Sander Granneman

MRC Senior Non-Clinical Research Fellow in RNA Biochemistry and Group Leader

Biography

Background

1998 - 2003    PhD, University of Nijmegen, The Netherlands

2003 - 2006    Post-doctoral fellow at the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven

2006 - 2011    Post-doctoral fellow at the Wellcome Trust Centre for Cell Biology, Edinburgh, UK

2011 - 2017    Wellcome Trust Research Career Development Fellow and PI at the Centre for Systems and Synthetic Biology (SynthSys), IQB3 UK

2018 -  Present    MRC non-clinical Senior Research Fellow and PI at the Centre for Systems and Synthetic Biology (SynthSys), IQB3 UK 

Undergraduate teaching

2018 – present:          Lecturer on Gene Expression & Microbial Regulation:

  • Two lectures on sRNAs and post-transcriptional regulation of gene expression.
  • Marking of exams.

     2017 – present:      Lecturer on Structure and Function of Proteins.

  • Two lectures on characterization of Macromolecules.
  • Web-based tutorial on protein purification.
  • Marking of exams and paper assignments.

     2015 – present:      Lecturer on Biochemistry B, MSc course.

  • Ribosome synthesis
  • Mechanism of translation.
  • Tutorials.
  • Marking of exams.
  • Marking of project reports.

     2015 + 2017:          Tutor on Biochemistry honours course.

  • 10 hours in Semester 1 and 2.

     2013 – present:      Lecturer on Tools for Synthetic Biology, MSc course.

  • Next Generation Sequencing.
  • Riboswitches.
  • Tutorials.

     2013 – present:      Lecturer on Gene Expression course.

        • Translation in prokaryotes.
        • Regulation of mRNA decay in eukaryotes.
        • Marking of exams.

     2012 –present:      Lecturer on The RNA world course.

        • Riboswitches.
        • Marking of reports and presentations.

     2011 – present:      Marking of ICB honour dissertations.

Open to PhD supervision enquiries?

Yes

Current PhD students supervised

Ongoing PhD research supervision:

- Secondary Supervisor Holly Kay (Royal Society; 2018 - present).

- Secondary Supervisor Pujitha Raja (Darwin Trust; 2018 – present).

- Secondary Supervisor Agata Wawszczyk (BBSRC; 2017 -  present)

- Primary Supervisor for Stuart McKellar (Wellcome Trust; 2016 – present).

Past PhD students supervised

Postgraduate research supervision, completed:

 - Primary PhD supervisor for Ira Iosub (Wellcome Trust; 2014-2018).

- Primary PhD supervisor for Elena Burlacu (Wellcome Trust; 2012-2016).

- Secondary PhD supervisor for Alina Selega (Informatics; 2014-2017).

- Project Supervision: five Biochemistry Honour students, six Erasmus students, two Masters student and one Bioinformatics student.

Research summary

My lab is interested in the role of RNA regulators and RNA binding proteins in the regulation of gene expression. Most of our research has focussed on the assembly of large macromolecular complexes, such as the yeast ribosome. However, more recently, we have also been working on understanding the role of RNA surveillance factors in the regulation of mRNA transcription and translation in both yeast and pathogenic bacteria. The goal of our research is to obtain detailed mechanistic insights into the strategies that organisms use for regulating gene expression during rapid adaptive responses. For our research we use highly innovative methodologies such as CRAC and CLASH and high-throughput structure probing methods. Our work is funded by the BBSRC, SULSA, the Wellcome Trust and the Medical Research Council.

Current research interests

My group is studying the role of riboregulators and RNA binding proteins in regulation of gene expression during adaptive responses. Many microorganisms, in particular human pathogens, have evolved clever mechanisms to be able to very rapidly adapt to stress caused by environmental changes, such as changes in host temperature and nutrient availability. This enables them to efficiently maintain cellular homeostasis even in hostile environments. Our goal is to gain mechanistic insights into regulatory strategies used by these organisms to adapt to stress. Our research focusses on riboregulators and RNA-binding proteins that play a key role in stress adaptation. In collaboration with Jay Tree (University of Sydney) and Ross Fitzgerald (Roslin) we are currently working on a number of bacterial pathogens to unravel the role of these factors in the post-transcriptional regulation of gene expression (see Tree J et al Mol Cell 2014).

Past research interests

We also study the mechanisms of ribosome synthesis and its relationship with cancer and cell division. Ribosomes are large RNA-protein complexes that translate mRNA into protein in the cytoplasm of eukaryotic cells. Ribosomes are largely synthesized in a subnuclear compartment called the nucleolus. In eukaryotes, three of the four ribosomal RNAs (rRNAs) are transcribed as a single precursor (35S pre-rRNA in yeast) that is processed at several well-defined sites to generate the mature 18S, 5.8S and 25S rRNA. Pre-rRNA processing takes place in large complexes called pre-ribosomes, which are the precursors to the ribosomes. A growing mammalian cell produces about 7500 ribosomes per minute, requiring around 600,000 ribosomal proteins and involve over 200 trans-acting factors, necessary for the synthesis of ribosomal RNA (rRNA) and ribosomal subunit assembly. In interphase cells the number and size of nucleoli and the rate of ribosome synthesis directly correlate with cell proliferation rates, and aberrant nucleolar morphology is a hallmark of cancer cells. However, little is known about how the process of ribosome assembly is coupled to cell proliferation and a detailed understanding of ribosome biogenesis is required to comprehend these links. The goal of our research is to gain molecular insights into the dynamics of ribosome assembly in yeast using biochemical and high-throughput approaches.

Knowledge exchange

Software development:

  • In collaboration with Guido Sanguinetti’s group we developed BUM_HMM, a machine learning tool for mining high-throughput RNA structure probing data (Selega et al Nature Methods, 2017).
  • We developed the pyCRAC software package that simplified the analysis of high-throughput protein-RNA cross-linking data. The open access package was published in Genome Biology (Webb et al Genome Biology2014).

 

Technology development and IP disclosure:

Together with UVO3we have designed and built a new UV irradiation unit to be able to more efficiently cross-link proteins to RNA. The goal was to develop a new CLIP method that would allow us to do time-resolved protein-RNA cross-linking studies. To support this project, we obtained from the Wellcome Trust (ISSF and Enhancement Awards). 

Affiliated research centres

View all 68 publications on Research Explorer

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