原创力文档an rna-seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncrnasrna-seq策略检测完成编码和非编码转录组,包括完整的印宏ncrnas.pdfVIP
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An RNA-Seq Strategy to Detect the Complete Coding and
Non-Coding Transcriptome Including Full-Length
Imprinted Macro ncRNAs
1 2 1 1 2 2
Ru Huang , Markus Jaritz , Philipp Guenzl , Irena Vlatkovic , Andreas Sommer , Ido M. Tamir , Hendrik
3 1 1 3 1
Marks , Thorsten Klampfl , Robert Kralovics , Hendrik G. Stunnenberg , Denise P. Barlow *, Florian M.
Pauler1*
1 CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria, 2 Research Institute of Molecular Pathology, Vienna, Austria,
3 Department of Molecular Biology, Faculty of Science, Nijmegen Center for Molecular Life Sciences (NCMLS), Radboud University Nijmegen, Nijmegen, The Netherlands
Abstract
Imprinted macro non-protein-coding (nc) RNAs are cis-repressor transcripts that silence multiple genes in at least three
imprinted gene clusters in the mouse genome. Similar macro or long ncRNAs are abundant in the mammalian genome.
Here we present the full coding and non-coding transcriptome of two mouse tissues: differentiated ES cells and fetal head
using an optimized RNA-Seq strategy. The data produced is highly reproducible in different sequencing locations and is
able to detect the full length of imprinted macro ncRNAs such as Airn and Kcnq1ot1, whose length ranges between 80–
118 kb. Transcripts show a more uniform read coverage when RNA is fragmented with RNA hydrolysis compared with cDNA
fragmentation by shearing. Irrespective of the fragmentation method, all coding and non-coding transcripts longer than
8 kb show a gradual loss of sequencing tags towards the 39 end. Comparisons to published RNA-Seq datasets sho
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