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In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.
KTH, School of Biotechnology (BIO), Gene Technology. (Division of Gene Technology)
KTH, School of Biotechnology (BIO), Gene Technology. (Division of Gene Technology)
KTH, School of Biotechnology (BIO), Gene Technology. (Division of Gene Technology)ORCID iD: 0000-0002-8879-9245
KTH, School of Biotechnology (BIO), Gene Technology. (Division of Gene Technology)ORCID iD: 0000-0003-4313-1601
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Several recent studies have indicated that transcription is pervasive in regions outside of protein coding genes and that short antisense transcripts can originate from the promoter and terminator regions of genes. Here we investigate transcription of fragments longer than 200 nucleotides, focusing on antisense transcription for known protein coding genes and intergenic transcription. We find that roughly 12% to 16% of all reads that originate from promoter and terminator regions, respectively, map antisense to the gene in question. Furthermore, we detect a high number of novel transcriptionally active regions (TARs) that are generally expressed at a lower level than protein coding genes. We also investigate the correlation between RNA-seq data and microarray data and conclude that the correlation is dependant on gene length such that longer genes show a better correlation.

Keyword [en]
Transcriptome, non-coding RNA, DNA sequencing, next generation sequencing
National Category
Other Biological Topics
Identifiers
URN: urn:nbn:se:kth:diva-11445OAI: oai:DiVA.org:kth-11445DiVA: diva2:276130
Note
QC 20100723Available from: 2009-11-10 Created: 2009-11-10 Last updated: 2010-07-23Bibliographically approved
In thesis
1. On Transcriptome Sequencing
Open this publication in new window or tab >>On Transcriptome Sequencing
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis is about the use of massive DNA sequencing to investigate the transcriptome. During recent decades, several studies have made it clear that the transcriptome comprises a more complex set of biochemical machinery than was previously believed. The majority of the genome can be expressed as transcripts; and overlapping and antisense transcription is widespread. New technologies for the interroga- tion of nucleic acids have made it possible to investigate such cellular phenomena in much greater detail than ever before. For each application, special requirements need to be met. The work presented in this thesis focuses on the transcrip- tome and the development of technology for its analysis. In paper I, we report our development of an automated approach for sample preparation. The procedure was benchmarked against a publicly available reference data set, and we note that our approach outperformed similar manual procedures in terms of reproducibility. In the work reported in papers II-IV, we used different massive sequencing technologies to investigate the transcriptome. In paper II we describe a concatemerization approach that increased throughput by 65% using 454 sequencing,and we identify classes of transcripts not previously described in Populus. Papers III and IV both report studies based on SOLiD sequencing. In the former, we investigated transcripts and proteins for 13% of the human gene and detected a massive overlap for the upper 50% transcriptional levels. In the work described in paper IV, we investigated transcription in non-genic regions of the genome and detected expression from a high number of previ- ously unknown loci.

Place, publisher, year, edition, pages
Stockholm: KTH, 2009. 52 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2009:26
Keyword
Transcriptome, RNA-seq, DNA sequencing, gene expression profiling, non-coding RNA, small RNA
National Category
Other Biological Topics Bioinformatics and Systems Biology Genetics Biochemistry and Molecular Biology Cell and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-11446 (URN)978-91-7415-490-0 (ISBN)
Public defence
2009-12-18, Oscar Klein (FR4), Roslagstullsbacken 21, Albanova University Center, Stockholm, 09:00 (Swedish)
Opponent
Supervisors
Note
QC 20100723Available from: 2009-12-03 Created: 2009-11-10 Last updated: 2010-07-23Bibliographically approved

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Emanuelsson, Olof

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