The complex transcriptional landscape of the anucleate human platelet

BMC Genomics. 2013 Jan 16;14:1. doi: 10.1186/1471-2164-14-1.

Abstract

Background: Human 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.

Results: From 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.

Conclusions: Our 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/.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blood Platelets / cytology*
  • Blood Platelets / metabolism*
  • Cell Nucleus*
  • Data Mining
  • Genomics*
  • Humans
  • Internet
  • Introns / genetics
  • Pseudogenes / genetics
  • RNA, Antisense / genetics
  • RNA, Messenger / genetics
  • RNA, Ribosomal / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, RNA
  • Transcription, Genetic*

Substances

  • RNA, Antisense
  • RNA, Messenger
  • RNA, Ribosomal