Gene Structure and Function

Theme Co-Leads

Professor Jo Morris

Professor Jo Morris

Professor of Molecular Genetics


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Professor Ferenc Mueller

Professor Ferenc Mueller

Professor in Developmental Genetics


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The DNA within the nuclei of our cells carries the information to generate the machinery of the cell, the cell itself, our tissues and then the whole human. While each DNA blueprint, or gene, encodes for a different machine or structure, the genome, the collection of DNA wrapped up inside the nucleus, is much more active than a quiet library of neatly stacked blue-prints.

The way the DNA is structured, wrapped and read is fundamental to how and when the blueprint genes are read. Promoters, enhancers and physical interactions between regions of DNA are important in ways that are only now becoming apparent, directing phases of development, and often perturbed in cancers. The proper copying and repair of DNA to maintain the correct sequence and structure of genomes is critical to the proper function of cells, and repair and replication is frequently disrupted in cancers and targeted by cancer treatments. Within the genome, many processes occur almost simultaneously so that the regulation of possibly chaotic access is tightly controlled. The Genome Structure Function section of the Institute of Cancer and Genomic Sciences  investigates the fundamentals of the active information database that is our genome, in normal and disease states. We aim to use our understanding of these processes to improve human health and prevent, and treat human disease.

Replication forkDNA Replication, Stability and Repair

Our research is defining the normal mechanisms of DNA replication and repair, with the aim of understanding how it is deregulated in cancer cells. We are investigating the impact of specific classes of gene mutations, such as ATM, BRCA1, and MYBL2 on genome integrity. We examine the impact that processes such as transcription and replication have on genome stability. 

We recently discovered new ways the BRCA1 gene functions which could help expand our understanding of the development of ovarian and breast cancers. Results showed BRCA1 changes shape in order to protect vulnerable DNA until the copying machinery can be restarted. In addition, in some patients with a personal or family history of breast and ovarian cancer, the protective role of BRCA1 in DNA-copying is disabled - while its break repair function is still active.

Gene regulation diagram

Gene Structure and Regulation

Our basic research covers cancer cell and stem cell biology, viral oncology (EBV and HPV) and genome biology. We use high throughput methods to determine how genetic abnormalities unravel the complex regulatory networks that underlie cancer. In parallel we are studying the molecular pathways that control the normal development and differentiation of stem cells.

Current research includes a £1.3 million grant from the MRC to test combinations of drugs that target the signalling molecule FLT3 together with the transcription factor RUNX1 in Acute Myeloid Leukaemia.


Spotlight on global analysis of enhancers that control blood cell development

New study uncovers the information encoded in our DNA required for the transcriptional control of blood cell development from embryonic stem cells

This publication from the Bonifer laboratory describes a novel genome-wide screen that identified and functionally characterised distinct subsets of gene regulatory elements that direct the different stages of the development of blood cells from embryonic stem cells (ESC)

Nature Communications 14:267 (2023). Edginton-White B, A Maytum, SG Kellaway, DK Goode, P Keane,. . . C Bonifer. A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification.

doi: 10.1038/s41467-023-35910-9

This study of the genome investigated the functions of all of the regulatory elements within our DNA that are required to express our genes in the right cells, at the right levels, and at the right time. These regulatory elements are called enhancers and are scattered over large distances within the the 3 billion bases of DNA that make up the geneome. Enhancers also function to integrate multiple highly specific intrinsic and extrinsic signals, whereby most regulatory elements only function in a subset of cells. The Bonifer laboratory developed a whole genome assay able to define the precise time course of activation of enhancers, and their responses to external signals, during the stepwise development of blood cells from ESCs. These analyses identified thousands of differentially active enhancers able to stimulate a promoter across different stages of blood cell development from ESCs. It also showed that blood cell-specific gene expression is controlled by the concerted action of thousands of differentiation stage-specific sets of enhancers and promoters, many of which respond to the cytokine signals promoting cell differentiation towards blood cells. This work highlights the mechanisms of how and where extrinsic signals program a cell type-specific regulatory landscape driving hematopoietic differentiation.

This methodology, which can now be adapted to any ESC-derived cell type, also provides a way to investigate how gene expression is sometimes perturbed by mutations in enhancers or external signals which cause disease. To understand how genes respond to outside signals and are deregulated in disease, we need to know where these enhancer elements are, when they are active and how they function. 

Spotlight on the metabolism of cancer cells

Elife 11 (2022). Vilaplana-Lopera N, V Cuminetti, R Almaghrabi, G Papatzikas, AK Rout, M Jeeves, . . . P Garcia. Crosstalk between AML and stromal cells triggers acetate secretion through the metabolic rewiring of stromal cells. 

Spotlight figure from Garcia Model figure in eLife.pdf cropped

AML cells are known to interact with and obtain support from niche cells through various mechanisms, including the secretion of soluble factors, cytokines or metabolites, resulting in a better support for AML cells at the expense of normal haematopoiesis. Here, the group of Paloma Garcia identified a novel metabolic crosstalk between AML and stromal cells whereby AML cells prompt stromal cells to secrete acetate for their own consumption to feed the tricarboxylic acid cycle (TCA) and lipid biosynthesis.  Acetate in stromal cells is derived from pyruvate via chemical conversion under the influence of reactive oxygen species (ROS) following ROS transfer from AML to stromal cells via gap junctions.  This newly identified metabolic communication between AML and stromal cells highlights two different molecular targets, ACSS2 and gap junctions, that could potentially be exploited for adjuvant therapy. 


Spotlight on protein modification crosstalk during DNA repair

Nature Communications 12: 6313 (2021). M-P Sanchez-Bailon M-P, S-Y Choi, ER Dufficy, K Sharma, GS McNee, E Gunnel, K Chiang, D Sahay, S Maslen, GS Stewart, JM Skehel, I Dreveny and CC Davies. Arginine methylation and ubiquitylation crosstalk controls DNA end-resection and homologous recombination repair.

PRMT1 is an arginine methyltransferase that promotes genome stability and is upregulated in many cancers. Here, the group of Clare Davies identify the deubiquitylating enzyme USP11 as a new PRMT1 substrate, and that methylation of USP11 is required for double strand break repair. They also show that PRMT1 is a substrate for USP11, and that deubiquitylation of PRMT1 promotes PRMT1 activity towards MRE11, a component of the MRN complex, leading to efficient DNA end resection at break points. This study demonstrates the complexity of post-translational modifications that safe-guards our genome against DNA damage, but also suggests that hyper-activation could lead to chemo-resistance in cancer cells following chemo-therapy.


Spotlight on Cancer Genomics

Nature Genetics 51:151-162 (2019). Assi SA, MR Imperato, DJL Coleman, A Pickin, S Potluri, A Ptasinska, . . . PN CockerillC Bonifer. Subtype-specific regulatory network rewiring in acute myeloid leukemia. 

Gene structure and regulation diagram as detailed below

A study by Constanze Bonifer and Peter Cockerill has revealed the roles that different types of gene mutations play in causing acute myeloid leukaemia. Epigenetic profiling of regulatory elements revealed that mutation-specific subsets of AML have distinct patterns of gene expression. Each subset was controlled by distinct gene regulatory networks linked to mutations in transcription factors and signalling molecules This research brings us one step closer to being able to provide tailored and targeted treatment specific to individual patients, increasing their chances of survival.


Spotlight on BRCA1 and DNA Replication

Nature  571: 521-527 (2019). Daza-Martin M, Starowicz K, Jamshad M, Tye S, Ronson GE, MacKay HL, Chauhan AS, Walker AK, Stone HR, Beesley JFJ, Coles JL, Garvin AJ, Stewart GS, McCorvie TJ, Zhang X, Densham RM, JR Morris. Isomerization of BRCA1-BARD1 promotes replication fork protection.  

Diagram of BRCA as described below

BRCA1 is a gene required for genome stability and is a frequent target of mutations in breast cancer. Here the group of Jo Morris shows that the functional activation of the BRCA1 protein involves a conformational change in its structure.

BRCA1 phosphorylation by CDK1/2 followed by isomerization by PIN1 enhances the ability of BARD1 to associate with RAD51 (brown) and thereby promotes replication fork protection.

Selected Highlights from DNA Replication, Stability and Repair

J Clin Invest 132 (2022). Abu-Libdeh B, SS Jhujh, S Dhar, JA Sommers, A Datta, GM Longo, . . . GS Stewart. RECON syndrome is a genome instability disorder caused by mutations in the DNA helicase RECQL1.

Mol Cell 82:1924-1939 e1910 (2022). Bayley R, V Borel, RJ Moss, E Sweatman, P Ruis, A Ormrod, . . . MR Higgs. H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ.

J Cell Sci 135 (2022). Faulkner EL, JA Pike, RM Densham, E Garlick, SG Thomas, RK Neely and JR Morris. Imaging nanoscale nuclear structures with expansion microscopy.

J Biol Chem 298:102234 (2022). Tarcan Z, D Poovathumkadavil, A Skagia and A Gambus. The p97 segregase cofactor Ubxn7 facilitates replisome disassembly during S-phase.

Viruses 13 (2021). Abualfaraj T, NC Hagkarim, R Hollingworth, L Grange, S Jhujh, GS Stewart and RJ Grand. The Promotion of Genomic Instability in Human Fibroblasts by Adenovirus 12 Early Region 1B 55K Protein in the Absence of Viral Infection.

EMBO Rep 22:e51120 (2021). Blakemore D, N Vilaplana-Lopera, R Almaghrabi, E Gonzalez, M Moya, C Ward, . . . P Garcia. MYBL2 and ATM suppress replication stress in pluripotent stem cells.

Nat Comm 12: 6313 (2021). M-P Sanchez-Bailon M-P, S-Y Choi, ER Dufficy, K Sharma, GS McNee, … CC Davies. Arginine methylation and ubiquitylation crosstalk controls DNA end-resection and homologous recombination repair.

J Clinical Investigation 130:4069-4080 (2020). Zarrizi R, MR Higgs, K Vossgrone, M Rossing, B Bertelsen, M Bose, . . . GS Stewart, FC Nielsen, CS Sorensen. Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability.

J Gen Virol 101:873-883 (2020). Hollingworth R, GS Stewart and RJ Grand. Productive herpesvirus lytic replication in primary effusion lymphoma cells requires S-phase entry.

Mol Psychiatry 10.1038 (2020). Kummeling J, DE Stremmelaar, N Raun, MRF Reijnders, MH Willemsen, M Ruiterkamp-Versteeg, . . . MR Higgs, JM Kramer, T Kleefstra. Characterization of SETD1A haploinsufficiency in humans and Drosophila defines a novel neurodevelopmental syndrome.

Nat Commun 11:4287 (2020). van Schie JJM, A Faramarz, JA Balk, GS Stewart, E Cantelli, AB Oostra, . . . J de Lange. Warsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to support sister chromatid cohesion.

J Clin Invest 130:4069-4080 (2020). Zarrizi R, MR Higgs, K Vossgrone, M Rossing, B Bertelsen, M Bose, . . . CS Sorensen. Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability.

Nat Commun 11:3951 (2020). Zhang J, MA Bellani, RC James, D Pokharel, Y Zhang, JJ Reynolds, . . . GS Stewart, MM Seidman. DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain.

Nature 571:521-527 (2019). Daza-Martin M, K Starowicz, M Jamshad, S Tye, GE Ronson, HL MacKay, . . . JR MorrisIsomerization of BRCA1-BARD1 promotes replication fork protection.

Genes Dev 33:333-347 (2019). Garvin AJ, AK Walker, RM Densham, AS Chauhan, HR Stone, HL Mackay, . . . JR Morris. The deSUMOylase SENP2 coordinates homologous recombination and nonhomologous end joining by independent mechanisms.

Cancer Res 78:5767-5779 (2018). Bayley R, D Blakemore, L Cancian, S Dumon, G Volpe, C Ward, . . . MR Higgs, GS Stewart, E Petermann, P GarciaMYBL2 supports DNA double strand break repair in haematopoietic stem cells.

Cell Rep 25:2061-2069 e2064 (2018). Bowry A, AL Piberger, P Rojas, M Saponaro and E PetermannBET Inhibition Induces HEXIM1- and RAD51-Dependent Conflicts between Transcription and Replication.

Mol Cell 71:25-41 e26 (2018). Higgs MR, K Sato, JJ Reynolds, S Begum, R Bayley, A Goula, . . . GS Stewart. Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2.

Nat Commun 9:746 (2018). Ronson GE, AL Piberger, MR Higgs, AL Olsen, GS Stewart, PJ McHugh, . . . E Petermann, ND Lakin. PARP1 and PARP2 stabilise replication forks at base excision repair intermediates through Fbh1-dependent Rad51 regulation.

Nat Commun 9:229 (2018). Uckelmann M, RM Densham, R Baas, HHK Winterwerp, A Fish, TK Sixma and JR MorrisUSP48 restrains resection by site-specific cleavage of the BRCA1 ubiquitin mark from H2A.

Nature 559:285-289 (2018). Zimmermann M, O Murina, MAM Reijns, A Agathanggelou, R Challis, Z Tarnauskaite, . . . T Stankovic, AP Jackson, D Durocher. CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions.


More Publications

Mol Cell 65:900-916 e907 (2017). Clarke TL, MP Sanchez-Bailon, K Chiang, JJ Reynolds, J Herrero-Ruiz, TM Bandeiras, . . . CC DaviesPRMT5-Dependent Methylation of the TIP60 Coactivator RUVBL1 Is a Key Regulator of Homologous Recombination.

J Virol 91 (2017). Campos-Leon K, K Wijendra, A Siddiqa, I Pentland, KM Feeney, A Knapman, . . . JL ParishAssociation of Human Papillomavirus 16 E2 with Rad50-Interacting Protein 1 Enhances Viral DNA Replication.

Cell Rep 21:3498-3513 (2017). Chiang K, AE Zielinska, AM Shaaban, MP Sanchez-Bailon, J Jarrold, TL Clarke, . . . CC DaviesPRMT5 Is a Critical Regulator of Breast Cancer Stem Cell Function via Histone Methylation and FOXP1 Expression.

Nat Genet 49:537-549 (2017). Reynolds JJ, LS Bicknell, P Carroll, MR Higgs, R Shaheen, JE Murray, . . . GS StewartMutations in DONSON disrupt replication fork stability and cause microcephalic dwarfism.

Nat Cell Biol 19:468-479 (2017). Sonneville R, SP Moreno, A Knebel, C Johnson, CJ Hastie, A Gartner, . . . K Labib. CUL-2LRR-1 and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis.

Cell 168:843-855 e813 (2017). Williamson L, M Saponaro, S Boeing, P East, R Mitter, T Kantidakis, . . . JQ Svejstrup. UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene.

Nat Commun 7:13087 (2016). Kotsantis P, LM Silva, S Irmscher, RM Jones, L Folkes, N Gromak and E PetermannIncreased global transcription activity as a mechanism of replication stress in cancer.

PLoS Genet 12:e1005945 (2016). Byrd PJ, GS Stewart, A Smith, C Eaton, AJ Taylor, C Guy, . . . AM TaylorA Hypomorphic PALB2 Allele Gives Rise to an Unusual Form of FA-N Associated with Lymphoid Tumour Development.

Nat Struct Mol Biol 23:647-655 (2016). Densham RM, AJ Garvin, HR Stone, J Strachan, RA Baldock, M Daza-Martin, . . . JR MorrisHuman BRCA1-BARD1 ubiquitin ligase activity counteracts chromatin barriers to DNA resection.

Nat Genet 48:36-43 (2016). Harley ME, O Murina, A Leitch, MR Higgs, LS Bicknell, G Yigit, . . . AP Jackson. TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism.

Genes Dev 30:408-420 (2016). Kantidakis T, M Saponaro, R Mitter, S Horswell, A Kranz, S Boeing, . . . JQ Svejstrup. Mutation of cancer driver MLL2 results in transcription stress and genome instability.

Blood 127:582-595 (2016). Kwok M, N Davies, A Agathanggelou, E Smith, C Oldreive, E Petermann, . . . T Stankovic. ATR inhibition induces synthetic lethality and overcomes chemoresistance in TP53- or ATM-defective chronic lymphocytic leukemia cells.

Dev Cell 38:358-370 (2016). Monteiro R, P Pinheiro, N Joseph, T Peterkin, J Koth, E Repapi, . . . R Patient. Transforming Growth Factor beta Drives Hemogenic Endothelium Programming and the Transition to Hematopoietic Stem Cells.

Mol Cell 59:462-477 (2015). Higgs MR, JJ Reynolds, A Winczura, AN Blackford, V Borel, ES Miller, . . . GS StewartBOD1L Is Required to Suppress Deleterious Resection of Stressed Replication Forks.

Science 346:477-481 (2014). Moreno SP, R Bailey, N Campion, S Herron and A GambusPolyubiquitylation drives replisome disassembly at the termination of DNA replication.

Cell 157:1037-1049 (2014). Saponaro M, T Kantidakis, R Mitter, GP Kelly, M Heron, H Williams, . . . JQ Svejstrup. RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress.

EMBO J 32:1556-1567 (2013). Davies CC, A Chakraborty, ME Diefenbacher, M Skehel and A Behrens. Arginine methylation of the c-Jun coactivator RACO-1 is required for c-Jun/AP-1 activation.

EMBO Rep 14:975-983 (2013). Garvin AJ, RM Densham, SA Blair-Reid, KM Pratt, HR Stone, D Weekes, . . . JR Morris. The deSUMOylase SENP7 promotes chromatin relaxation for homologous recombination DNA repair. 


Selected Highlights from Gene Structure and Regulation

Blood 2022019138 (2023). Clarke ML, RB Lemma, DS Walton, G Volpe, B Noyvert, OS Gabrielsen and J Frampton. MYB insufficiency disrupts proteostasis in hematopoietic stem cells leading to age-related neoplasia. doi: 10.1182/blood.2022019138

Nature Commun 14:267 (2023). Edginton-White B, A Maytum, SG Kellaway, DK Goode, P Keane,. . . C BoniferA genome-wide relay of signalling-responsive enhancers drives hematopoietic specification.

Dev Cell 58:155-170 e158 (2023). Hadzhiev Y, L Wheatley, L Cooper, F Ansaloni, C Whalley, Z Chen, . . . A Beggs, F Muller. The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation.

Blood doi: 10.1182/blood.2021015036 (2022). Tirtakusuma R, K Szoltysek, P Milne, V Grinev, A Ptasinska, PS Chin, . . . C Bonifer, O Heidenreich, S Bomken. Epigenetic regulator genes direct lineage switching in MLL/AF4 leukaemia.

Elife 11 (2022). Vilaplana-Lopera N, V Cuminetti, R Almaghrabi, G Papatzikas, AK Rout, M Jeeves, . . . P Garcia. Crosstalk between AML and stromal cells triggers acetate secretion through the metabolic rewiring of stromal cells.

Nat Genet 54:1037-1050 (2022). Baranasic D, M Hortenhuber, PJ Balwierz, T Zehnder, AK Mukarram, C Nepal, . . . F Muller. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.

Cancer Lett 501:172-186 (2021). Gleneadie HJ, AH Baker, N Batis, J Bryant, Y Jiang, SJH Clokie, H Mehanna, P Garcia, DMA Gendoo. . . JL Parish, FL Khanim, M Wiench. The anti-tumour activity of DNA methylation inhibitor 5-aza-2'-deoxycytidine is enhanced by the common analgesic paracetamol through induction of oxidative stress.

Front Immunol 12:642807 (2021). Bevington SL, R Fiancette, DW Gajdasik, P Keane, JK Soley, CM Willis, . . . PN Cockerill. Stable Epigenetic Programming of Effector and Central Memory CD4 T Cells Occurs Within 7 Days of Antigen Exposure In Vivo.

Life Science Alliance 4 (2021). Kellaway SG, P Keane, B Edginton-White, K Regha, E Kennett and C Bonifer. Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories.

Cell Reports 34:108759 (2021). Wang J, P Rojas, J Mao, M Muste Sadurni, O Garnier, S Xiao, . . . MR Higgs, P Garcia,  M Saponaro. Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M.

Frontiers in Immunology 12:642807 (2021). Bevington SL, R Fiancette, DW Gajdasik, P Keane, JK Soley, CM Willis, . . . PN Cockerill. Stable Epigenetic Programming of Effector and Central Memory CD4 T Cells Occurs Within 7 Days of Antigen Exposure In Vivo.

EMBO Reports 22:e51120 (2021). Blakemore D, N Vilaplana-Lopera, R Almaghrabi, E Gonzalez, M Moya, C Ward, . .A Gambus, E Petermann, GS Stewart, P Garcia. MYBL2 and ATM suppress replication stress in pluripotent stem cells.

Scientific Reports 11:3009 (2021). Halsall JA, S Andrews, F Krueger, CE Rutledge, G Ficz, W Reik and BM Turner. Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle.

Cell Reports 35:109010 (2021). Potluri S, SA Assi, PS Chin, DJL Coleman, A Pickin, S Moriya, . . . PN Cockerill, C Bonifer. Isoform-specific and signaling-dependent propagation of acute myeloid leukemia by Wilms tumor 1.

J General Virology 101:873-883 (2020). Hollingworth R, GS Stewart and RJ Grand. Productive herpesvirus lytic replication in primary effusion lymphoma cells requires S-phase entry.

EMBO J:e105220 (2020). Bevington SL, P Keane, JK Soley, S Tauch, DW Gajdasik, R Fiancette, . . . PN CockerillIL-2/IL-7-inducible factors pioneer the path to T cell differentiation in advance of lineage-defining factors. doi: 10.15252/embj.2020105220

Cell Rep 31:107748 (2020). Bevington SL, STH Ng, GJ Britton, P Keane, DC Wraith and PN CockerillChromatin Priming Renders T Cell Tolerance-Associated Genes Sensitive to Activation below the Signaling Threshold for Immune Response Genes.

Commun Biol 3:71 (2020). Dobrzycki T, CB Mahony, M Krecsmarik, C Koyunlar, R Rispoli, J Peulen-Zink, . . . R MonteiroDeletion of a conserved Gata2 enhancer impairs haemogenic endothelium programming and adult Zebrafish haematopoiesis.

Haematologica  (2020). Kellaway SG, P Keane, E Kennett and C BoniferRUNX1-EVI1 disrupts lineage determination and the cell cycle by interfering with RUNX1 and EVI1 driven gene regulatory networks. DOI: 10.3324/haematol.2019.241885

Life Sci Alliance 3 (2020). Kwon SY, K Massey, MA Watson, T Hussain, G Volpe, CD Buckley, . . . P BadenhorstOxidised metabolites of the omega-6 fatty acid linoleic acid activate dFOXO.

Cell Rep 31:107691 (2020). Nafria M, P Keane, ES Ng, EG Stanley, AG Elefanty and C BoniferExpression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells.

Nucleic Acids Res 48:8374-8392 (2020). Wragg JW, L Roos, D Vucenovic, N Cvetesic, B Lenhard and F MullerEmbryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation.

J Virol 10.1128  (2020). Molloy DP and RJ Grand. Structural determinants within the adenovirus early region 1A protein spacer region necessary for tumourigenesis.

Nat Genet 51:151-162 (2019). Assi SA, MR Imperato, DJL Coleman, A Pickin, S Potluri, A Ptasinska, . . . PN Cockerill, C BoniferSubtype-specific regulatory network rewiring in acute myeloid leukemia.

Nat Commun 10:3577 (2019). Bonkhofer F, R Rispoli, P Pinheiro, M Krecsmarik, J Schneider-Swales, IHC Tsang, . . . R Monteiro, T Peterkin, R Patient. Blood stem cell-forming haemogenic endothelium in zebrafish derives from arterial endothelium.

Nat Commun 10:691 (2019). Hadzhiev Y, HK Qureshi, L Wheatley, L Cooper, A Jasiulewicz, H Van Nguyen, . . . F Muller. A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation.

Cell Rep 28:3022-3031 e3027 (2019). Ptasinska A, A Pickin, SA Assi, PS Chin, L Ames, R Avellino, . . . C Bonifer. RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPalpha- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction.

Cancer Cell 34:674-689 e678 (2018). de Boer B, J Prick, MG Pruis, P Keane, MR Imperato, J Jaques, . . . C Bonifer, JJ Schuringa. Prospective Isolation and Characterization of Genetically and Functionally Distinct AML Subclones.

Cancer Cell 34:626-642 e628 (2018). Martinez-Soria N, L McKenzie, J Draper, A Ptasinska, H Issa, S Potluri, . . . C Bonifer, O Heidenreich. The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation.

Cell Rep 24:1496-1511 e1498 (2018). Ward C, G Volpe, P Cauchy, A Ptasinska, R Almaghrabi, D Blakemore, . . . P GarciaFine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic Reprogramming.

More Publications

J Immunol 199:2652-2667 (2017). Brignall R, P Cauchy, SL Bevington, B Gorman, AO Pisco, J Bagnall, . . . P Cockerill, P Paszek. Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells.

J Virol 91 (2017). Harris L, L McFarlane-Majeed, K Campos-Leon, S Roberts and JL ParishThe Cellular DNA Helicase ChlR1 Regulates Chromatin and Nuclear Matrix Attachment of the Human Papillomavirus 16 E2 Protein and High-Copy-Number Viral Genome Establishment.

Cell Rep 19:1654-1668 (2017). Loke J, SA Assi, MR Imperato, A Ptasinska, P Cauchy, Y Grabovska, . . . C BoniferRUNX1-ETO and RUNX1-EVI1 Differentially Reprogram the Chromatin Landscape in t(8;21) and t(3;21) AML.

Nucleic Acids Res 45:9874-9888 (2017). Stanulovic VS, P Cauchy, SA Assi and M HoogenkampLMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage.

Sci Rep 7:11148 (2017). Volpe G, DS Walton, DE Grainger, C Ward, P Cauchy, D Blakemore, . . . J FramptonPrognostic significance of high GFI1 expression in AML of normal karyotype and its association with a FLT3-ITD signature.

EMBO J 35:515-535 (2016). Bevington SL, P Cauchy, J Piper, E Bertrand, N Lalli, RC Jarvis, . . . PN CockerillInducible chromatin priming is associated with the establishment of immunological memory in T cells.

PLoS Genet 12:e1005969 (2016). Kwon SY, V Grisan, B Jang, J Herbert and P Badenhorst. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

Epigenetics Chromatin 9:52 (2016). Wiersma M, M Bussiere, JA Halsall, N Turan, R Slany, BM Turner and KP Nightingale. Protein kinase Msk1 physically and functionally interacts with the KMT2A/MLL1 methyltransferase complex and contributes to the regulation of multiple target genes.

Leukemia 10:1038 (2016). Clarke M, G Volpe, L Sheriff, D Walton, C Ward, W Wei, . . . J FramptonTranscriptional regulation of SPROUTY2 by MYB influences myeloid cell proliferation and stem cell properties by enhancing responsiveness to IL-3.

Dev Cell 36:572-587 (2016). Goode DK, N Obier, MS Vijayabaskar, ALM Lie, AJ Lilly, R Hannah, . . . C BoniferDynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation.

Dev Cell 38:358-370 (2016). Monteiro R, P Pinheiro, N Joseph, T Peterkin, J Koth, E Repapi, . . . R Patient. Transforming Growth Factor beta Drives Hemogenic Endothelium Programming and the Transition to Hematopoietic Stem Cells.

Cell Rep 12:821-836 (2015). Cauchy P, SR James, J Zacarias-Cabeza, A Ptasinska, MR Imperato, SA Assi, . . . PN CockerillChronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature.

J Virol 89:4770-4785 (2015). Paris C, I Pentland, I Groves, DC Roberts, SJ Powis, N Coleman, . . . JL ParishCCCTC-Binding Factor Recruitment to the Early Region of the Human Papillomavirus 18 Genome Regulates Viral Oncogene Expression.

Nat Commun 6:7203 (2015). Regha K, SA Assi, O Tsoulaki, J Gilmour, G Lacaud and C Bonifer. Developmental-stage-dependent transcriptional response to leukaemic oncogene expression.

Nature 507:381-385 (2014). Haberle V, N Li, Y Hadzhiev, C Plessy, C Previti, C Nepal, . . . F Muller, B Lenhard. Two independent transcription initiation codes overlap on vertebrate core promoters.

Cell reports 8:1974-1988 (2014). Ptasinska A, SA Assi, N Martinez-Soria, MR Imperato, J Piper, P Cauchy, . . . C BoniferIdentification of a Dynamic Core Transcriptional Network in t(8;21) AML that Regulates Differentiation Block and Self-Renewal.

Development 141:715-724 (2014). Roberts JA, I Miguel-Escalada, KJ Slovik, KT Walsh, Y Hadzhiev, R Sanges, . . . F Muller. Targeted transgene integration overcomes variability of position effects in zebrafish.

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