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, Huang Wen Chen, Paolo Fortina, Isidore Rigoutsos

Research output: Contribution to journalArticle

72 Citations (Scopus)

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 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, ~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/.

Original languageEnglish (US)
Number of pages1
JournalBMC Genomics
DOIs
StateAccepted/In press - Jan 16 2013

Fingerprint

Blood Platelets
RNA
Ribosomal RNA
Messenger RNA
Genome
Polymerase Chain Reaction
Untranslated RNA
Retroelements
Hemostasis
MicroRNAs
Transcriptome
Actins
Proteins
Thrombosis
Leukocytes
Nucleotides
Hemorrhage

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Bray, P. F., McKenzie, S. E., Edelstein, L. C., Nagalla, S., Delgrosso, K., Ertel, A., ... Rigoutsos, I. (Accepted/In press). The complex transcriptional landscape of the anucleate human platelet. BMC Genomics. https://doi.org/10.1186/1471-2164-14-1

The complex transcriptional landscape of the anucleate human platelet. / Bray, Paul F.; McKenzie, Steven E.; Edelstein, Leonard C.; Nagalla, Srikanth; Delgrosso, Kathleen; Ertel, Adam; Kupper, Joan; Jing, Yi; Londin, Eric; Loher, Phillipe; Chen, Huang Wen; Fortina, Paolo; Rigoutsos, Isidore.

In: BMC Genomics, 16.01.2013.

Research output: Contribution to journalArticle

Bray, PF, McKenzie, SE, Edelstein, LC, Nagalla, S, Delgrosso, K, Ertel, A, Kupper, J, Jing, Y, Londin, E, Loher, P, Chen, HW, Fortina, P & Rigoutsos, I 2013, 'The complex transcriptional landscape of the anucleate human platelet', BMC Genomics. https://doi.org/10.1186/1471-2164-14-1
Bray, Paul F. ; McKenzie, Steven E. ; Edelstein, Leonard C. ; Nagalla, Srikanth ; Delgrosso, Kathleen ; Ertel, Adam ; Kupper, Joan ; Jing, Yi ; Londin, Eric ; Loher, Phillipe ; Chen, Huang Wen ; Fortina, Paolo ; Rigoutsos, Isidore. / The complex transcriptional landscape of the anucleate human platelet. In: BMC Genomics. 2013.
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