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Open Access Research article

The complex transcriptional landscape of the anucleate human platelet

Paul F Bray1*, Steven E McKenzie1, Leonard C Edelstein1, Srikanth Nagalla1, Kathleen Delgrosso2, Adam Ertel2, Joan Kupper2, Yi Jing3, Eric Londin3, Phillipe Loher3, Huang-Wen Chen3, Paolo Fortina2 and Isidore Rigoutsos3*

Author affiliations

1 Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA

2 Cancer Genomics Laboratory, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA

3 Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, USA

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Citation and License

BMC Genomics 2013, 14:1  doi:10.1186/1471-2164-14-1

Published: 16 January 2013

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/ webcite.

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