BLENCOWE LAB
UNIVERSITY OF TORONTO


Publications

2017
Gueroussov, S., Weatheritt, R.J., O'Hanlon, D., Lin, Z.Y., Narula, A., Gingras, A.C. and Blencowe B.J. (2017). Regulatory Expansion in Mammals of Multivalent hnRNP Assemblies that Globally Control Alternative Splicing. Cell 170:324-339.[PUBMED]

Blencowe, B.J. (2017). The Relationship between Alternative Splicing and Proteomic Complexity. Trends Biochem Sci. 42:407-408.[PUBMED]

Muñoz, M.J., Nieto Moreno, N., Giono, L.E., Cambindo Botto, A.E., Dujardin, G., Bastianello, G., Lavore, S., Torres-Méndez, A., Menck, C.F., Blencowe, B.J., Irimia, M., Foiani, M. and Kornblihtt, A.R. (2017). Major Roles for Pyrimidine Dimers, Nucleotide Excision Repair, and ATR in the Alternative Splicing Response to UV Irradiation. Cell Rep. 18:2868-2879.[PUBMED]

Barrios-Rodiles, M., Ellis, J.D., Blencowe, B.J. and Wrana J.L. (2017). LUMIER: A Discovery Tool for Mammalian Protein Interaction Networks. Methods Mol. Biol. 1550:137-148.[PUBMED]

Han, H., Braunschweig, U., Gonatopoulos-Pournatzis, T., Weatheritt, R.J., Hirsch, C.J., Ha, K.C., Radovani, E., Sterne-Weiler, T., Wang, J., O’Hanlon, D., Pan, Q., Ray, D., Vizeacoumar, F., Datti, A., Magomedova, L., Cummins, L.C., Hughes, T.R., Greenblatt, J.F., Wrana, J.L., Moffat, J. and Blencowe, B.J. (2017). Multilayered control of alternative splicing regulatory networks by transcription factors. Mol. Cell. 65:539-55.[PUBMED]


2016
Quesnel-Vallières M., Dargaei Z., Irimia M., Gonatopoulos-Pournatzis T., Ip J., Wu M., Sterne-Weiler T., Nakagawa S., Woodin M.A., Blencowe B.J. and Cordes S.P. (2016) Misregulation of an activity-dependent splicing network as a common mechanism underlying autism spectrum disorders. Mol. Cell. 64:1023-1034.[PUBMED]

Parikshak, NN, Swarup, V., Belgard, T.G., Irimia, M., Ramaswami, G., Gandal, M.J., Hartl, C., Leppa, V., de la Torre Ubieta, L., Huang, J., Lowe, J.K., Blencowe, B.J., Horvath, S. and Geschwind, D.H. (2016). Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature. 540:423-427.[PUBMED]

Weatheritt, R.J., Sterne-Weiler, T. and Blencowe, B.J. (2016). The ribosome-engaged landscape of alternative splicing. Nat Struct Mol Biol. 23:1117-1123.[PUBMED]

Tahmasebi, S., Jafarnejad, S.M., Tam, I.S., Gonatopoulos-Pournatzis, T., Matta-Camacho, E., Tsukumo, Y., Yanagiya, A., Li, W., Atlasi, Y., Caron, M., Braunschweig, U., Pearl, D., Khoutorsky, A., Gkogkas, C.G., Nadon, R., Bourque, R., Yang, X.J., Tian, B., Stunnenberg, H.G., Yamanaka, Y., Blencowe, B.J., Giguere, V. and Sonenberg, N. (2016). Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2. Proc Natl Acad Sci USA. 113:12360-12367.[PUBMED]

Martin, S., Bellora, N., González-Vallinas, J., Irimia, M., Chebli, K., DeToledo, M., Raabe, M., Eyras, E., Urlaub, H., Blencowe, B.J. and Tazi, J. (2016) Preferential Binding of a stable G3BP Ribonucleoprotein Complex to Intron-retaining Transcripts in Mouse Brain and Modulation of their Expression in the Cerebellum. J Neurochem. 139:349-368.[PUBMED]

Rodrigues, D.C., Kim, D.S., Yang, G., Zaslavsky, K., Ha, K.C., Mok, R.S., Ross, P.J., Zhao M., Piekna A., Wei W., Blencowe B.J., Morris Q. and Ellis J. (2016) MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs. Cell Rep. 17:720-734.[PUBMED]

Tsalikis, J., Pan, Q., Tattoli, I., Maisonneuve, C., Blencowe, B.J., Philpott, D.J. and Girardin, S.E. (2016) The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress. BMC Genomics. 17:680.[PUBMED]

Solana, J., Irimia, M., Ayoub, S., Orejuela, M.R., Zywitza, V., Jens, M., Tapial, J., Ray, D., Morris, Q., Hughes, T.R., Blencowe, B.J. and Rajewsky, N. (2016) Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. Elife 5:e16797.[PUBMED]

Rodor, J., Pan, Q., Blencowe, B.J., Eyras, E. and Cáceres, J.F. (2016) The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation. RNA 9:1411-26.[PUBMED]

Ip, J.Y., Sone, M., Nashiki, C., Pan, Q., Kitaichi, K., Yanaka, K., Abe, T., Takao, K., Miyakawa, T., Blencowe, B.J. and Nakagawa, S. (2016) Gomafu lncRNA knockout mice exhibit mild hyperactivity with enhanced responsiveness to the psychostimulant methamphetamine. Sci Rep. 6:27204.[PUBMED]

Ennajdaoui H., Howard, J.M., Sterne-Weiler, T., Jahanbani, F., Coyne, D.J., Uren, P.J., Dargyte, M., Katzman, S., Draper, J.M., Wallace, A., Cazarez, O., Burns, S.C., Qiao, M., Hinck, L., Smith, A.D., Toloue, M.M., Blencowe, B.J., Penalva, L.O. and Sanford, J.R. (2016) IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC. Cell Rep. 15:1876-83.[PUBMED]

Sharma, E., Sterne-Weiler, T., O'Hanlon, D. and Blencowe, B.J. (2016) Global Mapping of Human RNA-RNA Interactions. Mol. Cell 62:618-626.[PUBMED]

Dominguez, D., Tsai, Y.H., Weatheritt, R., Wang, Y., Blencowe, B.J. and Wang, Z. (2016) An extensive program of periodic alternative splicing linked to cell cycle progression. eLife 5:e10288.[PUBMED]

Promponas, V.J., Katsani, K.R., Blencowe, B.J. and Ouzounis, C.A. (2016) Sequence evidence for common ancestry of eukaryotic endomembrane coatomers. Sci. Rep. 6:22311.[PUBMED]

Zhao, D.Y., Gish, G., Braunschweig, U., Li, Y., Ni, Z., Schmitges, F.W., Zhong, G., Liu, K., Li, W., Moffat, J., Vedadi, M., Min, J., Pawson, T.J., Blencowe, B.J. and Greenblatt, J.F. (2016) SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination Nature. 529:48.[PUBMED]


2015
Merico, D., Roifman, M., Braunschweig, U., Yuen, R., Alexandrova, R., Bates, A., Reid, B., Nalpathamkalam, T., Wang, Z., Thiruvahindrapuram, B., Gray, P., Kakakios, A., Peake, B., Hogarth, S., Manson, D., Buncic, R., Pereira, S., Herbrick J-A., Blencowe, B.J., Roifman, C. and Scherer, S. (2015) Compound heterozygous mutations in the noncoding RNU4ATAC cause Roifman Sydrome by disrupting minor intron splicing Nature Communications. 6:8718.[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, C.D., Irimia, M., Di Fiore, P.P., Blencowe, B.J., Dejana, E. and Ghigna, C. (2015). The alternative splicing factor Nova2 regulates vascular development and lumen formation Nat. Commun. 6: 8479. [PUBMED]

Gueroussov, S., Gonatopoulos-Pournatzis, T., Irimia, M., Raj, B., Lin, Z.Y., Gingras, A.C. and Blencowe, B.J. (2015). An alternative splicing event amplifies evolutionary differences between vertebrates. Science. 349(6250):868-873. [PUBMED]

Raj, B. and Blencowe, B.J. (2015). Alternative splicing in the mammalian nervous system: recent insights into mechanisms and functional roles. Neuron. 87(1):14-27. [PUBMED]

Tomsic, J., He, H., Akagi, K., Liyanarachchi, S., Pan, Q., Bertani, B., Nagy, R., Symer, D.E., Blencowe, B.J. and de la Chapelle, A. (2015). A germline mutation in SRRM2, a splicing factor gene, is implicated in papillary thyroid carcinoma predisposition. Sci. Rep. 5: 10566. [PUBMED]

Bagherie-Lachidan, M., Reginensi, A., Pan, Q., Zaveri, H.P., Scott, D.A., Blencowe, B.J., Helmbacher, F. and McNeill, H. (2015). Stromal Fat4 acts non-autonomously with Dchs1/2 to restrict the nephron progenitor pool. Development. 142(15): 2564-73. [PUBMED]

Hirsch, C.L., Coban Akdemir, Z., Wang, L., Jayakumaran, G., Trcka, D., Weiss, A., Hernandez, J.J., Pan, Q., Han, H., Xu, X., Xia, Z., Salinger, A.P., Wilson, M., Vizeacoumar, F., Datti, A., Li, W., Cooney, A.J., Barton, M.C., Blencowe, B.J., Wrana, J.L. and Dent, S.Y.R. (2015) Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes and Development. 29(8): 803-816. [PUBMED]

Quesnel-Vallieres, M., Irimia, M., Cordes, S.P. and Blencowe, B.J. (2015). Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development. Genes and Development. 29(7):746-759. [PUBMED]

Blencowe, B.J. (2015). Reflections for the 20th anniversary issue of RNA journal. RNA. 21(4): 573-575. [PUBMED]

Xiong, H.Y., Alipanahi, B., Lee, L.J., Bretschneider, H., Merico, D., Yuen, R.K., Hua, Y., Gueroussov, S., Najafabadi, H.S., Hughes, T.R., Morris, Q., Barash, Y., Krainer, A.R., Jojic, N., Scherer, S.W., Blencowe, B.J. and Frey, B.J. (2015). The human splicing code reveals new insights into the genetic determinants of disease. Science. 347(6218):1254806. [PUBMED]


2014
Irimia, M., Weatheritt, R.J., Ellis, J., Parikshak, N.N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallieres, M., Tapial, J., Raj, B., O'Hanlon, D., Barrios-Rodiles, M., Sternberg, M.J.E., Cordes, S.P., Roth, F.P., Wrana, J.L., Geschwind, D.H. and Blencowe, B.J. (2014). A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell. 159(7): 1511-1523. [PUBMED]

Raj, B., Irimia, M., Braunschweig, U., Sterne-Weiler, T., O’Hanlon, D., Lin, Z.Y., Chen, G.I., Easton, L., Ule, J., Gingras, AC., Eyras, E. and Blencowe, B.J. (2014). A global regulatory mechanism for activating an exon network required for neurogenesis. Molecular Cell. 56(1):90-103. [PUBMED]

Braunschweig, U., Barbosa-Morais, N.L., Pan, Q., Nachman, E., Alipanahi, B., Gonatopoulos-Pourtnazis, T., Frey, B., Irimia, M. & Blencowe, B.J. (2014). Widespread intron retention in mammals functionally tunes transcriptomes. Genome Research. 24(11): 1774-1786. [PUBMED].

Liu, Y., Noon, A.P., Aguiar Cabeza,E., Shen, J., Kuk,C., Ilczynski,C., Ni,R., Sukhu, B., Chan, K., Barbosa-Morais, N.L., Hermanns, T., Blencowe, B.J., Azad, A., van de Kwast, T.H., Catto, J.W., Zlotta, A.R., Wrana, J.L. (2014). Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer. European Urology. 66:982-986. [PUBMED].

Mansouri, S., Pan, Q., Blencowe, B.J., Claycomb, J. and Frappier, L. (2014). Epsten-Barr Virus EBNA1 protein regulates viral latency through effects on Let-7 microRNA and dicer. Journal of Virology. 88(19):11166-11177. [PUBMED]

Katsani, K., Irimia, M., Karapiperis, C., Scouras, Z., Blencowe, B.J., Promponas, V., & Ouzounis, C. (2014). Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins. Nature Scientific Reports. 4:4655. [PUBMED]

Uddin, M., Tammimies, K., Pellecchia, G., Alipanahi, B., Hu, P., Wang, Z., Pinto, D., Lau, L., Nalpathamkalam, T., Marshall, C.R., Blencowe, B.J., Frey, B.J., Merico, D.,Yuen, R.K. and Scherer, S.W. (2014). Brain-expressed exons under purifying selection are enriched for de novo mutations in Autism Spectrum Disorder. Nature Genetics. 46(7):742-747. [PUBMED]


2013
Sebé-Pedrós, A., Irimia, M., del Campo, J., Parra-Acero, H., Russ, C., Nusbaum, C., Blencowe, B.J. & Ruiz-Trillo, I. (2013). Regulated aggregative multicellularity in a close unicellular relative of Metazoa. eLife. 2013:2:e01287.[PUBMED]

Ray, D., Kazan, H., Cook, K.B., Weirauch, M.T., Najafabadi, H.S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., Na, H., Irimia, M., Matzah, L.H., Dale, R.K., Smith, S.A., Yarosh, C.A, Kelly, S.M., Nabet, B., Mecenas, D., Li, W., Laishram, R.S., Qiao, M., Lipshitz, H.D., Piano, F., Corbett, A.H., Carstens, R.P., Frey,B.J., Anderson R.A., Lynch, K.W., Penalva, L.O., Lei, E.P., Fraser, A.G., Blencowe, B.J., Morris, Q.D. and Hughes, T.R. (2013). A compendium of RNA-binding motifs for decoding gene regulation. Nature. 499: 172-177. [PUBMED]

Han, H.,Irimia, M., Ross, P.J., Sung, H-K., Alipanahi, B., David, L., Golipour, A., Gabut, M., Michael, I.P., Nachman, E., Wang, E., Trcka, D., Thompson, T., O'Hanlon, D., Slobodeniuc, V., Barbosa-Morais, N.L., Burge, C.B., Moffat, J., Frey, B.J., Nagy, A., Ellis, J., Wrana, J.L. and Blencowe, B.J.(2013). MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature. 498 241-245. [PUBMED]

Colak, R., Kim, T., Michaut, M., Sun, M., Irimia, M., Bellay, J., Myers, CL, Blencowe, B.J. and Kim, P.M. (2013). Distinct types of disorder in the human proteome: functional implications for alternative splicing. PLoS Comput Biol. 9(4): e1003030. [PUBMED]

Braunschweig, U., Gueroussov, S., Plocik, A.M., Graveley, B.R. and Blencowe, B.J. (2013). Dynamic integration of Splciing within Gene Regulatory Pathways. Cell. 152:1252-1269. [PUBMED]

2012
Barbosa-Morais, N.L., Irimia, M., Pan, Q., Xiong, H.Y., Gueroussov, S., Lee, L.J., Slobodeniuc, V., Kutter, C., Watt, S., Colak, R., Kim, T.H, Misquitta-Ali, C.M., Wilson, M.D., Kim, P.M., Odom, D.T., Frey, B.J. and Blencowe, B.J. (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science. 338: 1587-1593. [PUBMED]

Ward, M.C., Wilson, M.D., Barbosa-Morais, N.L., Schmidt, D., Stark, R., Pan, Q., Schwalie, P.C., Thybert, D., Kutter, C., Watt, S., Lukk, M., Flicek, P., Blencowe, B.J. and Odom, D.T. (2012). Latent Regulatory Potential of Human-Specific Repetitive Elements. Mol Cell. 49: 262-272. [PUBMED]

Khare, T., Pai, S., Koncevicius, K., Pal, M., Kriukiene, E., Liutkeviciute, Z., Irimia, M., Jia, P., Ptak, C., Xia, M., Tice, R., Tochigi, M., Moréra, S., Nazarians, A., Belsham, D., Wong, A.H., Blencowe, B.J., Wang, S.C., Kapranov, P., Kustra, R., Labrie, V., Klimasauskas, S. and Petronis, A. (2012). 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nature Structural and Molecular Biology. 24: 1037-1043. [PUBMED]

Labbé, R.M., Irimia, M., Currie, K.W., Lin, A., Zhu, S.J., Brown, D.D., Ross, E.J., Voisin, V., Bader, G.D., Blencowe,B.J. and Pearson, B.J. (2012). A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells. 30: 1734-1745. [PUBMED]

Ellis, J.D., Barrios-Rodiles, M., Çolak, R., Irimia, M., Kim, T., Calarco, J.A., Wang, X., Pan, Q., O'Hanlon, D., Kim, P.M., Wrana, J.L., and Blencowe, B.J. (2012). Tissue-specific alternative splicing remodels protein-protein interaction networks. Molecular Cell. 46: 884-892. [PUBMED]

Blencowe, B.J. (2012). An Exon-centric Perspective. Biochemistry and Cell Biology. 90: 603-612.[PUBMED]

Irimia, M. and Blencowe, B.J. (2012). Alternative splicing: decoding an expansive regulatory layer. Current Opinion in Cell Biology. 24: 323-332. [PUBMED]

Martinez, N.M., Pan, Q., Cole, B.S., Yarosh, C.A., Babcock, G.A., Heyd, F., Zhu, W., Ajith, S., Blencowe, B.J., and Lynch K.W. (2012). Alternative Splicing Networks Regulated by Signalling in Human T Cells. RNA. 18: 1029-1040. [PUBMED]

2011
Lahiry, P., Lee, L.J., Rupar, A., Siu, V., Blencowe, B.J. and Hegele, R.A. (2011). Transcriptional profiling of endocrine cerebro-osteodysplasia using exon microarray and deep sequencing. PLoS ONE. 6(9):e25400. [PUBMED]

Gabut, M., Samavarchi-Tehrani, P., Wang, X., Slobodeniuc, V., O'Hanlon, D., Sung, H.K., Alvarez, M., Talukder, S., Pan, Q., Mazzoni, E.O., Nedelec, S., Wichterle, H., Woltjen, K., Hughes, T.R., Zandstra, P.W., Nagy, A., Wrana, J.L., and Blencowe, B.J. (2011). An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell. 147: 132-146. [PUBMED]

Han, H., Nutiu, R., Moffat, J., and Blencowe, B.J. (2011). SnapShot: High-throughput sequencing applications. Cell. 146:1044. [PUBMED]

Raj, B., O'Hanlon, D., Vessey, J.P., Pan, Q., Ray, D., Buckley, N.J., Miller, F.D., and Blencowe, B.J. (2011). Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis. Mol Cell. 43: 843-850. [PUBMED]

Voineagu, I., Wang, X., Johnston, P., Lowe, J., Tian, Y., Horvath, S., Mill, J., Cantor, R., Blencowe, B.J., and Geschwind, D. (2011). Transcriptome Analysis of Autistic Brain Reveals Convergent Molecular Pathology. Nature. 474: 380-400. [PUBMED]

Calarco, J.A., Zhen, M. and Blencowe, B.J. (2011). Networking in a global world: Establishing functional connections between neural splicing regulators and their target transcripts. RNA. 17: 775-791. [PUBMED]

Saltzman, A.L., Pan, Q., and Blencowe, B.J. (2011). Regulation of alternative splicing by the core spliceosomal machinery. Genes and Development. 25: 373-384. [PUBMED]

Ramani, A.K., Calarco, J.A., Pan, Q., Mavandadi, S., Wang, Y., Nelson, A.C., Lee, L.J., Morris, Q., Blencowe, B.J., Zhen, M., and Fraser, A. (2011). Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Research. 21: 342-348. [PUBMED]

Ip, J.Y., Schmidt, D., Pan, Q., Ramani, A.K., Fraser, A.G., Odom, D.T., and Blencowe, B.J. (2011). Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Research. 21: 390-401. [PUBMED]

Misquitta-Ali, C.M., Cheng, E., O’Hanlon, D., Liu, N., McGlade, C.J., Tsao, M.S., and Blencowe, B.J. (2011). Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer. Mol. Cell Bio. 31: 138-150. [PUBMED]

2010
Tripathi, V., Ellis, J., Shen, Z., Song, D.Y., Pan, Q., Watt, A.T., Freier, S.M., Bennett, C.F., Sharma, A., Bubulya, P.A., Blencowe, B.J., Prasanth, S.G., and Prasanth, K.V. (2010). The Nuclear-retained Non-coding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation. Mol. Cell. 39: 925-938. [PUBMED]

McIlwain, D.R., Pan, Q., Reilly, P.T., Elia, A.J., McCracken, S., Wakeham, A.C., Itie-Youten, A., Blencowe, B.J., and Mak, T.W. (2010). Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay. Proc. Natl. Acad. Sci. USA.107: 12186-12191. [PUBMED]

Barash Y., Blencowe B.J., and Frey B.J. (2010). Model-based detection of alternative splicing signals. Bioinformatics. 26: i325-i333. [PUBMED]

Van Bakel, H., Nislow, C., Blencowe, B.J., and Hughes, T. (2010). Most “dark matter” transcripts are associated with known genes. PLoS Biol. 8(5): e1000371. [PUBMED]

Barash, Y., Calarco, J.A., Gao, W., Pan, Q., Wang, X., Shai, O., Blencowe, B.J., and Frey, B.J. (2010). Deciphering the splicing code. Nature. 465: 53-59. [PUBMED]

Luco, R.F., Pan, Q., Tominaga, K., Blencowe, B.J., Pereira-Smith, O.M. and Misteli, T. (2010). Regulation of alternative splicing by histone modifications. Science. 327:996-1000. [PUBMED]

2009
Kornblihtt, A.R., Schor, I.E., Allo, M. and Blencowe, B.J. (2009). When chromatin meets splicing. Nat. Struct. Mol. Biol. 16: 902-903. [PUBMED]

Khanna, M., Van Bakel, H., Tang, X., Calarco, J.A., Babak, T., Guo, G., Emili, A., Greenblatt, J.F., Hughes, T.R., Krogan, N. and Blencowe, B.J. (2009). A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300 RNA. RNA. 15: 2174-2185. [PUBMED]

Calarco, J., Superina, S., O'Hanlon, D., Gabut, M., Raj, B., Pan, Q., Skalska, U., Clarke, L., Gelinas, D., van der Kooy, D., Zhen, M., Ciruna, B., and Blencowe, B.J. (2009). Regulation of Vertebrate Nervous System-Specific Alternative Splicing and Development by an SR-Related Protein. Cell, 138: 898-910. [PUBMED]

Ray, D., Kazan, H., Chan, E., Castillo, L.P., Chaudhry, S., Talukder, S., Blencowe, B.J., Morris, Q., and Hughes, T.R. (2009). RNAcompete: a method for rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nature Biotech. 27: 667-670. [PUBMED]

Blencowe, B.J., Ahmad, S., and Lee, L.J. (2009). Current generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes and Dev. 23: 1379-1386. [PUBMED]

Blencowe, B.J., Brenner, S., Hughes, T., and Morris, Q. (2009). Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization. Pap. Symp. Biocomput., 545-8. [PUBMED]

2008
Pan, Q., Shai, O., Lee, L., Frey, B.J., and Blencowe, B.J. (2008). Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40:1413-1415. [PUBMED]

*Aznarez, I., *Barash, Y., Shai, O., He, D., Zielenski, J., Tsui, L.C., Parkinson, J., Frey, B.J., Rommens, J.M., and Blencowe, B.J. (2008). A systematic analysis of intronic sequences downstream of 5´ splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation.Genome Res. 18:1247-58. [PUBMED]

Saltzman, A., Kim, Y.K., Pan, Q., Fagnani, M., Maquat, L.E., and Blencowe, B.J. (2008). Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Molecular and Cellular Biology. 28: 4320-30. [PUBMED]

Gabut, M., Chaudhry, S. and Blencowe, B.J. (2008). SnapShot: The splicing regulatory machinery. Cell. 133: 192, 192.e1. [PUBMED]

2007
Blencowe, B.J. and Graveley, B.R. (2007). Editors. Alternative Splicing in the Postgenomic Era. Advances in Experimental Medicine and Biology. Landes Bioscience + Springer Science and Business Media. 623. [PRESS]

Calarco, J.A., Saltzman, A., Ip, J.Y., Blencowe, B.J. (2007). Technologies for the global discovery and analysis of alternative splicing. In: Alternative Splicing in the Postgenomic Era. B.J. Blencowe and B.R. Graveley, Editors. Advances in Experimental Medicine and Biology. Landes Bioscience + Springer Science and Business Media. 623: 64-84. [PUBMED]

*Huang, J.C., *Babak, T., Corson, T.W., Chua, G., Khan, S., Gallie, B.L., Hughes, T.R., Blencowe, B.J., Frey, B.J., Morris, Q.D. (2007). Using expression profiling to identify human microRNA targets. Nat Methods. 4: 1045-1049. [PUBMED]

Calarco, J.A., Xing, Y., Caceres, M., Calarco, J.P., Xiao, X., Pan, Q., Lee, C., Preuss, T.M., Blencowe, B.J. (2007). Global analysis of alternative splicing differences between humans and chimpanzees. Genes and Dev. 21: 2963-2975. [PUBMED]

*Fagnani, M., *Barash, Y., Ip, J., Misquitta, C., Pan, Q., Saltzman, A.L., Shai, O., Lee, L., Rozenhek, A., Mohammad, N., Willaime-Morawek, S., Babak, T., Zhang, W., Hughes, T.R., van der Kooy, D., Frey, B.J., Blencowe, B.J. (2007). Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol. 8: R108. [PUBMED]

Fortes, P., Longman, D., McCracken, S., Ip, J.Y., Poot, R., Mattaj, I.W., Caceres, J.F., Blencowe, B.J. (2007). Identification and characterization of RED120: A conserved PWI domain protein with links to splicing and 3'-end formation. FEBS Lett. 581: 3087-3097. [PUBMED]

Blencowe, B.J., Khanna, M. (2007). Molecular biology: RNA in control. Nature. 447: 391-393. [PUBMED]

Aznarez, I., Zielenski, J., Rommens, J.M., Blencowe, B.J., Tsui, L.C. (2007). Exon skipping through the creation of a putative exonic splicing silencer as a consequence of the cystic fibrosis mutation R553X. J. Med. Genet. 44: 341-346. [PUBMED]

Ip, J.Y., Tong, A., Pan, Q., Topp, J.D., Blencowe, B.J., Lynch, K.W. (2007). Global analysis of alternative splicing during T-cell activation. RNA. 13: 563-572. [PUBMED]

Babak, T., Blencowe, B.J., Hughes, T.R. (2007). Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinformatics. 8: 33. [PUBMED]

2006
Ule, J., Stefani, G., Mele, M., Ruggiu, M. Wang, X., Taneri, B., Gaasterland, T., Blencowe, B.J. and Darnell, R.B. (2006). An RNA map predicting Nova-dependent splicing regulation. Nature. 444: 580-586. [PUBMED]

Hughes, T.R., Hiley, S.L., Saltzman, A.J., Babak, T., and Blencowe, B.J. (2006). Microarray analysis of RNA processing and modification. In: Methods in Enzymology. Elsevier Life Sciences. 410: 300-316. [PUBMED]

Blencowe, B.J. (2006). Alternative splicing: New insights from global analyses. Cell. 126: 37-47. [PUBMED]

Shai, O., Morris, Q.D., Blencowe, B.J., and Frey, B.J. (2006). Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics. 22: 606-613. [PUBMED]

Lopez-Bigas, N., Blencowe, B.J., and Ouzounis, C.A. (2006). Highly consistent patterns for inherited human diseases at the molecular level. Bioinformatics. 22: 269-277. [PUBMED]

*Pan, Q., *Saltzman, A.L., Kim, Y.K., Misquitta, C., Shai, O., Maquat, L.E., Frey, B.J., and Blencowe, B.J. (2006). Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes and Dev. 20: 153-158. [PUBMED]

2005
McCracken, S., Longman, D., Marcon, E., Moens, P., Downey, M., Nickerson, J.A., Jessberger, R., Wilde, A., Caceres, J.F., Emili, A., and Blencowe, B.J. (2005). Proteomic analysis of SRm160-containing complexes reveals a conserved association with cohesin. J. Biol. Chem. 280: 42227-42236. [PUBMED]

*Frey, B.J., *Mohammad, N., *Morris, Q.D., *Zhang, W., Robinson, M.D., Mnaimneh, S., Chang, R., Pan, Q., Sat, E., Rossant, J., Bruneau, B.G., Aubin, J., Blencowe, B.J., and Hughes, T.R. (2005). Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nat. Genet. 37: 991-996. [PUBMED]

Babak, T., Blencowe, B.J., Hughes, T.R. (2005). A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics. 6: 104. [PUBMED]

Blencowe, B.J. (2005). Splicing on the brain. Nat. Genet. 37: 796-797. [PUBMED]

*Rosonina, E., *Ip, J.Y.Y., Calarco, J.A., Bakowski, M.A., Emili, A., McCracken, S., Tucker, P., Ingles., C.J., and Blencowe, B.J. (2005). A role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol. Cell Biol. 25: 6734-6746. [PUBMED]

Pan, Q., Bakowski, M.A., Morris, Q., Zhang, W., Frey, B., Hughes, T.R., and Blencowe, B.J. (2005). Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet. 21: 73-77. [PUBMED]

2004
*Pan, Q., *Shai, O., Misquitta, C., Zhang, W., Saltzman, A.L., Mohammad, N., Babak, T., Siu, H., Hughes, T.R., Morris, Q.D., Frey, B.J., and Blencowe, B.J. (2004). Revealing global regulatory features of mammalian alternative splicing by using a quantitative microarray platform. Mol. Cell 16: 929-941. [PUBMED]

*Zhang, W., *Morris, Q.D., Chang, R., Shai, O., Bakowski, M.A., Mitsakakis, N., Mohammad, N., Robinson, M.D., Zirnglibl, R., Somogyi, E., Laurin, N., Eftekharpour, E., Sat, E., Grigull, J., Pan, Q., Peng, W., Krogan, N., Greenblatt, J., Felhings, M., van der Kooy, D., Aubin, J., Bruneau, B.G., Rossant, J., Blencowe, B.J., Frey, B.J., and Hughes, T.R. (2004). The functional landscape of mouse gene expression. J. Biol. 3: 21. [PUBMED]

Babak, T., Zhang, W., Morris, Q., Blencowe, B.J., Hughes, T.R. (2004). Probing miRNAs with microarrays: tissue specificity and functional inference. RNA 10: 1813-1819. [PUBMED]

Custódio, N., Carvalho, C., Condado, I., Antoniou, M., Izaurralde, E., Blencowe, B.J., and Carmo-Fonseca, M. (2004). In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA 10: 622-633. [PUBMED]

Rosonina, E., and Blencowe, B.J. (2004). Analysis of the role of RNA polymerase II CTD heptapeptide repeats in pre-mRNA processing. RNA 10: 581-589. [PUBMED]

Lew, J.M., Fei, Y.L., Aleck, K., Blencowe, B.J., Weksberg, R., and Sadowski, P.D. (2004). CDKN1C mutation in Wiedemann-Beckwith syndrome patients reduces RNA splicing efficiency and identifies a splicing enhancer. Am. J. Med. Gen. 127A: 268-276. [PUBMED]

2003
McCracken, S., Longman, D., Johnstone, I.L., Caceres, J.F. and Blencowe, B.J. (2003). An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation. J. Biol. Chem. 278: 44153-44160. [PUBMED]

Rosonina, E., Bakowski, M.A., McCracken, S., and Blencowe, B.J. (2003). Transcriptional activators control splicing and 3'-end cleavage levels. J. Biol. Chem. 278: 43034-43040. [PUBMED]

Aznarez, I., Chan, E.M., Zilenski, J., Blencowe, B.J., and Tsui, L.-C. (2003). Characterization of disease-associated mutations affecting an exonic splicing enhancer and two cryptic splice sites in exon 13 of the cystic fibrosis transmembrane conductance regulator gene. Hum. Mol. Genet. 12: 2031-2040. [PUBMED]

Szymczyna, B.R., Bowman, J.A., McCracken, S., Pineda-Lucena, A., Lu, Y., Cox, B., Lambermon, M., Gravely, B.R., Arrowsmith, C.H., and Blencowe, B.J. (2003). Structure and function of the PWI motif: a novel nucleic acid binding domain that facilitates pre-mRNA processing. Genes and Dev. 17: 461-475. [PUBMED]

Blencowe, B.J. (2003) Splicing Regulation: The Cell Cycle Connection. Curr. Biol. 13: R149-151. [PUBMED]

2002
Emili, A., Shales, M., McCracken, S., Xie, W., Tucker, P.W., Kobayashi, R., Blencowe, B., and Ingles, C.J. (2002) Splicing and transcription-associated proteins PSF and p54nrb/NonO bind to the RNA polymerase II CTD. RNA 8: 1102-1111. [PUBMED]

Rosonina, E., and Blencowe, B.J. (2002) Gene Expression: The Close Coupling of Transcription and Splicing. Curr. Biol. 12: R319-R321. [PUBMED]

Blencowe, B.J. (2002) Transcription: Surprising role for an elusive small nuclear RNA. Curr. Biol. 12: R147-R149. [PUBMED]

McCracken, S., Lambermon, M., and Blencowe, B.J. (2002) The SRm160 splicing coactivator promotes transcript 3'-end cleavage. Mol. Cell. Biol. 22: 148-160. [PUBMED]

2001
Boucher, L., Ouzounis, C.A., Enright, A., and Blencowe, B.J. (2001) A genome-wide survey of SR domain proteins. RNA. 7: 1693-1701. [PUBMED]

Longman, D., McGarvey, T., McCracken, S., Johnstone, I.L., Blencowe, B.J., and Caceres, J.F. (2001) Multiple interactions between SRm160 and SR family proteins in enhancer-dependent splicing and developement of C. elegans. Curr. Biol. 11: 1923-1933. [PUBMED]

Rodrigues, J.P., Rode, M., Gatfield, D., Blencowe, B.J., Carmo-Fonseca, M., and Izauralde, E. (2001) REF proteins mediate the export of apliced and unspliced mRNAs from the nucleus. Proc. Natl. Acad. Sci. U.S.A. 98: 1030-1035. [PUBMED]

2000
McGarvey, T., Rosonina, E., McCracken, S., Li., Q., Arnaout, R., Mientjes, E., Nickerson, J., Awrey, D., Greenblatt, J., Grosveld, J., and Blencowe, B.J. (2000)The acute myeloid leukemia-associated protein, DEK, forms a splicing-dependent interaction with exon-product complexes. J. Cell Biol. 150: 309-320. [PUBMED]

Blencowe, B.J. (2000) Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem. Science 25: 106-110. [PUBMED]

Blencowe, B.J., Bauren, G., Eldridge, A.E., Issner, R., Nickerson, J.A., Rosonina, E., and Sharp, P.A. (2000) The SRm160/300 splicing coactivator subunits. RNA 6: 111-120. [PUBMED]

B.J. Blencowe publications prior to 2000

Li, Y. and Blencowe, B.J. (1999) Distinct factor requirements for exonic splicing enhancer function and binding of the U2 snRNP auxiliary factor to the polypyrimidine tract. J. Biol. Chem. 274: 35074-35079. [PUBMED]

Blencowe, B.J., Bowman, J.A.L., McCracken S., Rosonina E. (1999) SR-related proteins and the processing of mRNA precursors. Biochem. Cell Biol. 77: 1-15. [PUBMED]

Blencowe, B.J., and Lamond, A.I. (1999) Purification and depletion of RNP particles by antisense affinity chromatography. Methods in Molecular Biology 118: 275-287. [PUBMED]

Eldridge, A., Li, Y., Sharp, P.A., and Blencowe, B.J. (1999) The SRm160/300 splicing coactivator is required for exon-enhancer function. Proc. Natl. Acad. Sci. USA 96: 6125-6130 [PUBMED]

Blencowe, B.J. and Ouzounis, C.A. (1999) The "PWI" Motif: a new protein domain in splicing factors. Trends Biochem. Sci. 24: 179-180 [PUBMED]

Blencowe, B.J., Issner, R., Nickerson, J.A. and Sharp, P.A. (1998) A coactivator of Pre-mRNA splicing. Genes and Dev. 12: 996-1009 [PUBMED]

Penman, S., Blencowe, B.J., and Nickerson, J.A. (1997). The nuclear matrix: past and present. In: Nuclear Structure and Gene Expression. New York, Academic Press. p.3-24.

Mortillaro, M., Blencowe, B.J., Wei, X., Nakayasu, H., Du, L., Warren, S., Sharp, P.A., and Berezney, R. (1996). A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix. Proc. Natl. Acad. Sci. USA. 93: 8253-8257 [PUBMED]

Blencowe, B.J., Issner, R., Kim, J., McCaw, P. and Sharp, P.A. (1995). New proteins related to the Ser-Arg family of splicing factors. RNA. 1: 852-865. [PUBMED]

Nickerson, J.A. Blencowe, B.J. and S. Penman (1995). The architectural organization of nuclear metabolism. Int. Rev. Cyt. 162: 67-124. [PUBMED]

Blencowe, B.J. and Barabino, S.M.L. (1995). Antisense affinity depletion of ribonucleoprotein particles. In: Methods in Molecular Biology. Vol. 37. Humana Press. 67-76. [PUBMED]

Blencowe, B.J., Nickerson, J.A., Issner, R., Penman, S. and Sharp, P.A. (1994). Association of nuclear matrix antigens with exon-containing splicing complexes. J. Cell Biol. 127: 593-607. [PUBMED]

Crispino, J.D., Blencowe, B.J. and Sharp, P.A. (1994). Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP. Science. 265: 1866-1869. [PUBMED]

Blencowe, B.J., Carmo-Fonseca, M., Behrens, S.-E., Lührmann, R., and A.I. Lamond (1993). Interaction of the human autoantigen p150 with splicing snRNPs. J. Cell Science. 105: 685-697. [PUBMED]

Ouzounis, C.A. and Blencowe, B.J. (1991). Bacterial DNA replication initiation factor priA is related to proteins belonging to the 'DEAD-box' family. Nucl. Acids Res. 19: 6953. [PUBMED]

Lamm, G.M., Blencowe, B.J., Sproat, B.S., Iribarren, A.M., Ryder, U. and Lamond, A.I. (1991). Antisense probes containing 2-aminoadenosine allow efficient depletion of U5 snRNP from HeLa splicing extracts. Nucl. Acids Res. 19: 3193-3197. [PUBMED]

Barabino, S.M.L., Blencowe, B.J., Ryder, U., Sproat, B.S., and Lamond, A.I. (1990). Targeted snRNP depletion reveals an additional role for mammalian U1 snRNP in spliceosome assembly. Cell 63: 293-302. [PUBMED]

Lamond, A.I., Barabino, S., Blencowe, B.J., Sproat, B.S. and Ryder, U. (1990). Studying pre-mRNA splicing using antisense 2'-OMe RNA oligonucleotides. Mol. Biol. Rep. 14: 201. [PUBMED]

Sibbald, P.R. and Blencowe, B.J. (1990). A completely conserved rat U6 snRNA pseudogene coding sequence is sandwiched between a cytochrome c retropseudogene and a LINE-like sequence. Nucl. Acids Res. 18: 1063. [PUBMED]

Lamond, A.I., Barabino, S. and Blencowe, B.J. (1990). The Mammalian pre-mRNA splicing apparatus. In: Nucleic Acids and Molecular Biology vol. 4. Springer Verlag. 243-257.

Barabino, S., Sproat, B.S., Ryder, U., Blencowe, B.J., and Lamond, A.I. (1989). Mapping U2 snRNP-pre-mRNA interactions using biotinylated oligonucleotides made of 2'-OMe RNA. EMBO J. 8: 4171-4178. [PUBMED]

Blencowe, B.J., Sproat, B.S., Ryder, U., Barabino, S., and Lamond, A.I. (1989). Antisense probing of the human U4/U6 snRNP with biotinylated 2'- OMe RNA oligonucleotides. Cell 59: 531-539. [PUBMED]