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SUMMARY:Exon / Intron-Split Analysis Quantifies both Transcriptional and P
 ost-Transcriptional Contributions to Differential Expression in RNA-Seq
DTSTART:20140624T121500
DTSTAMP:20260430T074532Z
UID:38a94285f9b04e8342601cf8cae103c0ead2b3c4b3c332c7b7535b7c
CATEGORIES:Conferences - Seminars
DESCRIPTION:Michael Stadler\, Ph.D.\, Friedrich-Miescher Institute\, Basel
  (CH)\nBIOENGINEERING SEMINARAbstract:\nEukaryotic RNA expression is contr
 olled at multiple regulatory layers including transcription\, splicing\, n
 uclear export and RNA decay. The steady-state levels of mature RNAs are th
 e net result of the concerted activity of all of these layers. While these
  levels can be directly quantified using RNA-seq\, obtaining information a
 bout the transcriptional layer is experimentally challenging and requires 
 specific experimental procedures. It has recently been shown that primary 
 transcripts are also captured during RNA-seq library preparation\, suggest
 ing that intronic reads could be used to infer differences in transcriptio
 n without the need for specialized experimental approaches.\nWe can demons
 trate in several experimental systems that intronic reads mostly stem from
  nuclear RNA and that changes in intronic read counts accurately predict c
 hanges in transcriptional activity. We also found that the comparison of i
 ntronic and exonic levels\, which we refer to as "Exon/Intron-split analys
 is"\, allows the direct separation of transcriptional and post-transcripti
 onal contributions to mRNA expression changes. Our findings suggest that a
  standard RNA-seq experiment does not only allow the assessment of transcr
 ipt levels and structures\, but also reveals transcriptional and posttrans
 criptional responses to cellular perturbations\, increasing the value of e
 xisting and newly generated RNA-seq data.Bio:\n1999 MS in Immunology\, Uni
 versity of Bern\n2001 MS in Bioinformatics\, Universities of Geneva & Laus
 anne\n2003 PhD in Computational Immunology\, Insel Hospital\, University o
 f Bern\n2004-2006 postdoc at MIT\, Cambdridge\, USA with Chris Burge on tr
 anscription and splicing\n2006-   FMI Computational Biology group
LOCATION:SV1717A http://map.epfl.ch/?room=sv1717a
STATUS:CONFIRMED
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