Publications In 'Birmingham Centre for Genome Biology' Birmingham Centre for Genome BiologySeminarsOur CentreResearchNews and eventsOur teamPublicationsRecent grant funding from BCGB group leadersManagement of the CentreContact us Recent major publications from BCGB group leaders (for a full list please refer to each group’s home page) Last updated October 2020 Akerman: Nat Commun 11:4826 (2020). Akerman I, et al. A predictable conserved DNA base composition signature defines human core DNA replication origins. Akerman: Cell Metab 25:400-411 (2017). Akerman I, et al. Human Pancreatic beta Cell lncRNAs Control Cell-Specific Regulatory Networks. Akerman: Genes Dev 30:502-507 (2016). Arnes L, et al. betalinc1 encodes a long noncoding RNA that regulates islet beta-cell formation and function. Badenhorst: Life Sci Alliance 3 (2020). Kwon SY, et al. Oxidised metabolites of the omega-6 fatty acid linoleic acid activate dFOXO. Badenhorst: PLoS Genet 12:e1005969 (2016). Kwon SY, et al. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators. Bicknell: Oncogene 34:5821-5831 (2015). Noy PJ, et al. Blocking CLEC14A-MMRN2 binding inhibits sprouting angiogenesis and tumour growth. Bonifer: Cell Rep 31:107691 (2020). Nafria M, et al. Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells. Bonifer: Cancer Cell 34:674-689 e678 (2018). de Boer B, et al. Prospective Isolation and Characterization of Genetically and Functionally Distinct AML Subclones. Bonifer: Cancer Cell 34:626-642 e628 (2018). Martinez-Soria N, et al. The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation. Bonifer: Developmental Cell 36:572-587 (2016). Goode et al. Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation. Brogna: ELife 8: e41444 (2019). Singh AK, et al. The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci. Brogna: Elife 5 (2016). Choudhury SR, et al. Exon junction complex proteins bind nascent transcripts independently of pre-mRNA splicing in Drosophila melanogaster. Brogna: Mol Cell Biol 31:639-651 (2011). Guo J, et al. Poly(A) signals located near the 5' end of genes are silenced by a general mechanism that prevents premature 3'-end processing. Brown: Genome Res 25:1692-1702 (2015). Stoiber MH, et al. Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila. Brown: Nat Biotechnol 32:341-346 (2014). Boley N, et al. Genome-guided transcript assembly by integrative analysis of RNA sequence data. Brown: Nature 512:393-399 (2014). Brown JB, et al. Diversity and dynamics of the Drosophila transcriptome. Busby: Proc Natl Acad Sci U S A 112:5503-5508 (2015). Alsharif G, et al. Host attachment and fluid shear are integrated into a mechanical signal regulating virulence in Escherichia coli O157:H7. Busby: Nucleic Acids Res 42:9209-9216 (2014). Zhou Y, et al. Spacing requirements for Class I transcription activation in bacteria are set by promoter elements. Cockerill: EMBO J:e105220 (2020). Bevington SL, et al. IL-2/IL-7-inducible factors pioneer the path to T cell differentiation in advance of lineage-defining factors. Cockerill: Cell Rep 31:107748 (2020). Bevington SL, et al. Chromatin Priming Renders T Cell Tolerance-Associated Genes Sensitive to Activation below the Signaling Threshold for Immune Response Genes. Cockerill and Bonifer: Nat Genet 51:151-162 (2019). Assi SA, et al. Subtype-specific regulatory network rewiring in acute myeloid leukemia. Cockerill: EMBO J 35:515-535 (2016). Bevington SL, et al. Inducible chromatin priming is associated with the establishment of immunological memory in T cells. Cockerill and Bonifer: Cell Rep 12:821-836 (2015). Cauchy P, et al. Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature. Davies: Cell Rep 21:3498-3513 (2017). Chiang K, et al. PRMT5 Is a Critical Regulator of Breast Cancer Stem Cell Function via Histone Methylation and FOXP1 Expression. Davies :Mol Cell 65:900-916 e907 (2017). Clarke TL, et al. PRMT5-Dependent Methylation of the TIP60 Coactivator RUVBL1 Is a Key Regulator of Homologous Recombination. Fan: Dev Cell 30:48-60 (2014). Fan Y, Bergmann A. Multiple mechanisms modulate distinct cellular susceptibilities toward apoptosis in the developing Drosophila eye. Fan: PLoS Genet 10:e1004131 (2014). Fan Y, et al. Genetic models of apoptosis-induced proliferation decipher activation of JNK and identify a requirement of EGFR signaling for tissue regenerative responses in Drosophila. Gambus: Life Science Alliance e201900390 (2019) Priego Moreno S, et al Mitotic replisome disassembly depends on TRAIP ubiquitin ligase activity. Gambus: Nature Cell Biology 18:468-479(2018). Sonneville R, et al. CUL-2LRR-1 and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis. Gambus: Nat Cell Biol 19:468-479 (2017). Sonneville R, et al. CUL-2LRR-1 and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis. Garcia: Cancer Res (2018). Bayley R, et al. MYBL2 supports DNA double strand break repair in haematopoietic stem cells. Garcia: Cell Rep 24:1496-1511 e1498 (2018). Ward C, et al. Fine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic Reprogramming. Garcia and Frampton: Leukemia 31:957-966 (2017). Clarke M, et al. Transcriptional regulation of SPROUTY2 by MYB influences myeloid cell proliferation and stem cell properties by enhancing responsiveness to IL-3. Garcia and Frampton: Sci Rep 7:11148 (2017). Volpe G, et al. Prognostic significance of high GFI1 expression in AML of normal karyotype and its association with a FLT3-ITD signature. Grainger: Genes Dev 28:214-219 (2014). Singh SS, et al. Widespread suppression of intragenic transcription initiation by H-NS. Grzechnik: Nature Communications 9: 1783 (2018). Nuclear fate of yeast snoRNA is determined by co-transcriptional Rnt1 cleavage. Grzechnik: Genes Devel. 29: 849-61 (2015). Pcf11 orchestrates transcription termination pathways in yeast. Hotchin: J Cell Sci 125:3202-3209 (2012). Ryan KR, et al. Plakoglobin-dependent regulation of keratinocyte apoptosis by Rnd3. Monteiro: Commun Biol 3:71 (2020). Dobrzycki T, et al. Deletion of a conserved Gata2 enhancer impairs haemogenic endothelium programming and adult Zebrafish haematopoiesis. Monteiro: Dev Cell 38:358-370 (2016). Monteiro R, et al. Transforming Growth Factor beta Drives Hemogenic Endothelium Programming and the Transition to Hematopoietic Stem Cells. Morris: Nature 571:521-527 (2019). Daza-Martin M, et al. Isomerization of BRCA1-BARD1 promotes replication fork protection. Morris: Genes Dev 33:333-347 (2019). Garvin et al. The deSUMOylase SENP2 coordinates homologous recombination and nonhomologous end joining by independent mechanisms. Morris: Nat Struct Mol Biol 23:647-655 (2016). Densham RM, et al. Human BRCA1-BARD1 ubiquitin ligase activity counteracts chromatin barriers to DNA resection. Mueller: Nat Commun 11:168 (2020). Nepal C, et al. Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing. Mueller: Nucleic Acids Res 48:8374-8392 (2020). Wragg JW, et al. Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation. Mueller: Nature Communications 10:691(2019). Hadzhiev Y, et al. A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation. Mueller: Nat Neurosci 21:1482-1492 (2018). Dong X, et al. Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease. Mueller: Nature 507:381-385 (2014). Haberle V, et al. Two independent transcription initiation codes overlap on vertebrate core promoters. Parish: PLoS Biology 16: e2005752 (2018).Pentland I, et al. Disruption of CTCF-YY1-dependent looping of the human papillomavirus genome activates differentiation-induced viral oncogene transcription. Parish :J Virol 91: e02305-16 (2017). Campos-Leon K, et al. Association of Human Papillomavirus 16 E2 with Rad50-Interacting Protein 1 Enhances Viral DNA Replication. Parish and Roberts: J Virol 91(1). pii: e01853-16 (2017). Harris L, et al. The Cellular DNA Helicase ChlR1 Regulates Chromatin and Nuclear Matrix Attachment of the Human Papillomavirus 16 E2 Protein and High-Copy-Number Viral Genome Establishment. Parish and Roberts: J Virol 89:4770-4785 (2015). Paris C, et al. CCCTC-Binding Factor Recruitment to the Early Region of the Human Papillomavirus 18 Genome Regulates Viral Oncogene Expression. Petermann: Cell Reports 25:2061-2069(2018). Bowry A, et al. BET Inhibition Induces HEXIM1- and RAD51-Dependent Conflicts between Transcription and Replication Petermann: Nat Commun 9:746 (2018). Ronson GE, et al. PARP1 and PARP2 stabilise replication forks at base excision repair intermediates through Fbh1-dependent Rad51 regulation. Petermann: Nat Commun 7:13087 (2016). Kotsantis P, et al. Increased global transcription activity as a mechanism of replication stress in cancer. Saponaro: Cell 168:843-855 e813 (2017). Williamson L, et al. UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene. Saponaro: Genes Dev 30:408-420 (2016). Kantidakis T, et al. Mutation of cancer driver MLL2 results in transcription stress and genome instability. Saponaro: Cell 157:1037-1049 (2014). Saponaro M, et al. RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Soller: Nature 540:301-304 (2016). Haussmann IU, et al. m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination. Soller: Mol Cell Biol 35:3104-3115 (2015). Zaharieva E, et al. Concentration and Localization of Coexpressed ELAV/Hu Proteins Control Specificity of mRNA Processing. Stankovic: Nature 559:285-289 (2018). Zimmermann M, et al. CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions. Stankovic and Taylor: PLoS Genet 12:e1005945 (2016). Byrd PJ, et al. A Hypomorphic PALB2 Allele Gives Rise to an Unusual Form of FA-N Associated with Lymphoid Tumour Development. Stankovic and Taylor: Blood 127:582-595 (2016). Kwok M, et al. ATR inhibition induces synthetic lethality and overcomes chemoresistance in TP53- or ATM-defective chronic lymphocytic leukemia cells. Stewart: Nat Commun 11:3951 (2020). Zhang J, et al. DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain. Stewart and Higgs: J Clin Invest 130:4069-4080 (2020). Zarrizi R, et al. Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability. Stewart and Higgs: Mol Cell 71:25-41 e26 (2018). Higgs MR, et al. Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2. Stewart and Higgs: Nat Genet 49:537-549 (2017). Reynolds JJ et al. DONSON encodes a novel replication fork protection factor mutated in microcephalic dwarfism. Stewart and Higgs: Nat Genet 48:36-43 (2016). Harley ME, et al. TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism. Turner: Epigenetics Chromatin 8:29 (2015). Halsall JA, et al. Cells adapt to the epigenomic disruption caused by histone deacetylase inhibitors through a coordinated, chromatin-mediated transcriptional response.