title: Over 20% of human transcripts might form sense-antisense pairs.
abstract: The major challenge to identifying natural sense- antisense (SA) transcripts from public databases is how to determine the correct orientation for an expressed sequence, especially an expressed sequence tag sequence. In this study, we established a set of very stringent criteria to identify the correct orientation of each human transcript. We used these orientation-reliable transcripts to create 26 741 transcription clusters in the human genome. Our analysis shows that 22% (5880) of the human transcription clusters form SA pairs, higher than any previous estimates. Our orientation-specific RT-PCR results along with the comparison of experimental data from previous studies confirm that our SA data set is reliable. This study not only demonstrates that our criteria for the prediction of SA transcripts are efficient, but also provides additional convincing data to support the view that antisense transcription is quite pervasive in the human genome. In-depth analyses show that SA transcripts have some significant differences compared with other types of transcripts, with regard to chromosomal distribution and Gene Ontology-annotated categories of physiological roles, functions and spatial localizations of gene products.
authors.affiliation: Department of Medicine, University of Chicago, 5841 S. Maryland Avenue, MC2115, Chicago, IL 60637, USA. jchen@medicine.bsd.uchicago.edu
authors.forename: Jianjun
authors.initials: J
authors.lastname: Chen
authors.forename: Miao
authors.initials: M
authors.lastname: Sun
authors.forename: W James
authors.initials: WJ
authors.lastname: Kent
authors.forename: Xiaoqiu
authors.initials: X
authors.lastname: Huang
authors.forename: Hanqing
authors.initials: H
authors.lastname: Xie
authors.forename: Wenquan
authors.initials: W
authors.lastname: Wang
authors.forename: Guolin
authors.initials: G
authors.lastname: Zhou
authors.forename: Run Zhang
authors.initials: RZ
authors.lastname: Shi
authors.forename: Janet D
authors.initials: JD
authors.lastname: Rowley
mesh_terms: D020029:Base Pairing; D002877:Chromosomes, Human; D015894:Genome, Human; D006801:Humans; D016372:RNA, Antisense / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
chemical_list: D016372:RNA, Antisense; D012333:RNA, Messenger