Genomics of gene expression
One of the biggest challenges in biology is to understand how apparently identical cells respond differently to the same stimulus. We are especially interested in understanding how the intrinsic complexity of gene expression contributes to non-genetic cellular adaptation. To deliver an integrated view of the mechanisms driving the appearance of divergent cellular phenotypes, as well as to refine our knowledge of the basic process of gene expression, we study: the epigenetic status, transcript isoform usage and post-transcriptional mRNA regulation.
In addition to our interest in the fundamental dissection of gene expression, our lab actively develops novel sequencing technologies. We have developed a diversity of approaches to study gene expression, chromatin organization and to improve clinical analysis. We investigate the complexity of overlapping human transcript isoforms simultaneously sequencing both the 5’ and 3’ ends of each RNA molecule (TIF-Seq). Our lab has also shown how the existence of widespread co-translational mRNA degradation allows studying ribosome dynamics by sequencing mRNA degradation intermediates (5P-Seq). By combining experimental and computational biology, we aim to decrease the gap between research fields and contribute to a better mechanistically understanding of the gene expression process.
Alisa Alekseenko, PhD student
Bingnan Li, Postdoc
Donal Barrett, Research Technician
Eva Brinkman, Postdoc
Jingwen Wang, Postdoc
Lilit Nersisyan, Postdoc
Ryan Hull, Postdoc
Sueli Marques, Senior Lab Manager
Susanne Huch, Postdoc
Xiushan Yin, Visiting Professor
Yerma Pareja Sanchez, PhD student
Yujie Zhang, PhD student
- Pelechano V*, Wei W*, and Steinmetz LM. Widespread co-translational RNA decay reveals ribosome dynamics. Cell 2015 Jun 4;161(6):1400-12.
- Chabbert CD*, Adjalley SH*, Klaus B, Fritsch ES, Gupta I, Pelechano V#, and Steinmetz LM#. High-throughput ChIP-Seq for large-scale chromatin studies. Mol Syst Biol. 2015 Jan 12;11(1):777.
- Gupta I, Clauder-Münster S, Klaus B, Järvelin AI, Aiyar RS, Benes V, Huber W, Pelechano V# and Steinmetz LM#. Alternative polyadenylation diversifies post-transcriptional regulation through selective RNA-protein interactions. Mol Syst Biol. 2014 Feb 25;10(2):719.
- Pelechano V*, Wei W*, Steinmetz LM. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature. 2013 May 2;497(7447):127-3
- Wilkening S*, Pelechano V*, Järvelin AI*, Tekkedil MM, Anders S, Benes V, Steinmetz LM. An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res. 2013 Mar 1;41(5):e65
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Photo credit of my portrait: Magnus Bergström