Faculty of Biological Sciences

Dr Joan Boyes

BA, Oxford; PhD 1991, IMP, University of Vienna.
Associate Professor
School of Molecular and Cellular Biology

Background: Postdoctoral work NIH, Bethesda, MD, USA (1991-1997); Kay Kendall Leukaemia Fellowship and Lister Fellowship, Institute of Cancer Research London (1998-2004). Joined University of Leeds November 2004.

Contact:  Miall 10.01, +44(0) 113 34 33147, email address for  

Research Interests

Regulation of Gene Transcription and V(D)J Recombination by Chromatin Modifications

Multicellular organisms absolutely require that genes are activated in the right cell type and at the right time during development. We are investigating two key aspects of gene regulation. Firstly, we are investigating the chromatin changes associated with the regulation of immunoglobulin genes and V(D)J recombination. Secondly, we are investigating the role of protein modifications in the control of transcription factor levels, which in turn modulate the levels of gene transcription.

 

V(D)J Recombination and Genome Instability

V(D)J recombination enables a highly diverse repertoire of immunoglobulin and T cell receptor genes to be generated. However, since the recombination reaction involves the breakage and rejoining of DNA, it is also inherently risky and the price humans pay for having such an effective immune system is genome instability and cancer. We are investigating the mechanism by which V(D)J recombination is regulated and how mistakes in this reaction can lead to oncogene activation.

 

Regulation of V(D)J recombination

V(D)J recombination generates diversity of the variable exon of immunoglobulin and T cell receptor genes by the stochastic joining of individual V, D and J gene segment. All gene segments with the potential to be recombined are flanked by the same recombination signal sequences (RSSs). Moreover, the same lymphoid-specific proteins, RAG1 and RAG2, recognize these RSSs to initiate recombination in both B and T cells. Despite using the same signal sequences and the same proteins, V(D)J recombination is strictly regulated in a cell-, locus- and stage-specific manner. An important question is how this cell and stage specificity is achieved. The key regulatory step is thought to be the specific disruption of the chromatin packaging at the RSSs.

 

figure 1We are investigating the chromatin changes associated with V(D)J recombination, using the mouse immunoglobulin lambda light chain locus (Ig lambda) as a model. This is the smallest antigen receptor locus with only six functional recombining gene segments. We have identified a critical enhancer that regulates recombination of this locus and notably, this enhancer is bound by only two B-cell specific factors, PU.1 and IRF4. The Ig lambda locus rearranges primarily in pre-B cells but we showed that increased levels just of IRF4 at the earlier pro-B cell stage are enough to completely activate the Ig lambda locus. Using this system, we showed that even when all the known chromatin changes associated with recombination are present, this is not sufficient to completely trigger recombination. Instead, we find a strong correlation between the level of non-coding transcription and recombination of the light chain loci. We showed further that the transient loss of H2A/H2B dimers from nucleosomes, triggered by ongoing transcription is needed to generate a fully active chromatin structure and the initiation of V(D)J recombination. We propose that by fully opening the chromatin for recombination only transiently, this prevents excessive RAG cutting, which could lead to genome instability.

Future projects aim to further investigate the critical steps in long range locus activation.

 

Role of recombination by-products in triggering genome instability

During V(D)J recombination, the recombining gene segments are brought together and the intervening DNA is excised. The reactive ends of this excised DNA are joined into a circle, the excised signal circle (ESC), which was thought to be lost during cell division. However, more recent studies have shown that the ESC can be (re-)bound by RAG proteins and re-integrated at RSSs and cryptic RSSs in the genome. Since a number of cryptic RSSs lie next to oncogenes, this can lead to oncogene activation and tumourogenesis. We are investigating the regulation of re-integration and also developing probes to detect the sites of re-integration.

 

Regulation of the level of Gene Transcription

Many studies of gene regulation have focused on how transcription initiation is regulated. However, equally important to turning a gene on is the ability to turn transcription off. figure 2Recently, it has become apparent that active transcription factors at promoters are degraded via the ubiquitin/proteasome pathway. This thereby limits their half-life at promoters and thus the level of gene transcription. Although there is good evidence that active transcription factors are degraded, nothing is known about how this degradation is controlled. We are investigating this question using the haemopoietic transcription factor, GATA-1. In particular, we are analyzing the role of protein modifications in triggering degradation and how these transcription factor modifications, in turn, are regulated. The long term goal is to understand how eukaryotic transcription levels are regulated in response to environmental signals.

Sources of funding: MRC, NC3Rs, Yorkshire Cancer Research, the Lady Tata Memorial Trust, Children with Cancer.

 

Faculty Research and Innovation



Studentship information

See also:

Modules managed

BIOC2301 - Intermediate Integrated Biochemistry

Modules taught

BIOC1301 - Introductory Integrated Biochemistry: the Molecules and Processes of Life
BIOC1303 - Introductory Biochemistry: Problem Solving and Data Handling
BIOC2301 - Intermediate Integrated Biochemistry
BIOC2302 - Intermediate Biochemistry: Practicals
BIOC2303 - Intermediate Biochemistry: Skills
BIOC3160 - Laboratory/Literature/Computing Research Project
BIOL2111/BIOC2301 - Integrated Biochemistry/Genetic Engineering
BIOL2301/03/05/MICR2320 - Skills for Biol Sci, Biosciences and Microbiology
BIOL3399 - Extended Research Project Preparation
BLGY3152 - Advanced Topics in Human Genetics

Group Leader Dr Joan Boyes  (Associate Professor)

Regulation of Gene Transcription and V(D)J Recombination by Chromatin Modifications 

Postgraduates

Zeqian Gao (Primary supervisor) 90% FTE
James Scott (Primary supervisor) 70% FTE
Alastair Smith (Primary supervisor) 90% FTE
Daniel Thwaites (Primary supervisor) 90% FTE
Xiaoling Wang (Primary supervisor) 80% FTE
Mohd Azinuddin Ahmad Mokhtar (Co-supervisor) 10% FTE
Fatin Zainul Abidin (Co-supervisor) 10% FTE