Publications In 'Birmingham Centre for Genome Biology' Birmingham Centre for Genome BiologySeminarsOur CentreResearchFunctional Genome Biology - MResNews 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. Colbourne: Nat Commun 12:4306 (2021). Chaturvedi A, et al. Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia. Colbourne: PLoS Genet 16:e1008518 (2020). Rago A, et al. Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis. Colbourne: Chromosoma 125:769-787 (2016). Gomez R, et al. Male meiosis in Crustacea: synapsis, recombination, epigenetics and fertility in Daphnia magna. Colbourne: Proc Natl Acad Sci U S A 110:16532-16537 (2013). Weston DP, et al. Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean, Hyalella azteca. 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.