The complex transcriptional landscape of the anucleate human platelet.
BMC Genomics
; 14: 1, 2013 Jan 16.
Article
en En
| MEDLINE
| ID: mdl-23323973
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 ß-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/.
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Base de datos:
MEDLINE
Asunto principal:
Transcripción Genética
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Plaquetas
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Núcleo Celular
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Genómica
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
BMC Genomics
Asunto de la revista:
GENETICA
Año:
2013
Tipo del documento:
Article