Genomewide characterization of non-polyadenylated RNAs

• Published in: Genome biology Vol. 12; no. 2; p. R16
• Main Authors: Yang, Li, Duff, Michael O, Graveley, Brenton R, Carmichael, Gordon G, Chen, Ling-Ling
• Format: Journal Article
• Language: English
• Published: England BioMed Central 16.02.2011
• Subjects: Animals; Cell Differentiation; Computational Biology - methods; Embryonic Stem Cells - metabolism; Eukaryota; Gene Expression Regulation; Genome; HeLa Cells; High-Throughput Nucleotide Sequencing; Histones - genetics; Histones - metabolism; Humans; Introns - genetics; Poly A - genetics; Protein Isoforms - genetics; Protein Isoforms - metabolism; RNA - genetics; Transcriptome
• ISSN: 1474-760X; 1465-6906; 1474-760X; 1465-6914
• DOI: 10.1186/gb-2011-12-2-r16

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. 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. 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.