Journal
BMC GENOMICS
Volume 14, Issue -, Pages -Publisher
BMC
DOI: 10.1186/1471-2164-14-1
Keywords
Platelet; Transcriptome; Ribosomal RNA; Non-coding RNA; miRNA; Repeat elements; Antisense transcripts
Funding
- Cardeza Foundation for Hematological Research (Philadelphia, PA)
- Kimmel Cancer Center (Philadelphia, PA)
- NIH-NCI Cancer Center [P30-CA-56036]
- NIH-NHLBI [R01-HL-102482]
- NIH-NIAID [2U19AI056363-06/2030984]
- William M. Keck Foundation
- TJU funds
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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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