title: Poly A- transcripts expressed in HeLa cells.
abstract: BACKGROUND
  Transcripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3' poly A tail. Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown.
  
  
  RESULTS
  We developed the TRD (Total RNA Detection) system for transcript identification. The system detects the transcripts through the following steps: 1) depleting the abundant ribosomal and small-size transcripts; 2) synthesizing cDNA without regard to the status of the 3' poly A tail; 3) applying the 454 sequencing technology for massive 3' EST collection from the cDNA; and 4) determining the genome origins of the detected transcripts by mapping the sequences to the human genome reference sequences. Using this system, we characterized the cytoplasmic transcripts from HeLa cells. Of the 13,467 distinct 3' ESTs analyzed, 24% are poly A-, 36% are poly A+, and 40% are bimorphic with poly A+ features but without the 3' poly A tail. Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved. Experiments confirmed the authenticity of the detected poly A- transcripts.
  
  
  CONCLUSIONS
  Our study provides the first large-scale sequence evidence for the presence of poly A- transcripts in eukaryotes. The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts.
authors.affiliation: Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America.
authors.forename: Qingfa
authors.initials: Q
authors.lastname: Wu
authors.forename: Yeong C
authors.initials: YC
authors.lastname: Kim
authors.forename: Jian
authors.initials: J
authors.lastname: Lu
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Xuan
authors.forename: Jun
authors.initials: J
authors.lastname: Chen
authors.forename: Yonglan
authors.initials: Y
authors.lastname: Zheng
authors.forename: Tom
authors.initials: T
authors.lastname: Zhou
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
authors.forename: Chung-I
authors.initials: CI
authors.lastname: Wu
authors.forename: San Ming
authors.initials: SM
authors.lastname: Wang
mesh_terms: D020413:3' Untranslated Regions; D003593:Cytoplasm / Q000378:metabolism; D020224:Expressed Sequence Tags; D015870:Gene Expression; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006367:HeLa Cells; D006657:Histones / Q000378:metabolism; D006801:Humans; D008954:Models, Biological; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D011061:Poly A; D012333:RNA, Messenger / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D020413:3' Untranslated Regions; D006657:Histones; D012333:RNA, Messenger; D011061:Poly A