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The complex transcriptional landscape of the anucleate human platelet
Journal article   Open access   Peer reviewed

The complex transcriptional landscape of the anucleate human platelet

Paul F. Bray, Steven E. McKenzie, Leonard C. Edelstein, Srikanth Nagalla, Kathleen Delgrosso, Adam Ertel, Joan Kupper, Yi Jing, Eric Londin, Phillipe Loher, …
BMC genomics, v 14(1), pp 1-1
16 Jan 2013
PMID: 23323973
url
https://doi.org/10.1186/1471-2164-14-1View
Published, Version of Record (VoR)CC BY V4.0 Open

Abstract

Biotechnology & Applied Microbiology Genetics & Heredity Life Sciences & Biomedicine Science & Technology
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 similar to 1 billion reads revealed that coding and non-coding platelet transcripts span a very wide dynamic range (>= 16 PCR cycles beyond beta-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, similar to 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/.

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Web of Science research areas
Biotechnology & Applied Microbiology
Genetics & Heredity
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