CDB Student Publications -

To find out more about the scientific discoveries made by CDB students take a look at the peer reviewed papers listed below....

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WT CDB Student publications (2008 – 2018)

 

58 publications

28 first author publications, including: Nature (1); Nature Cell Biol (1); Nature Comm. (1); Molecular Cell (5); Elife (3); Genes & Development (2); Cell Reports (3); Genome Research (1); Journal of Cell Biol (1); Current Biol (1)

(Alphabetical order, WT CDB students in bold)

 

Almeida M, Pintacuda G, Masui O, Koseki Y, Gdula M, Cerase A, Brown D, Mould A, Innocent C, Nakayama M, Schermelleh L, Nesterova TB, Koseki H, Brockdorff N (2017) PCGF3/5-PRC1 initiates Polycomb recruitment in X chromosome inactivation. Science (New York, NY) 356: 1081-1084

 

Blackledge NP, Farcas AM, Kondo T, King HW, McGouran JF, Hanssen LL, Ito S, Cooper S, Kondo K, Koseki Y, Ishikura T, Long HK, Sheahan TW, Brockdorff N, Kessler BM, Koseki H, Klose RJ (2014) Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 157: 1445-59

 

Blackledge NP, Long HK, Zhou JC, Kriaucionis S, Patient R, Klose RJ (2012) Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. Nucleic acids research 40: e32

 

Brown DA, Di Cerbo V, Feldmann A, Ahn J, Ito S, Blackledge NP, Nakayama M, McClellan M, Dimitrova E, Turberfield AH, Long HK, King HW, Kriaucionis S, Schermelleh L, Kutateladze TG, Koseki H, Klose RJ (2017) The SET1 Complex Selects Actively Transcribed Target Genes via Multivalent Interaction with CpG Island Chromatin. Cell Rep 20: 2313-2327

 

Conduit PT, Richens JH, Wainman A, Holder J, Vicente CC, Pratt MB, Dix CI, Novak ZA, Dobbie IM, Schermelleh L, Raff JW (2014) A molecular mechanism of mitotic centrosome assembly in Drosophila. Elife 3: e03399

 

Cooper S, Grijzenhout A, Underwood E, Ancelin K, Zhang T, Nesterova TB, Anil-Kirmizitas B, Bassett A, Kooistra SM, Agger K, Helin K, Heard E, Brockdorff N (2016) Jarid2 binds mono-ubiquitylated H2A lysine 119 to mediate crosstalk between Polycomb complexes PRC1 and PRC2. Nature communications 7: 13661

 

Corrigan L, Redhai S, Leiblich A, Fan SJ, Perera SM, Patel R, Gandy C, Wainwright SM, Morris JF, Hamdy F, Goberdhan DC, Wilson C (2014) BMP-regulated exosomes from Drosophila male reproductive glands reprogram female behavior. The Journal of cell biology 206: 671-88

 

Cundell MJ, Hutter LH, Nunes Bastos R, Poser E, Holder J, Mohammed S, Novak B, Barr FA (2016) A PP2A-B55 recognition signal controls substrate dephosphorylation kinetics during mitotic exit. The Journal of cell biology 214: 539-54

 

Davidson A, Parton RM, Rabouille C, Weil TT, Davis I (2016) Localized Translation of gurken/TGF-alpha mRNA during Axis Specification Is Controlled by Access to Orb/CPEB on Processing Bodies. Cell Rep 14: 2451-62

 

Dimitrova E, Turberfield AH, Klose RJ (2015) Histone demethylases in chromatin biology and beyond. EMBO reports 16: 1620-39

 

Ding SS, Woollard A (2017) Non-muscle myosin II is required for correct fate specification in the Caenorhabditis elegans seam cell divisions. Scientific reports 7: 3524

 

Dobrzycki T, Krecsmarik M, Bonkhofer F, Patient R, Monteiro R (2018) An optimised pipeline for parallel image-based quantification of gene expression and genotyping after in situ hybridisation. Biology open 7

 

Farcas AM, Blackledge NP, Sudbery I, Long HK, McGouran JF, Rose NR, Lee S, Sims D, Cerase A, Sheahan TW, Koseki H, Brockdorff N, Ponting CP, Kessler BM, Klose RJ (2012) KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife 1: e00205

 

Fischl H, Howe FS, Furger A, Mellor J (2017) Paf1 Has Distinct Roles in Transcription Elongation and Differential Transcript Fate. Molecular cell 65: 685-698.e8

 

Freter S, Fleenor SJ, Freter R, Liu KJ, Begbie J (2013) Cranial neural crest cells form corridors prefiguring sensory neuroblast migration. Development (Cambridge, England) 140: 3595-600

 

Grijzenhout A, Godwin J, Koseki H, Gdula MR, Szumska D, McGouran JF, Bhattacharya S, Kessler BM, Brockdorff N, Cooper S (2016) Functional analysis of AEBP2, a PRC2 Polycomb protein, reveals a Trithorax phenotype in embryonic development and in ESCs. Development (Cambridge, England) 143: 2716-23

 

Halstead JM, Lin YQ, Durraine L, Hamilton RS, Ball G, Neely GG, Bellen HJ, Davis I (2014) Syncrip/hnRNP Q influences synaptic transmission and regulates BMP signaling at the Drosophila neuromuscular synapse. Biology open 3: 839-49

 

Hanssen LLP, Kassouf MT, Oudelaar AM, Biggs D, Preece C, Downes DJ, Gosden M, Sharpe JA, Sloane-Stanley JA, Hughes JR, Davies B, Higgs DR (2017) Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nature cell biology 19: 952-961

 

Howe FS, Boubriak I, Sale MJ, Nair A, Clynes D, Grijzenhout A, Murray SC, Woloszczuk R, Mellor J (2014) Lysine acetylation controls local protein conformation by influencing proline isomerization. Molecular Cell 55: 733-44

 

Howe FS, Russell A, Lamstaes AR, El-Sagheer A, Nair A, Brown T, Mellor J (2017) CRISPRi is not strand-specific at all loci and redefines the transcriptional landscape. Elife 6

 

Hughes S, Wilkinson H, Gilbert SP, Kishida M, Ding SS, Woollard A (2014) The C. elegans TPR Containing Protein, TRD-1, Regulates Cell Fate Choice in the Developing Germ Line and Epidermis. PLoS One 9: e114998

 

King HW, Fursova NA, Blackledge NP, Klose RJ (2018) Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes. Genome research 28: 1494-1507

 

King HW, Klose RJ (2017) The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells. Elife 6

 

Kirmizitas A, Meiklejohn S, Ciau-Uitz A, Stephenson R, Patient R (2017) Dissecting BMP signaling input into the gene regulatory networks driving specification of the blood stem cell lineage. Proceedings of the National Academy of Sciences of the United States of America 114: 5814-5821

 

Leiblich A, Marsden L, Gandy C, Corrigan L, Jenkins R, Hamdy F, Wilson C (2012) Bone morphogenetic protein- and mating-dependent secretory cell growth and migration in the Drosophila accessory gland. Proceedings of the National Academy of Sciences of the United States of America 109: 19292-7

 

Liang CC, Zhan B*, Yoshikawa Y, Haas W, Gygi SP, Cohn MA (2015) UHRF1 Is a Sensor for DNA Interstrand Crosslinks and Recruits FANCD2 to Initiate the Fanconi Anemia Pathway. Cell Rep 10: 1947-56

 

Long HK, Blackledge NP, Klose RJ (2013) ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection. Biochem Soc Trans 41: 727-40

 

Long HK, King HW, Patient RK, Odom DT, Klose RJ (2016) Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved. Nucleic acids research 44: 6693-706

 

Long HK, Sims D, Heger A, Blackledge NP, Kutter C, Wright ML, Grutzner F, Odom DT, Patient R, Ponting CP, Klose RJ (2013) Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife 2: e00348

 

Maher GJ, Ralph HK*, Ding Z, Koelling N, Mlcochova H, Giannoulatou E, Dhami P, Paul DS, Stricker SH, Beck S, McVean G, Wilkie AO, Goriely A (2018) Selfish mutations dysregulating RAS-MAPK signaling are pervasive in aged human testes. Genome research

 

McDermott SM, Yang L, Halstead JM, Hamilton RS, Meignin C, Davis I (2014) Drosophila Syncrip modulates the expression of mRNAs encoding key synaptic proteins required for morphology at the neuromuscular junction. RNA 20: 1593-606

 

Mogni ME, Costa A, Ioannou C, Bell SD (2009) The glutamate switch is present in all seven clades of AAA+ protein. Biochemistry 48: 8774-5

 

Moindrot B, Cerase A, Coker H, Masui O, Grijzenhout A, Pintacuda G, Schermelleh L, Nesterova TB, Brockdorff N (2015) A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing. Cell Rep 12: 562-72

 

Motnenko A, Liang CC, Yang D, Lopez-Martinez D, Yoshikawa Y, Zhan B, Ward KE, Tian J, Haas W, Spingardi P, Kessler BM, Kriaucionis S, Gygi SP, Cohn MA (2018) Identification of UHRF2 as a novel DNA interstrand crosslink sensor protein. PLoS genetics 14: e1007643

 

Murray SC, Haenni S, Howe FS, Fischl H, Chocian K, Nair A, Mellor J (2015) Sense and antisense transcription are associated with distinct chromatin architectures across genes. Nucleic acids research 43: 7823-37

 

Nguyen T, Fischl H, Howe FS, Woloszczuk R, Serra Barros A, Xu Z, Brown D, Murray SC, Haenni S, Halstead JM, O'Connor L, Shipkovenska G, Steinmetz LM, Mellor J (2014) Transcription mediated insulation and interference direct gene cluster expression switches. Elife 3: e03635

 

Novak ZA, Conduit PT, Wainman A, Raff JW (2014) Asterless licenses daughter centrioles to duplicate for the first time in Drosophila embryos. Curr Biol 24: 1276-82

 

Oudelaar AM, Davies JOJ, Hanssen LLP, Telenius JM, Schwessinger R, Liu Y, Brown JM, Downes DJ, Chiariello AM, Bianco S, Nicodemi M, Buckle VJ, Dekker J, Higgs DR, Hughes JR (2018) Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nature genetics

 

Oudelaar AM, Hanssen LLP, Hardison RC, Kassouf MT, Hughes JR, Higgs DR (2017) Between form and function: the complexity of genome folding. Human molecular genetics 26: R208-r215

 

Parton RM, Davidson A, Davis I, Weil TT (2014) Subcellular mRNA localisation at a glance. J Cell Sci 127: 2127-33

 

Pintacuda G, Wei G, Roustan C, Kirmizitas BA, Solcan N, Cerase A, Castello A, Mohammed S, Moindrot B, Nesterova TB, Brockdorff N (2017) hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing. Molecular cell 68: 955-969.e10

 

Pogna EA, Clayton AL, Mahadevan LC (2010) Signalling to chromatin through post-translational modifications of HMGN. Biochim Biophys Acta 1799: 93-100

 

Redhai S, Hellberg JE, Wainwright M, Perera SW, Castellanos F, Kroeger B, Gandy C, Leiblich A, Corrigan L, Hilton T, Patel B, Fan SJ, Hamdy F, Goberdhan DC, Wilson C (2016) Regulation of Dense-Core Granule Replenishment by Autocrine BMP Signalling in Drosophila Secondary Cells. PLoS genetics 12: e1006366

 

Ridings-Figueroa R, Stewart ER, Nesterova TB, Coker H, Pintacuda G, Godwin J, Wilson R, Haslam A, Lilley F, Ruigrok R, Bageghni SA, Albadrani G, Mansfield W, Roulson JA, Brockdorff N, Ainscough JFX, Coverley D (2017) The nuclear matrix protein CIZ1 facilitates localization of Xist RNA to the inactive X-chromosome territory. Genes & development 31: 876-888

 

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

 

Rose NR, King HW, Blackledge NP, Fursova NA, Ember KJ, Fischer R, Kessler BM, Klose RJ (2016) RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes. Elife 5

 

Saurya S, Roque H, Novak ZA, Wainman A, Aydogan MG, Volanakis A, Sieber B, Pinto DM, Raff JW (2016) Drosophila Ana1 is required for centrosome assembly and centriole elongation. J Cell Sci 129: 2514-25

 

Senft AD, Costello I, King HW, Mould AW, Bikoff EK, Robertson EJ (2018) Combinatorial Smad2/3 Activities Downstream of Nodal Signaling Maintain Embryonic/Extra-Embryonic Cell Identities during Lineage Priming. Cell Rep 24: 1977-1985.e7

 

Skourti-Stathaki K, Kamieniarz-Gdula K, Proudfoot NJ (2014) R-loops induce repressive chromatin marks over mammalian gene terminators. Nature

 

Skourti-Stathaki K, Proudfoot NJ (2013) Histone 3 s10 phosphorylation: "caught in the R loop!". Molecular cell 52: 470-2

 

Skourti-Stathaki K, Proudfoot NJ (2014) A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression. Genes & development 28: 1384-96

 

Skourti-Stathaki K, Proudfoot NJ, Gromak N (2011) Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Molecular cell 42: 794-805

 

Sun Q, Csorba T, Skourti-Stathaki K, Proudfoot NJ, Dean C (2013) R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science (New York, NY) 340: 619-21

 

Volanakis A, Kamieniarz-Gdula K, Schlackow M, Proudfoot NJ (2017) WNK1 kinase and the termination factor PCF11 connect nuclear mRNA export with transcription. Genes & development 31: 2175-2185

 

Weil TT, Parton RM, Herpers B, Soetaert J, Veenendaal T, Xanthakis D, Dobbie IM, Halstead JM, Hayashi R, Rabouille C, Davis I (2012) Drosophila patterning is established by differential association of mRNAs with P bodies. Nature cell biology 14: 1305-13

 

Wojtas M, Peralta B, Ondiviela M, Mogni M, Bell SD, Abrescia NG (2011) Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit. Biochem Soc Trans 39: 25-30

 

Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia NG (2012) Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA. Nucleic acids research 40: 9941-52

 

Yang CP, Samuels TJ, Huang Y, Yang L, Ish-Horowicz D, Davis I, Lee T (2017) Imp and Syp RNA-binding proteins govern decommissioning of Drosophila neural stem cells. Development (Cambridge, England) 144: 3454-3464

 

 

*joint first author