title: Genomewide characterization of non-polyadenylated RNAs.
abstract: BACKGROUND
  RNAs can be physically classified into poly(A)+ or poly(A)- transcripts according to the presence or absence of a poly(A) tail at their 3' ends. Current deep sequencing approaches largely depend on the enrichment of transcripts with a poly(A) tail, and therefore offer little insight into the nature and expression of transcripts that lack poly(A) tails.
  
  
  RESULTS
  We have used deep sequencing to explore the repertoire of both poly(A)+ and poly(A)- RNAs from HeLa cells and H9 human embryonic stem cells (hESCs). Using stringent criteria, we found that while the majority of transcripts are poly(A)+, a significant portion of transcripts are either poly(A)- or bimorphic, being found in both the poly(A)+ and poly(A)- populations. Further analyses revealed that many mRNAs may not contain classical long poly(A) tails and such messages are overrepresented in specific functional categories. In addition, we surprisingly found that a few excised introns accumulate in cells and thus constitute a new class of non-polyadenylated long non-coding RNAs. Finally, we have identified a specific subset of poly(A)- histone mRNAs, including two histone H1 variants, that are expressed in undifferentiated hESCs and are rapidly diminished upon differentiation; further, these same histone genes are induced upon reprogramming of fibroblasts to induced pluripotent stem cells.
  
  
  CONCLUSIONS
  We offer a rich source of data that allows a deeper exploration of the poly(A)- landscape of the eukaryotic transcriptome. The approach we present here also applies to the analysis of the poly(A)- transcriptomes of other organisms.
authors.affiliation: Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT 06030-6403, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Yang
authors.forename: Michael O
authors.initials: MO
authors.lastname: Duff
authors.forename: Brenton R
authors.initials: BR
authors.lastname: Graveley
authors.forename: Gordon G
authors.initials: GG
authors.lastname: Carmichael
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D019295:Computational Biology / Q000379:methods*; D053595:Embryonic Stem Cells / Q000378:metabolism; D056890:Eukaryota; D005786:Gene Expression Regulation; D016678:Genome; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D007438:Introns / Q000235:genetics*; D011061:Poly A / Q000235:genetics; D020033:Protein Isoforms / Q000235:genetics* / Q000378:metabolism; D012313:RNA / Q000235:genetics*; D059467:Transcriptome
chemical_list: D006657:Histones; D020033:Protein Isoforms; D011061:Poly A; D012313:RNA