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Items: 1 to 50 of 193

1.

Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.

Feng H, Bao S, Rahman MA, Weyn-Vanhentenryck SM, Khan A, Wong J, Shah A, Flynn ED, Krainer AR, Zhang C.

Mol Cell. 2019 Jun 20;74(6):1189-1204.e6. doi: 10.1016/j.molcel.2019.02.002.

PMID:
31226278
2.

PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis.

Lin KT, Krainer AR.

Bioinformatics. 2019 May 28. pii: btz438. doi: 10.1093/bioinformatics/btz438. [Epub ahead of print]

PMID:
31135034
3.

Delivery of GalNAc-Conjugated Splice-Switching ASOs to Non-hepatic Cells through Ectopic Expression of Asialoglycoprotein Receptor.

Scharner J, Qi S, Rigo F, Bennett CF, Krainer AR.

Mol Ther Nucleic Acids. 2019 Jun 7;16:313-325. doi: 10.1016/j.omtn.2019.02.024. Epub 2019 Mar 13.

4.

Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia.

Wang E, Lu SX, Pastore A, Chen X, Imig J, Chun-Wei Lee S, Hockemeyer K, Ghebrechristos YE, Yoshimi A, Inoue D, Ki M, Cho H, Bitner L, Kloetgen A, Lin KT, Uehara T, Owa T, Tibes R, Krainer AR, Abdel-Wahab O, Aifantis I.

Cancer Cell. 2019 Mar 18;35(3):369-384.e7. doi: 10.1016/j.ccell.2019.01.010. Epub 2019 Feb 21.

PMID:
30799057
5.

Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites.

Wong MS, Kinney JB, Krainer AR.

Mol Cell. 2018 Sep 20;71(6):1012-1026.e3. doi: 10.1016/j.molcel.2018.07.033. Epub 2018 Aug 30.

PMID:
30174293
6.

Mechanism of Nonsense-Mediated mRNA Decay Stimulation by Splicing Factor SRSF1.

Aznarez I, Nomakuchi TT, Tetenbaum-Novatt J, Rahman MA, Fregoso O, Rees H, Krainer AR.

Cell Rep. 2018 May 15;23(7):2186-2198. doi: 10.1016/j.celrep.2018.04.039.

7.

Antisense oligonucleotides correct the familial dysautonomia splicing defect in IKBKAP transgenic mice.

Sinha R, Kim YJ, Nomakuchi T, Sahashi K, Hua Y, Rigo F, Bennett CF, Krainer AR.

Nucleic Acids Res. 2018 Jun 1;46(10):4833-4844. doi: 10.1093/nar/gky249.

8.

A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma.

Lin KT, Ma WK, Scharner J, Liu YR, Krainer AR.

Genome Res. 2018 Feb 15. doi: 10.1101/gr.227181.117. [Epub ahead of print]

9.

Downregulation of Survivin contributes to cell-cycle arrest during postnatal cardiac development in a severe spinal muscular atrophy mouse model.

Sheng L, Wan B, Feng P, Sun J, Rigo F, Bennett CF, Akerman M, Krainer AR, Hua Y.

Hum Mol Genet. 2018 Feb 1;27(3):486-498. doi: 10.1093/hmg/ddx418.

10.

Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers.

Sivaramakrishnan M, McCarthy KD, Campagne S, Huber S, Meier S, Augustin A, Heckel T, Meistermann H, Hug MN, Birrer P, Moursy A, Khawaja S, Schmucki R, Berntenis N, Giroud N, Golling S, Tzouros M, Banfai B, Duran-Pacheco G, Lamerz J, Hsiu Liu Y, Luebbers T, Ratni H, Ebeling M, Cléry A, Paushkin S, Krainer AR, Allain FH, Metzger F.

Nat Commun. 2017 Nov 14;8(1):1476. doi: 10.1038/s41467-017-01559-4.

11.

A-44G transition in SMN2 intron 6 protects patients with spinal muscular atrophy.

Wu X, Wang SH, Sun J, Krainer AR, Hua Y, Prior TW.

Hum Mol Genet. 2017 Jul 15;26(14):2768-2780. doi: 10.1093/hmg/ddx166.

12.

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage.

Jangi M, Fleet C, Cullen P, Gupta SV, Mekhoubad S, Chiao E, Allaire N, Bennett CF, Rigo F, Krainer AR, Hurt JA, Carulli JP, Staropoli JF.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):E2347-E2356. doi: 10.1073/pnas.1613181114. Epub 2017 Mar 7.

13.

A Broad Set of Chromatin Factors Influences Splicing.

Allemand E, Myers MP, Garcia-Bernardo J, Harel-Bellan A, Krainer AR, Muchardt C.

PLoS Genet. 2016 Sep 23;12(9):e1006318. doi: 10.1371/journal.pgen.1006318. eCollection 2016 Sep.

14.

RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns.

Doktor TK, Hua Y, Andersen HS, Brøner S, Liu YH, Wieckowska A, Dembic M, Bruun GH, Krainer AR, Andresen BS.

Nucleic Acids Res. 2017 Jan 9;45(1):395-416. doi: 10.1093/nar/gkw731. Epub 2016 Aug 23.

15.

Splicing-factor alterations in cancers.

Anczuków O, Krainer AR.

RNA. 2016 Sep;22(9):1285-301. doi: 10.1261/rna.057919.116. Review.

16.

Global identification of hnRNP A1 binding sites for SSO-based splicing modulation.

Bruun GH, Doktor TK, Borch-Jensen J, Masuda A, Krainer AR, Ohno K, Andresen BS.

BMC Biol. 2016 Jul 5;14:54. doi: 10.1186/s12915-016-0279-9.

17.

Differentiation of mammary tumors and reduction in metastasis upon Malat1 lncRNA loss.

Arun G, Diermeier S, Akerman M, Chang KC, Wilkinson JE, Hearn S, Kim Y, MacLeod AR, Krainer AR, Norton L, Brogi E, Egeblad M, Spector DL.

Genes Dev. 2016 Jan 1;30(1):34-51. doi: 10.1101/gad.270959.115. Epub 2015 Dec 23.

18.

Antisense oligonucleotide-directed inhibition of nonsense-mediated mRNA decay.

Nomakuchi TT, Rigo F, Aznarez I, Krainer AR.

Nat Biotechnol. 2016 Feb;34(2):164-6. doi: 10.1038/nbt.3427. Epub 2015 Dec 14.

19.

The spliceosome, a potential Achilles heel of MYC-driven tumors.

Anczuków O, Krainer AR.

Genome Med. 2015 Oct 22;7:107. doi: 10.1186/s13073-015-0234-3.

20.

SRSF1-Regulated Alternative Splicing in Breast Cancer.

Anczuków O, Akerman M, Cléry A, Wu J, Shen C, Shirole NH, Raimer A, Sun S, Jensen MA, Hua Y, Allain FH, Krainer AR.

Mol Cell. 2015 Oct 1;60(1):105-17. doi: 10.1016/j.molcel.2015.09.005.

21.

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.

Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, Ren B, Krainer AR, Maniatis T, Wu Q.

Cell. 2015 Aug 13;162(4):900-10. doi: 10.1016/j.cell.2015.07.038.

22.

Differential connectivity of splicing activators and repressors to the human spliceosome.

Akerman M, Fregoso OI, Das S, Ruse C, Jensen MA, Pappin DJ, Zhang MQ, Krainer AR.

Genome Biol. 2015 Jun 6;16:119. doi: 10.1186/s13059-015-0682-5.

23.

Splicing: still so much to learn.

Krainer AR.

RNA. 2015 Apr;21(4):500-1. doi: 10.1261/rna.050641.115. No abstract available.

24.

Rescue of gene-expression changes in an induced mouse model of spinal muscular atrophy by an antisense oligonucleotide that promotes inclusion of SMN2 exon 7.

Staropoli JF, Li H, Chun SJ, Allaire N, Cullen P, Thai A, Fleet CM, Hua Y, Bennett CF, Krainer AR, Kerr D, McCampbell A, Rigo F, Carulli JP.

Genomics. 2015 Apr;105(4):220-8. doi: 10.1016/j.ygeno.2015.01.007. Epub 2015 Jan 31.

25.

Motor neuron cell-nonautonomous rescue of spinal muscular atrophy phenotypes in mild and severe transgenic mouse models.

Hua Y, Liu YH, Sahashi K, Rigo F, Bennett CF, Krainer AR.

Genes Dev. 2015 Feb 1;29(3):288-97. doi: 10.1101/gad.256644.114. Epub 2015 Jan 12.

26.

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, Blencowe BJ, Frey BJ.

Science. 2015 Jan 9;347(6218):1254806. doi: 10.1126/science.1254806. Epub 2014 Dec 18.

27.

HIV-1 transcription is regulated by splicing factor SRSF1.

Paz S, Krainer AR, Caputi M.

Nucleic Acids Res. 2014 Dec 16;42(22):13812-23.

28.

Emerging functions of SRSF1, splicing factor and oncoprotein, in RNA metabolism and cancer.

Das S, Krainer AR.

Mol Cancer Res. 2014 Sep;12(9):1195-204. doi: 10.1158/1541-7786.MCR-14-0131. Epub 2014 May 7. Review.

29.

Pharmacology of a central nervous system delivered 2'-O-methoxyethyl-modified survival of motor neuron splicing oligonucleotide in mice and nonhuman primates.

Rigo F, Chun SJ, Norris DA, Hung G, Lee S, Matson J, Fey RA, Gaus H, Hua Y, Grundy JS, Krainer AR, Henry SP, Bennett CF.

J Pharmacol Exp Ther. 2014 Jul;350(1):46-55. doi: 10.1124/jpet.113.212407. Epub 2014 Apr 30.

30.

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.

Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, Krainer AR, Darnell RB, Zhang C.

Cell Rep. 2014 Mar 27;6(6):1139-1152. doi: 10.1016/j.celrep.2014.02.005. Epub 2014 Mar 6.

31.

Splicing factor SRSF6 promotes hyperplasia of sensitized skin.

Jensen MA, Wilkinson JE, Krainer AR.

Nat Struct Mol Biol. 2014 Feb;21(2):189-97. doi: 10.1038/nsmb.2756. Epub 2014 Jan 19.

32.

Pathological impact of SMN2 mis-splicing in adult SMA mice.

Sahashi K, Ling KK, Hua Y, Wilkinson JE, Nomakuchi T, Rigo F, Hung G, Xu D, Jiang YP, Lin RZ, Ko CP, Bennett CF, Krainer AR.

EMBO Mol Med. 2013 Oct;5(10):1586-601. doi: 10.1002/emmm.201302567. Epub 2013 Sep 9.

33.

Isolated pseudo-RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition.

Cléry A, Sinha R, Anczuków O, Corrionero A, Moursy A, Daubner GM, Valcárcel J, Krainer AR, Allain FH.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):E2802-11. doi: 10.1073/pnas.1303445110. Epub 2013 Jul 8.

34.

A new path to oncogene-induced senescence: at the crossroads of splicing and translation.

Das S, Fregoso OI, Krainer AR.

Cell Cycle. 2013 May 15;12(10):1477-9. doi: 10.4161/cc.24749. Epub 2013 Apr 22. No abstract available.

35.

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.

Wu J, Anczuków O, Krainer AR, Zhang MQ, Zhang C.

Nucleic Acids Res. 2013 May 1;41(10):5149-63. doi: 10.1093/nar/gkt216. Epub 2013 Apr 9.

36.

Splicing-factor oncoprotein SRSF1 stabilizes p53 via RPL5 and induces cellular senescence.

Fregoso OI, Das S, Akerman M, Krainer AR.

Mol Cell. 2013 Apr 11;50(1):56-66. doi: 10.1016/j.molcel.2013.02.001. Epub 2013 Mar 7.

37.

Pick one, but be quick: 5' splice sites and the problems of too many choices.

Roca X, Krainer AR, Eperon IC.

Genes Dev. 2013 Jan 15;27(2):129-44. doi: 10.1101/gad.209759.112. Review.

38.

Manipulation of PK-M mutually exclusive alternative splicing by antisense oligonucleotides.

Wang Z, Jeon HY, Rigo F, Bennett CF, Krainer AR.

Open Biol. 2012 Oct;2(10):120133. doi: 10.1098/rsob.120133.

39.

Antisense-based therapy for the treatment of spinal muscular atrophy.

Rigo F, Hua Y, Krainer AR, Bennett CF.

J Cell Biol. 2012 Oct 1;199(1):21-5. doi: 10.1083/jcb.201207087.

40.

TSUNAMI: an antisense method to phenocopy splicing-associated diseases in animals.

Sahashi K, Hua Y, Ling KK, Hung G, Rigo F, Horev G, Katsuno M, Sobue G, Ko CP, Bennett CF, Krainer AR.

Genes Dev. 2012 Aug 15;26(16):1874-84. doi: 10.1101/gad.197418.112.

41.

A generalizable pre-clinical research approach for orphan disease therapy.

Beaulieu CL, Samuels ME, Ekins S, McMaster CR, Edwards AM, Krainer AR, Hicks GG, Frey BJ, Boycott KM, Mackenzie AE.

Orphanet J Rare Dis. 2012 Jun 15;7:39. Review.

42.

Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides.

Roca X, Akerman M, Gaus H, Berdeja A, Bennett CF, Krainer AR.

Genes Dev. 2012 May 15;26(10):1098-109. doi: 10.1101/gad.190173.112.

43.

Oncogenic splicing factor SRSF1 is a critical transcriptional target of MYC.

Das S, Anczuków O, Akerman M, Krainer AR.

Cell Rep. 2012 Feb 23;1(2):110-7.

44.

Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing.

Rigo F, Hua Y, Chun SJ, Prakash TP, Krainer AR, Bennett CF.

Nat Chem Biol. 2012 Apr 15;8(6):555-61. doi: 10.1038/nchembio.939.

45.

Antisense-mediated exon inclusion.

Hua Y, Krainer AR.

Methods Mol Biol. 2012;867:307-23. doi: 10.1007/978-1-61779-767-5_20.

46.

RNA therapeutics: beyond RNA interference and antisense oligonucleotides.

Kole R, Krainer AR, Altman S.

Nat Rev Drug Discov. 2012 Jan 20;11(2):125-40. doi: 10.1038/nrd3625. Review.

47.

The splicing factor SRSF1 regulates apoptosis and proliferation to promote mammary epithelial cell transformation.

Anczuków O, Rosenberg AZ, Akerman M, Das S, Zhan L, Karni R, Muthuswamy SK, Krainer AR.

Nat Struct Mol Biol. 2012 Jan 15;19(2):220-8. doi: 10.1038/nsmb.2207.

48.

Mechanisms of activation and repression by the alternative splicing factors RBFOX1/2.

Sun S, Zhang Z, Fregoso O, Krainer AR.

RNA. 2012 Feb;18(2):274-83. doi: 10.1261/rna.030486.111. Epub 2011 Dec 19.

49.

Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons.

Wang Z, Chatterjee D, Jeon HY, Akerman M, Vander Heiden MG, Cantley LC, Krainer AR.

J Mol Cell Biol. 2012 Apr;4(2):79-87. doi: 10.1093/jmcb/mjr030. Epub 2011 Nov 1.

50.

Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model.

Hua Y, Sahashi K, Rigo F, Hung G, Horev G, Bennett CF, Krainer AR.

Nature. 2011 Oct 5;478(7367):123-6. doi: 10.1038/nature10485.

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