FY2013 Annual Report

Genomics and Regulatory Systems Unit

Assistant (Adjunct) Professor Nicholas Luscombe


Cellular life must recognise and respond appropriately to diverse internal and external stimuli. By ensuring the correct expression of specific genes at the appropriate times, the transcriptional regulatory system plays a central role in controlling many biological processes: these range from cell cycle progression and maintenance of intracellular metabolic and physiological balance, to cellular differentiation and developmental time-courses. Numerous diseases result from a breakdown in the regulatory system and a third of human developmental disorders have been attributed to dysfunctional transcription factors (TFs). Furthermore, alterations in the activity and regulatory specificity of TFs are now established as major sources for species diversity and evolutionary adaptation. Indeed, increased sophistication of the regulatory system appears to have been a principal requirement for the emergence of metazoan life.

Our research is dedicated to understanding on a genomic scale: (i) how transcription is regulated and (ii) how this regulatory system controls biologically interesting phenomena. Much of our work until now has been purely computational, either analysing publicly available data or in collaboration with experimental laboratories performing functional genomic investigations.

1. Staff

  • Nicholas M. Luscombe, Assistant Professor (Adjunct)
  • Dr Garth Ilsley, Research Scientist
  • Dr Takeshi Noda, Researcher
  • Dr.Ritsuko Suyama, Research Scientist
  • Sachiko Blank, Administrative Assistant

2. Collaborations

  • Theme: Single cell analysis of transcriptional regulation in developing chordate embryos
    • Type of collaboration: Joint research
    • Researchers: Professor, Nori Satoh, OIST Graduate University

3. Activities and Findings

Garth Ilsley, Takeshi Noda, Ritsuko SuyamaNicholas Luscombe in collaboration with Nori Satoh

Until now, molecular biology techniques have been limited in the ability to measure gene expression levels in single cells, meaning that only average measurements for entire embryos were available. In collaboration with Nori Satoh’s unit, we have developed approaches to measure gene expression and thus model transcriptional regulatory processes in individual cells, as they differentiate into specific cell types. We have been developing and testing this approach with single cells of the early Ciona intestinalis (sea squirt) embryo. Although the adult form appear distinct to vertebrates, the Cionalarva is clearly a chordate, thus offering us an opportunity to understand aspects of vertebrate evolution and development. We are currently assembling a dataset of gene expression by RNA-Seq in every cell of the Ciona embryo at the 16, 32 and 64-cell stages.

4. Publications

4-1 Journals

Ilsley, G. R., Fisher, J., Apweiler, R., DePace, A. H. & Luscombe, N. M. Cellular resolution models for even skipped regulation in the entire Drosophila embryo. eLife 2, (2013).

4-2 Oral and poster presentation

Noting to report

4.3 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

Nothing to report

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6.Organized events(Symposia/Workshop) and Meetings

6-1  Hands-on Training at OIST: Practical workshop on High-Throughput Sequencing data Analysis 2013

Date: September 30 to October 4, 2013
Venue:OIST Seaside House
Organizer: Nicholas M Luscombe (OIST)
Co-organizers:Jonathan Miller (OIST) and Mikita Suyama (University of Kyushu) John Marioni(EMBL European Bioinformatics Institute,UK)


  • Piero Carninci, Riken Omics Science Centre, Japan
  • Byung-Kwan Cho, Korean Advanced Institute of Science & Technology, Korea
  • Jing-Dong Jackie Han, CAS-MPG Institute for Computational Biology, Shanghai, China
  • Nicolas Delhomme, Umeå University, Sweden
  • Benilton Carvalho, State University of Campinas (UNICAMP), Brazil
  • Gabriella Rustici, EMBL European Bioinformatics Institute, UK 
  • Kathi Zarnack, CRUK London Research Institute, UK 
  • Bori Gerle, University College London, UK 

7. Other

Nicholas Luscombe elected EMBO Member 2013