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 - Intermediate Skills - BIOL/MICR
BIOL5382M - Extended Research Project
BIOL5394M - Specialised Research Topics and Skills
BLGY3152 - Advanced Topics in Human Genetics

Committees

Member of Graduate School Committee (Progression Tutor (SMCB/Astbury))

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
Stephen Higgins (Primary supervisor) 100% FTE
Alastair Smith (Primary supervisor) 90% FTE
Daniel Thwaites (Primary supervisor) 90% FTE
Xiaoling Wang (Primary supervisor) 80% FTE
Samar Yahya (Primary supervisor) 100% FTE
Fatin Zainul Abidin (Co-supervisor) 10% FTE

Scott JNF, Kupinski AP, Boyes J Targeted genome regulation and modification using transcription activator-like effectors. FEBS J 281 4583-4597, 2014
DOI:10.1111/febs.12973
View abstract

Yan R, Hallam A, Stockley PG, Boyes J Oncogene dependency and the potential of targeted RNAi-based anti-cancer therapy. Biochemical Journal 461 1-13, 2014
View abstract

Scott JNF, Kupinski AP, Kirkham CM, Tuma R, Boyes JM Tale proteins bind to both active and inactive chromatin Biochemical Journal 458 153-158, 2014
DOI:10.1042/BJ20131327
View abstract

Kirkham CM, Scott JN, Boyes J, Bevington S The Molecular Basis of B Cell Development and the Role of Deregulated Transcription and Epigenetics in Leukaemia and Lymphoma TRANSCRIPTIONAL AND EPIGENETIC MECHANISMS REGULATING NORMAL AND ABERRANT BLOOD CELL DEVELOPMENT 331-363, 2014
DOI:10.1007/978-3-642-45198-0_13

Haque SFY, Bevington SL, Boyes J The E lambda(3-1) enhancer is essential for V(D)J recombination of the murine immunoglobulin lambda light chain locus BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 441 482-487, 2013
DOI:10.1016/j.bbrc.2013.10.087

Bevington S, Boyes J Transcription-coupled eviction of histones H2A/H2B governs V(D)J recombination. The EMBO Journal 32 1381-1392, 2013
DOI:10.1038/emboj.2013.42
View abstract

Palacios D, Summerbell D, Rigby PWJ, Boyes J Interplay between DNA Methylation and Transcription Factor Availability: Implications for Developmental Activation of the Mouse Myogenin Gene MOL CELL BIOL 30 3805-3815, 2010
DOI:10.1128/MCB.00050-10

de Thonel A, Vandekerckhove J, Lanneau D, Selvakumar S, Courtois G, Hazoume A, Brunet M, Maurel S, Hammann A, Ribeil JA, Zermati Y, Gabet AS, Boyes J, Solary E, Hermine O, Garrido C HSP27 controls GATA-1 protein level during erythroid cell differentiation BLOOD 116 85-96, 2010
DOI:10.1182/blood-2009-09-241778

Grange S, Boyes J Chromatin opening is tightly linked to enhancer activation at the kappa light chain locus BIOCHEM BIOPH RES CO 363 223-228, 2007
DOI:10.1016/j.bbrc.2007.08.171

Nightingale KP, Baumann M, Eberharter A, Mamais A, Becker PB, Boyes J Acetylation increases access of remodelling complexes to their nucleosome targets to enhance initiation of V(D)J recombination NUCLEIC ACIDS RES 35 6311-6321, 2007
DOI:10.1093/nar/gkm650

Hernandez-Hernandez A, Ray P, Litos G, Ciro M, Ottolenghi S, Beug H, Boyes J Acetylation and MAPK phosphorylation cooperate to regulate the degradation of active GATA-1 EMBO J 25 3264-3274, 2006
DOI:10.1038/sj.emboj.7601228

Baumann M, Mamais A, McBlane F, Xiao H, Boyes J Regulation of V(D)J recombination by nucleosome positioning at recombination signal sequences EMBO J 22 5197-5207, 2003

McBlane F, Boyes J Stimulation of V(D)J recombination by histone acetylation CURR BIOL 10 483-486, 2000

Boyes JM Preparation of Chromatin Templates for Transcription Studies In Transcription Factors: A Practical Approach, 2nd Edition , 1999

Boyes J, Byfield P, Nakatani Y, Ogryzko V Regulation of activity of the transcription factor GATA-1 by acetylation NATURE 396 594-598, 1998

Boyes J, Omichinski J, Clark D, Pikaart M, Felsenfeld G Perturbation of nucleosome structure by the erythroid transcription factor GATA-1. J Mol Biol 279 529-544, 1998
DOI:10.1006/jmbi.1998.1783
View abstract

Bell A, Boyes J, Chung J, Pikaart M, Prioleau MN, Recillas F, Saitoh N, Felsenfeld G The establishment of active chromatin domains. Cold Spring Harb Symp Quant Biol 63 509-514, 1998

Felsenfeld G, Boyes J, Chung J, Clark D, Studitsky V Chromatin structure and gene expression. Proc Natl Acad Sci U S A 93 9384-9388, 1996
View abstract

Boyes J, Felsenfeld G Tissue-specific factors additively increase the probability of the all-or-none formation of a hypersensitive site. EMBO J 15 2496-2507, 1996
View abstract

FELSENFELD G, BOYES J, BRESNICK E, CHUNG J, CLARK D, STUDITSKY V CHROMATIN STRUCTURE AND THE REGULATION OF GLOBIN GENE-EXPRESSION FASEB J 8 A1326-A1326, 1994

Boyes J, Bird A Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J 11 327-333, 1992
View abstract

Boyes J, Bird A DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell 64 1123-1134, 1991
View abstract

Antequera F, Boyes J, Bird A High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines. Cell 62 503-514, 1990
View abstract