Donnelly Centre for Cellular and Biomolecular Research

Selected Publications

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Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL. ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development. Nucleic Acids Research. 2019; [Pubmed]

Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H. A physical and genetic map of identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Research. 2019; 29(1):146-156. [Pubmed]

Gonatopoulos-Pournatzis T, Wu M, Braunschweig U, Roth J, Han H, Best AJ, Raj B, Aregger M, O'Hanlon D, Ellis JD, Calarco JA, Moffat J, Gingras AC, Blencowe BJ. Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons. Molecular Cell. 2018; 72(3):510-524.e12. [Pubmed]

Sterne-Weiler T, Weatheritt RJ, Best AJ, Ha KCH, Blencowe BJ. Efficient and accurate quantitative profiling of alternative splicing patterns of any complexity on a laptop. Molecular Cell. 2018; 72(1):187-200.e6. [Pubmed]

Tapial J, Ha KCH, Sterne-Weiler T, Gohr A, Braunschweig U, Hermoso-Pulido A, Quesnel-Vallières M, Permanyer J, Sodaei R, Marquez Y, Cozzuto L, Wang X, Gómez-Velázquez M, Rayon T, Manzanares M, Ponomarenko J, Blencowe BJ, Irimia M. An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Genome Research. 2017; 27(10):1759-1768. [Pubmed]

Gueroussov S, Weatheritt RJ, O'Hanlon D, Lin ZY, Narula A, Gingras AC, Blencowe BJ. Regulatory expansion in mammals of multivalent hnRNP assemblies that globally control alternative splicing. Cell. 2017; 170(2):324-339.e23. [Pubmed]

Han H, Braunschweig U, Gonatopoulos-Pournatzis T, Weatheritt RJ, Hirsch CL, Ha KCH, Radovani E, Nabeel-Shah S, Sterne-Weiler T, Wang J, O'Hanlon D, Pan Q, Ray D, Zheng H, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR, Greenblatt JF, Wrana JL, Moffat J, Blencowe BJ. Multilayered control of alternative splicing regulatory networks by transcription factors. Molecular Cell. 2017; 65(3):539-553.e7. [Pubmed]

Quesnel-Vallières M, Dargaei Z, Irimia M, Gonatopoulos-Pournatzis T, Ip JY, Wu M, Sterne-Weiler T, Nakagawa S, Woodin MA, Blencowe BJ, Cordes SP. Misregulation of an activity-dependent splicing network as a common mechanism underlying autism spectrum disorders. Molecular Cell. 2016; 64(6):1023-1034. [Pubmed]

Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR. Multiparameter functional diversity of human C2H2 zinc finger proteins. Genome Research. 2016; 26(12):1742-1752. [Pubmed]

van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Ušaj MM, Pechlaner M, Takar M, Ušaj M, VanderSluis B, Andrusiak K, Bansal P, Baryshnikova A, Boone CE, Cao J, Cote A, Gebbia M, Horecka G, Horecka I, Kuzmin E, Legro N, Liang W, et al. Exploring genetic suppression interactions on a global scale. Science (New York, N.Y.). 2016; 354(6312). [Pubmed]

Liang L, Gnaneshan S, Garduño RA, Mallo GV. Genome sequence of Listeria monocytogenes Plasmid pLM-C-273 carrying genes related to stress resistance. Genome Announcements. 2016; 4(5):. [Pubmed]

Tsalikis J, Pan Q, Tattoli I, Maisonneuve C, Blencowe BJ, Philpott DJ, Girardin SE. The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress. BMC Genomics. 2016; 17:680. [Pubmed]

Teatero S, Lemire P, Dewar K, Wasserscheid J, Calzas C, Mallo GV, Li A, Athey TB, Segura M, Fittipaldi N. Genomic recombination leading to decreased virulence of group B Streptococcus in a mouse model of adult invasive disease. Pathogens (Basel, Switzerland). 2016; 5(3):. [Pubmed]

Rodor J, Pan Q, Blencowe BJ, Eyras E, Cáceres JF. The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation. RNA (New York, N.Y.). 2016; 22(9):1411-26. [Pubmed]

Ip JY, Sone M, Nashiki C, Pan Q, Kitaichi K, Yanaka K, Abe T, Takao K, Miyakawa T, Blencowe BJ, Nakagawa S. Gomafu lncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine. Scientific Reports. 2016; 6:27204. [Pubmed]

Stubenhaus BM, Dustin JP, Neverett ER, Beaudry MS, Nadeau LE, Burk-McCoy E, He X, Pearson BJ, Pellettieri J. Light-induced depigmentation in planarians models the pathophysiology of acute porphyrias. eLife. 2016; 5:. [Pubmed]

Sharma E, Sterne-Weiler T, O'Hanlon D, Blencowe BJ. Global mapping of human RNA-RNA interactions. Molecular Cell. 2016; 62(4):618-26. [Pubmed]

Labrie V, Buske OJ, Oh E, Jeremian R, Ptak C, Gasiūnas G, Maleckas A, Petereit R, Žvirbliene A, Adamonis K, Kriukienė E, Koncevičius K, Gordevičius J, Nair A, Zhang A, Ebrahimi S, Oh G, Šikšnys V, Kupčinskas L, Brudno M, Petronis A. Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Nature Structural & Molecular Biology. 2016; 23(6):566-73. [Pubmed]

Winick-Ng W, Caetano FA, Winick-Ng J, Morey TM, Heit B, Rylett RJ. 82-kDa choline acetyltransferase and SATB1 localize to β-amyloid induced matrix attachment regions. Scientific Reports. 2016; 6:23914. [Pubmed]

Currie KW, Brown DD, Zhu S, Xu C, Voisin V, Bader GD, Pearson BJ. HOX gene complement and expression in the planarian Schmidtea mediterranea. EvoDevo. 2016; 7:7. [Pubmed]

Gnaneshan S, Hsueh YC, Liang L, Teatero S, Fittipaldi N, Mallo GV. Genome sequence of Listeria monocytogenes strain F6540 (sequence type 360) collected from food samples in Ontario, Canada. Genome Announcements. 2016; 4(1). [Pubmed]

Zhao DY, Gish G, Braunschweig U, Li Y, Ni Z, Schmitges FW, Zhong G, Liu K, Li W, Moffat J, Vedadi M, Min J, Pawson TJ, Blencowe BJ, Greenblatt JF. SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination. Nature. 2016; 529(7584):48-53. [Pubmed]

Tjhung KF, Kitov PI, Ng S, Kitova EN, Deng L, Klassen JS, Derda R. Silent encoding of chemical post-translational modifications in phage-displayed libraries. Journal of the American Chemical Society. 2016; 138(1):32-5. [Pubmed]

Dibitetto D, Ferrari M, Rawal CC, Balint A, Kim T, Zhang Z, Smolka MB, Brown GW, Marini F, Pellicioli A. Slx4 and Rtt107 control checkpoint signalling and DNA resection at double-strand breaks. Nucleic Acids Research. 2016; 44(2):669-82. [Pubmed]

Giampietro C, Deflorian G, Gallo S, Di Matteo A, Pradella D, Bonomi S, Belloni E, Nyqvist D, Quaranta V, Confalonieri S, Bertalot G, Orsenigo F, Pisati F, Ferrero E, Biamonti G, Fredrickx E, Taveggia C, Wyatt CD, Irimia M, Di Fiore PP, Blencowe BJ, Dejana E, Ghigna C. The alternative splicing factor Nova2 regulates vascular development and lumen formation. Nature Communications. 2015; 6:8479. [Pubmed]

Jablonowski CM, Cussiol JR, Oberly S, Yimit A, Balint A, Kim T, Zhang Z, Brown GW, Smolka MB. Termination of replication stress signaling via concerted action of the Slx4 scaffold and the PP4 phosphatase. Genetics. 2015; 201(3):937-49. [Pubmed]

van Leeuwen J, Andrews B, Boone C, Tan G. Construction of Multifragment Plasmids by Homologous Recombination in Yeast. Cold Spring Harbor Protocols. 2015; 2015(9):pdb.top084111. [Pubmed]

van Leeuwen J, Andrews B, Boone C, Tan G. Rapid and Efficient Plasmid Construction by Homologous Recombination in Yeast. Cold Spring Harbor Protocols. 2015; 2015(9):pdb.prot085100. [Pubmed]

Gueroussov S, Gonatopoulos-Pournatzis T, Irimia M, Raj B, Lin ZY, Gingras AC, Blencowe BJ. An alternative splicing event amplifies evolutionary differences between vertebrates. Science (New York, N.Y.). 2015; 349(6250):868-73. [Pubmed]

Bagherie-Lachidan M, Reginensi A, Pan Q, Zaveri HP, Scott DA, Blencowe BJ, Helmbacher F, McNeill H. Stromal Fat4 acts non-autonomously with Dchs1/2 to restrict the nephron progenitor pool. Development (Cambridge, England). 2015; 142(15):2564-73. [Pubmed]

Zhu SJ, Hallows SE, Currie KW, Xu C, Pearson BJ. A mex3 homolog is required for differentiation during planarian stem cell lineage development. eLife. 2015; 4. [Pubmed]

Balint A, Kim T, Gallo D, Cussiol JR, Bastos de Oliveira FM, Yimit A, Ou J, Nakato R, Gurevich A, Shirahige K, Smolka MB, Zhang Z, Brown GW. Assembly of Slx4 signaling complexes behind DNA replication forks. The EMBO Journal. 2015; 34(16):2182-97. [Pubmed]

Pal M, Ebrahimi S, Oh G, Khare T, Zhang A, Kaminsky ZA, Wang SC, Petronis A. High precision DNA modification analysis of HCG9 in major psychosis. Schizophrenia Bulletin. 2016; 42(1):170-7. [Pubmed]

Cussiol JR, Jablonowski CM, Yimit A, Brown GW, Smolka MB. Dampening DNA damage checkpoint signalling via coordinated BRCT domain interactions. The EMBO Journal. 2015; 34(12):1704-17. [Pubmed]

O'Meara TR, Veri AO, Ketela T, Jiang B, Roemer T, Cowen LE. Global analysis of fungal morphology exposes mechanisms of host cell escape. Nature Communications. 2015; 6:6741. [Pubmed]

Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, Barrios-Rodiles M, Sternberg MJ, Cordes SP, Roth FP, Wrana JL, Geschwind DH, Blencowe BJ. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell. 2014; 159(7):1511-23. [Pubmed]

Ali SS, Soo J, Rao C, Leung AS, Ngai DH, Ensminger AW, Navarre WW. Silencing by H-NS potentiated the evolution of Salmonella. PLoS Pathogens. 2014; 10(11):e1004500. [Pubmed]

Mansouri S, Pan Q, Blencowe BJ, Claycomb JM, Frappier L. Epstein-Barr virus EBNA1 protein regulates viral latency through effects on let-7 microRNA and dicer. Journal of Virology. 2014; 88(19):11166-77. [Pubmed]

Marcon E, Ni Z, Pu S, Turinsky AL, Trimble SS, Olsen JB, Silverman-Gavrila R, Silverman-Gavrila L, Phanse S, Guo H, Zhong G, Guo X, Young P, Bailey S, Roudeva D, Zhao D, Hewel J, Li J, Gräslund S, Paduch M, Kossiakoff AA, Lupien M, Emili A, Wodak SJ, Greenblatt J. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Cell Reports. 2014; 8(1):297-310. [Pubmed]

Parts L, Liu YC, Tekkedil MM, Steinmetz LM, Caudy AA, Fraser AG, Boone C, Andrews BJ, Rosebrock AP. Heritability and genetic basis of protein level variation in an outbred population. Genome Research. 2014; 24(8):1363-70. [Pubmed]

Lin AY, Pearson BJ. Planarian yorkie/YAP functions to integrate adult stem cell proliferation, organ homeostasis and maintenance of axial patterning. Development (Cambridge, England). 2014; 141(6):1197-208. [Pubmed]

Matochko WL, Cory Li S, Tang SK, Derda R. Prospective identification of parasitic sequences in phage display screens. Nucleic Acids Research. 2014; 42(3):1784-98. [Pubmed]

Kittanakom S, Arnoldo A, Brown KR, Wallace I, Kunavisarut T, Torti D, Heisler LE, Surendra A, Moffat J, Giaever G, Nislow C. Miniature short hairpin RNA screens to characterize antiproliferative drugs. G3 (Bethesda, Md.). 2013; 3(8):1375-87. [Pubmed]

Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature. 2013; 498(7453):241-5. [Pubmed]

Rao C, Benhabib H, Ensminger AW. Phylogenetic reconstruction of the Legionella pneumophila Philadelphia-1 laboratory strains through comparative genomics. PLoS One. 2013; 8(5):e64129. [Pubmed]

Li Y, Zhao DY, Greenblatt JF, Zhang Z. RIPSeeker: A statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Research. 2013; 41(8):e94. [Pubmed]

Zhu SJ, Pearson BJ. The Retinoblastoma pathway regulates stem cell proliferation in freshwater planarians. Developmental Biology. 2013; 373(2):442-52. [Pubmed]

Douglas AC, Smith AM, Sharifpoor S, Yan Z, Durbic T, Heisler LE, Lee AY, Ryan O, Göttert H, Surendra A, van Dyk D, Giaever G, Boone C, Nislow C, Andrews BJ. Functional analysis with a barcoder yeast gene overexpression system. G3 (Bethesda, Md.). 2012; 2(10):1279-89. [Pubmed]

Smith AM, Durbic T, Kittanakom S, Giaever G, Nislow C. Barcode sequencing for understanding drug-gene interactions. Methods in Molecular Biology (Clifton, N.J.). 2012; 910:55-69. [Pubmed]

Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM. MUSI: An integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. Nucleic Acids Research. 2012; 40(6):e47. [Pubmed]

van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG, Hughes TR, Page JE. The draft genome and transcriptome of Cannabis sativa. Genome Biology. 2011; 12(10):R102. [Pubmed]

Han H, Nutiu R, Moffat J, Blencowe BJ. SnapShot: High-throughput sequencing applications. Cell. 2011; 146(6):1044, 1044.e1-2. [Pubmed]

Gabut M, Samavarchi-Tehrani P, Wang X, Slobodeniuc V, O'Hanlon D, Sung HK, Alvarez M, Talukder S, Pan Q, Mazzoni EO, Nedelec S, Wichterle H, Woltjen K, Hughes TR, Zandstra PW, Nagy A, Wrana JL, Blencowe BJ. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell. 2011; 147(1):132-46. [Pubmed]

Smith AM, Durbic T, Oh J, Urbanus M, Proctor M, Heisler LE, Giaever G, Nislow C. Competitive genomic screens of barcoded yeast libraries. Journal of Visualized Experiments: JoVE. 2011; [Pubmed]

Ketela T, Heisler LE, Brown KR, Ammar R, Kasimer D, Surendra A, Ericson E, Blakely K, Karamboulas D, Smith AM, Durbic T, Arnoldo A, Cheung-Ong K, Koh JL, Gopal S, Cowley GS, Yang X, Grenier JK, Giaever G, Root DE, Moffat J, Nislow C. A comprehensive platform for highly multiplexed mammalian functional genetic screens. BMC Genomics. 2011; 12:213. [Pubmed]