Publications

Recent major publications from BCGB group leaders (for a full list please refer to each group’s home page) 

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.

Bicknell: Oncogene 31:293-305 (2012). Mura M, et al. Identification and angiogenic role of the novel tumor endothelial marker CLEC14A.

Bonifer: Developmental Cell. 36:572-587 (2016). Goode et al. Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation.

Bonifer: Nat Commun 6:7203 (2015). Regha K, et al. Developmental-stage-dependent transcriptional response to leukaemic oncogene expression.

Bonifer: Cell Reports 8:1974-1988 (2014). Ptasinska A, et al. Identification of a Dynamic Core Transcriptional Network in t(8;21) AML that Regulates Differentiation Block and Self-Renewal.

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.

Brogna: EMBO J 29:1537-1551 (2010). Wen J, Brogna S Splicing-dependent NMD does not require the EJC in Schizosaccharomyces pombe.

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 and Bonifer: 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.

Cockerill: J Immunol 189:4459-4469 (2012). Baxter EW, et al. The inducible tissue-specific expression of the human IL-3/GM-CSF locus is controlled by a complex array of developmentally regulated enhancers.

Colborne: 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 :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.

Davies: EMBO J 32:1556-1567 (2013). Davies CC, et al. Arginine methylation of the c-Jun coactivator RACO-1 is required for c-Jun/AP-1 activation.

Davies: Nat Cell Biol 12:963-972 (2010). Davies CC, et al. Identification of a co-activator that links growth factor signalling to c-Jun/AP-1 activation.

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: 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.

Gambus: Science 346:477-481 (2014). Moreno SP, et al. Polyubiquitylation drives replisome disassembly at the termination of DNA replication.

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: Leukemia 27:661-670 (2013). Clarke M, et al. MYBL2 haploinsufficiency increases susceptibility to age-related haematopoietic neoplasia.

Garcia and Frampton: Leukemia 27:1487-1496 (2013). Volpe G, et al. C/EBPalpha and MYB regulate FLT3 expression in AML.

Grainger: Genes Dev 28:214-219 (2014). Singh SS, et al. Widespread suppression of intragenic transcription initiation by H-NS.

Grainger: PLoS Genet 9:e1003152 (2013). Chintakayala K, et al. E. coli Fis protein insulates the cbpA gene from uncontrolled transcription.

Grainger: PLoS Genet 9:e1003589 (2013). Singh SS, Grainger DC H-NS can facilitate specific DNA-binding by RNA polymerase in AT-rich gene regulatory regions.

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.

Jayaraman: Oncogene 33:5592-5600 (2014). Kershaw RM, et al. PRH/HHex inhibits the migration of breast and prostate epithelial cells through direct transcriptional regulation of Endoglin.

Jayaraman: Nucleic Acids Res 40:9008-9020 (2012). Noy P, et al. Protein kinase CK2 inactivates PRH/Hhex using multiple mechanisms to de-repress VEGF-signalling genes and promote cell survival.

Jayaraman: Mol Cell Biol 30:2120-2134 (2010). Noy P, et al. PRH/Hhex controls cell survival through coordinate transcriptional regulation of vascular endothelial growth factor signaling.

Kanhere: Nat Commun 3:1268 (2012). Kanhere A, et al. T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements.

Kanhere: Mol Cell 38:675-688 (2010). Kanhere A, et al. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2.

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.

Morris: EMBO J 31:3918-3934 (2012). Butler LR, et al. The proteasomal de-ubiquitinating enzyme POH1 promotes the double-strand DNA break response.

Morris: Cancer Cell 20:797-809 (2011). Drost R, et al. BRCA1 RING function is essential for tumor suppression but dispensable for therapy resistance.

Müller: Nature 507:381-385 (2014). Haberle V, et al. Two independent transcription initiation codes overlap on vertebrate core promoters.

Müller: Development 141:715-724 (2014). Roberts JA, et al. Targeted transgene integration overcomes variability of position effects in zebrafish.

Müller: Genome Res 23:1938-1950 (2013). Nepal C, et al. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.

Nightingale: Epigenetics Chromatin 9:52 (2016). Wiersma M, et al. Protein kinase Msk1 physically and functionally interacts with the KMT2A/MLL1 methyltransferase complex and contributes to the regulation of multiple target genes.

Parish :J Virol 91(5). pii: 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 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: Nat Commun 7:13087 (2016). Kotsantis P, et al. Increased global transcription activity as a mechanism of replication stress in cancer.

Petermann: Oncogene 32:3744-3753 (2013). Jones RM, et al. Increased replication initiation and conflicts with transcription underlie Cyclin E-induced replication stress.

Petermann: Mol Cell 37:492-502 (2010). Petermann E, et al. Hydroxyurea-stalled replication forks become progressively inactivated and require two different RAD51-mediated pathways for restart and repair.

Roberts: J Virol 88:12599-12611 (2014). Prescott EL, et al. Human papillomavirus type 1 E1^E4 protein is a potent inhibitor of the serine-arginine (SR) protein kinase SRPK1 and inhibits phosphorylation of host SR proteins and of the viral transcription and replication regulator E2.

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 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.

Stankovic and Taylor: Blood 116:4578-4587 (2010). Weston VJ, et al. The PARP inhibitor olaparib induces significant killing of ATM-deficient lymphoid tumor cells in vitro and in vivo.

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.

Stewart and Higgs: Mol Cell 59:462-477 (2015). Higgs MR, et al. BOD1L Is Required to Suppress Deleterious Resection of Stressed Replication Forks.

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.

Turner: Nat Genet 43:1169-1170 (2011). Lin H, et al. Relative overexpression of X-linked genes in mouse embryonic stem cells is consistent with Ohno's hypothesis.