The complex transcriptional landscape of the anucleate human platelet

BMC Genomics

Research Article

Joan Kupper¹  Kathleen Delgrosso¹  Adam Ertel¹  Paolo Fortina¹  Leonard C Edelstein²  Paul F Bray²  Steven E McKenzie²  Srikanth Nagalla²  Isidore Rigoutsos³  Eric Londin³  Huang-Wen Chen³  Phillipe Loher³  Yi Jing³ 

[1] Cancer Genomics Laboratory, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA;Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA;Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA;

关键词: Platelet;    Transcriptome;    Ribosomal RNA;    Non-coding RNA;    miRNA;    Repeat elements;    Antisense transcripts;   

DOI  :  10.1186/1471-2164-14-1

 received in 2012-06-28, accepted in 2012-12-05,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundHuman blood platelets are essential to maintaining normal hemostasis, and platelet dysfunction often causes bleeding or thrombosis. Estimates of genome-wide platelet RNA expression using microarrays have provided insights to the platelet transcriptome but were limited by the number of known transcripts. The goal of this effort was to deep-sequence RNA from leukocyte-depleted platelets to capture the complex profile of all expressed transcripts.ResultsFrom each of four healthy individuals we generated long RNA (≥40 nucleotides) profiles from total and ribosomal-RNA depleted RNA preparations, as well as short RNA (<40 nucleotides) profiles. Analysis of ~1 billion reads revealed that coding and non-coding platelet transcripts span a very wide dynamic range (≥16 PCR cycles beyond β-actin), a result we validated through qRT-PCR on many dozens of platelet messenger RNAs. Surprisingly, ribosomal-RNA depletion significantly and adversely affected estimates of the relative abundance of transcripts. Of the known protein-coding loci, ~9,500 are present in human platelets. We observed a strong correlation between mRNAs identified by RNA-seq and microarray for well-expressed mRNAs, but RNASeq identified many more transcripts of lower abundance and permitted discovery of novel transcripts.ConclusionsOur analyses revealed diverse classes of non-coding RNAs, including: pervasive antisense transcripts to protein-coding loci; numerous, previously unreported and abundant microRNAs; retrotransposons; and thousands of novel un-annotated long and short intronic transcripts, an intriguing finding considering the anucleate nature of platelets. The data are available through a local mirror of the UCSC genome browser and can be accessed at:http://cm.jefferson.edu/platelets_2012/.

【 授权许可】

CC BY   
© Bray et al.; licensee BioMed Central Ltd. 2013