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 language | English (US) |
|---|---|
| Number of pages | 1 |
| Journal | BMC Genomics |
| DOIs | |
| State | Accepted/In press - Jan 16 2013 |
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ASJC Scopus subject areas
- Biotechnology
- Genetics
Cite this
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 journal › Article
}
TY - JOUR
T1 - The complex transcriptional landscape of the anucleate human platelet
AU - Bray, Paul F.
AU - McKenzie, Steven E.
AU - Edelstein, Leonard C.
AU - Nagalla, Srikanth
AU - Delgrosso, Kathleen
AU - Ertel, Adam
AU - Kupper, Joan
AU - Jing, Yi
AU - Londin, Eric
AU - Loher, Phillipe
AU - Chen, Huang Wen
AU - Fortina, Paolo
AU - Rigoutsos, Isidore
PY - 2013/1/16
Y1 - 2013/1/16
N2 - 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/.
AB - 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/.
UR - http://www.scopus.com/inward/record.url?scp=84872183938&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84872183938&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-14-1
DO - 10.1186/1471-2164-14-1
M3 - Article
C2 - 23323973
AN - SCOPUS:84872183938
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
ER -