chemical_list: D062085:RNA, Long Noncoding; D034741:RNA, Small Interfering
keywords: Inflammation; Innate immunity; Long noncoding RNA (lncRNA); RNA sequencing; TLR signaling; shRNA