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Claudia Kutter Group

Claudia Kutter

Functional interactions of mammalian coding and noncoding transcriptomes

Over 200 highly specialized cells with diverse morphologies and functionalities exist in the human body, yet virtually every cell in the body contains the same genetic information. To exert cell-specific functions high fidelity mechanisms evolved to restrict the synthesis and processing of discrete sets of regulatory RNA molecules. Abnormal cell behavior as seen in many fatal human diseases, such as cancer, is often the consequence of aberrant transcripts formation.

The focus of our research is understanding the regulatory interdependencies of protein-coding and noncoding RNAs (ncRNAs). ncRNAs are RNA molecules that are not translated into protein products. They are implicated in diverse cellular processes, which include the control of transcription, RNA maturation and protein synthesis. Our group studies coding and noncoding RNAs (long noncoding, transfer and small RNAs) at the transcriptome-wide level in mammalian somatic tissues and in the germline. We aim to gain mechanistic insights into the transcriptional and post-transcriptional regulation and processing of RNAs during organ development, cell differentiation and disease progression.

We are particularly interested in:

  • revealing the origin, evolution and disease association of ncRNAs
  • deciphering the molecular mechanism underpinning regulation by ncRNAs and
  • validating ncRNA functions.

Our experimental approaches include:

  • applying and developing high-throughput RNA sequencing methodologies and epigenetic profiling coupled to powerful computational analysis,
  • detailed biochemical assays and
  • phenotypic characterization using genome editing tools in mammalian cell lines and tissues.

We are an integrated team of experimental and computational scientists working in close collaboration to pursue individual research projects. Our group is affiliated to MTC and the Science for Life Laboratory where our laboratory is located.

Science for Life Laboratory

Group Members

Wallenberg Academy Fellow Claudia Kutter: Junk may prove to be gold in the fight against cancer

Publications

The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity.
Ernst C, Odom DT, Kutter C
Nat Commun 2017 11;8(1):1411

Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis.
Ernst C, Pike J, Aitken SJ, Long HK, Eling N, Stojic L, et al
Elife 2016 11;5():

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, et al
PLoS Genet. 2016 05;12(5):e1006024

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.
Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, et al
Elife 2014 Oct;3():e02626

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
Schmitt B, Rudolph K, Karagianni P, Fonseca N, White R, Talianidis I, et al
Genome Res. 2014 Nov;24(11):1797-807

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders.
Blanco S, Dietmann S, Flores J, Hussain S, Kutter C, Humphreys P, et al
EMBO J. 2014 Sep;33(18):2020-39

Global gene expression profiling reveals SPINK1 as a potential hepatocellular carcinoma marker.
Marshall A, Lukk M, Kutter C, Davies S, Alexander G, Odom DT
PLoS ONE 2013 ;8(3):e59459

The evolutionary landscape of alternative splicing in vertebrate species.
Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, et al
Science 2012 Dec;338(6114):1587-93

Latent regulatory potential of human-specific repetitive elements.
Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, et al
Mol. Cell 2013 Jan;49(2):262-72

Rapid turnover of long noncoding RNAs and the evolution of gene expression.
Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, Ponting CP, et al
PLoS Genet. 2012 ;8(7):e1002841

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, et al
Cell 2012 Jan;148(1-2):335-48

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.
Kutter C, Brown GD, Gonçalves A, Wilson MD, Watt S, Brazma A, et al
Nat. Genet. 2011 Aug;43(10):948-55

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, et al
Science 2010 May;328(5981):1036-40

 

Vacancies

Enquiries (with CV) about experimental and computational postdoctoral positions are welcome