The complex transcriptional landscape of the anucleate human platelet

• DOI: 10.1186/1471-2164-14-1
• Publication Date: 2013-01-16T06:15:39Z
• Authors: 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
• Keywords: Coding region

Human blood platelets are essential to maintaining normal hemostasis, and platelet dysfunction often causes bleeding or thrombosis. Estimates of genome-wide RNA expression using microarrays have provided insights the transcriptome but were limited by number known transcripts. The goal this effort was deep-sequence from leukocyte-depleted capture complex profile all expressed From each four healthy individuals we generated long (≥40 nucleotides) profiles total ribosomal-RNA depleted preparations, as well short (<40 profiles. Analysis ~1 billion reads revealed that coding non-coding transcripts span a very wide dynamic range (≥16 PCR cycles beyond β-actin), result validated through qRT-PCR on many dozens messenger RNAs. Surprisingly, depletion significantly adversely affected estimates relative abundance Of protein-coding loci, ~9,500 present in human platelets. We observed strong correlation between mRNAs identified RNA-seq microarray for well-expressed mRNAs, RNASeq more lower permitted discovery novel Our analyses diverse classes RNAs, including: pervasive antisense loci; numerous, previously unreported abundant microRNAs; retrotransposons; thousands un-annotated intronic transcripts, an intriguing finding considering anucleate nature data available local mirror UCSC genome browser can be accessed at: http://cm.jefferson.edu/platelets_2012/ .