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Blocking late stages of splicing quickly limits pre-spliceosome assembly in vivo.

Mendoza-Ochoa GI, Barrass JD, Maudlin IE, Beggs JD.

RNA Biol. 2019 Dec;16(12):1775-1784. doi: 10.1080/15476286.2019.1657788. Epub 2019 Sep 4.


Extremely Rapid and Specific Metabolic Labelling of RNA In Vivo with 4-Thiouracil (Ers4tU).

Barrass JD, Beggs JD.

J Vis Exp. 2019 Aug 22;(150). doi: 10.3791/59952.


Tuning Degradation to Achieve Specific and Efficient Protein Depletion.

Barrass JD, Mendoza-Ochoa GI, Maudlin IE, Sani E, Beggs JD.

J Vis Exp. 2019 Jul 20;(149). doi: 10.3791/59874.


Spt5 modulates cotranscriptional spliceosome assembly in Saccharomyces cerevisiae.

Maudlin IE, Beggs JD.

RNA. 2019 Oct;25(10):1298-1310. doi: 10.1261/rna.070425.119. Epub 2019 Jul 9.


Mutagenesis of Snu114 domain IV identifies a developmental role in meiotic splicing.

Gautam A, Beggs JD.

RNA Biol. 2019 Feb;16(2):185-195. doi: 10.1080/15476286.2018.1561145. Epub 2019 Jan 23.


A fast and tuneable auxin-inducible degron for depletion of target proteins in budding yeast.

Mendoza-Ochoa GI, Barrass JD, Terlouw BR, Maudlin IE, de Lucas S, Sani E, Aslanzadeh V, Reid JAE, Beggs JD.

Yeast. 2019 Jan;36(1):75-81. doi: 10.1002/yea.3362. Epub 2018 Nov 12.


A Nuclear Export Block Triggers the Decay of Newly Synthesized Polyadenylated RNA.

Tudek A, Schmid M, Makaras M, Barrass JD, Beggs JD, Jensen TH.

Cell Rep. 2018 Aug 28;24(9):2457-2467.e7. doi: 10.1016/j.celrep.2018.07.103.


Corrigendum: Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.

Aslanzadeh V, Huang Y, Sanguinetti G, Beggs JD.

Genome Res. 2018 Apr;28(4):606.2. doi: 10.1101/gr.236265.118. No abstract available.


Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.

Aslanzadeh V, Huang Y, Sanguinetti G, Beggs JD.

Genome Res. 2018 Feb;28(2):203-213. doi: 10.1101/gr.225615.117. Epub 2017 Dec 18. Erratum in: Genome Res. 2018 Apr;28(4):606.2.


RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit.

Milligan L, Sayou C, Tuck A, Auchynnikava T, Reid JE, Alexander R, Alves FL, Allshire R, Spanos C, Rappsilber J, Beggs JD, Kudla G, Tollervey D.

Elife. 2017 Oct 13;6. pii: e27082. doi: 10.7554/eLife.27082.


Extremely fast and incredibly close: cotranscriptional splicing in budding yeast.

Wallace EWJ, Beggs JD.

RNA. 2017 May;23(5):601-610. doi: 10.1261/rna.060830.117. Epub 2017 Feb 2. Review.


Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling.

Barrass JD, Reid JE, Huang Y, Hector RD, Sanguinetti G, Beggs JD, Granneman S.

Genome Biol. 2015 Dec 17;16:282. doi: 10.1186/s13059-015-0848-1.


Cwc21p promotes the second step conformation of the spliceosome and modulates 3' splice site selection.

Gautam A, Grainger RJ, Vilardell J, Barrass JD, Beggs JD.

Nucleic Acids Res. 2015 Mar 31;43(6):3309-17. doi: 10.1093/nar/gkv159. Epub 2015 Mar 3.


Brr2p carboxy-terminal Sec63 domain modulates Prp16 splicing RNA helicase.

Cordin O, Hahn D, Alexander R, Gautam A, Saveanu C, Barrass JD, Beggs JD.

Nucleic Acids Res. 2014 Dec 16;42(22):13897-910. doi: 10.1093/nar/gku1238. Epub 2014 Nov 26.


A splicing-dependent transcriptional checkpoint associated with prespliceosome formation.

Chathoth KT, Barrass JD, Webb S, Beggs JD.

Mol Cell. 2014 Mar 6;53(5):779-90. doi: 10.1016/j.molcel.2014.01.017. Epub 2014 Feb 20.


A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation.

Aitken S, Alexander RD, Beggs JD.

J R Soc Interface. 2013 Jun 26;10(86):20130438. doi: 10.1098/rsif.2013.0438. Print 2013 Sep 6.


Structural basis for dual roles of Aar2p in U5 snRNP assembly.

Weber G, Cristão VF, Santos KF, Jovin SM, Heroven AC, Holton N, Lührmann R, Beggs JD, Wahl MC.

Genes Dev. 2013 Mar 1;27(5):525-40. doi: 10.1101/gad.213207.113. Epub 2013 Feb 26.


RNA helicases in splicing.

Cordin O, Beggs JD.

RNA Biol. 2013 Jan;10(1):83-95. doi: 10.4161/rna.22547. Epub 2012 Dec 10. Review.


Brr2p-mediated conformational rearrangements in the spliceosome during activation and substrate repositioning.

Hahn D, Kudla G, Tollervey D, Beggs JD.

Genes Dev. 2012 Nov 1;26(21):2408-21. doi: 10.1101/gad.199307.112.


Kinetic analysis of pre-ribosome structure in vivo.

Swiatkowska A, Wlotzka W, Tuck A, Barrass JD, Beggs JD, Tollervey D.

RNA. 2012 Dec;18(12):2187-200. doi: 10.1261/rna.034751.112. Epub 2012 Oct 23.


Structure, function and regulation of spliceosomal RNA helicases.

Cordin O, Hahn D, Beggs JD.

Curr Opin Cell Biol. 2012 Jun;24(3):431-8. doi: 10.1016/ Epub 2012 Mar 29. Review.


Modelling reveals kinetic advantages of co-transcriptional splicing.

Aitken S, Alexander RD, Beggs JD.

PLoS Comput Biol. 2011 Oct;7(10):e1002215. doi: 10.1371/journal.pcbi.1002215. Epub 2011 Oct 13.


Mechanism for Aar2p function as a U5 snRNP assembly factor.

Weber G, Cristão VF, de L Alves F, Santos KF, Holton N, Rappsilber J, Beggs JD, Wahl MC.

Genes Dev. 2011 Aug 1;25(15):1601-12. doi: 10.1101/gad.635911. Epub 2011 Jul 15.


Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast.

Kudla G, Granneman S, Hahn D, Beggs JD, Tollervey D.

Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):10010-5. doi: 10.1073/pnas.1017386108. Epub 2011 May 24.


Splicing-dependent RNA polymerase pausing in yeast.

Alexander RD, Innocente SA, Barrass JD, Beggs JD.

Mol Cell. 2010 Nov 24;40(4):582-93. doi: 10.1016/j.molcel.2010.11.005.


RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae.

Alexander RD, Barrass JD, Dichtl B, Kos M, Obtulowicz T, Robert MC, Koper M, Karkusiewicz I, Mariconti L, Tollervey D, Dichtl B, Kufel J, Bertrand E, Beggs JD.

RNA. 2010 Dec;16(12):2570-80. doi: 10.1261/rna.2162610. Epub 2010 Oct 25.


Cross-talk in transcription, splicing and chromatin: who makes the first call?

Alexander R, Beggs JD.

Biochem Soc Trans. 2010 Oct;38(5):1251-6. doi: 10.1042/BST0381251. Review.


Brr2p RNA helicase with a split personality: insights into structure and function.

Hahn D, Beggs JD.

Biochem Soc Trans. 2010 Aug;38(4):1105-9. doi: 10.1042/BST0381105. Review.


Prognosis for splicing factor PRPF8 retinitis pigmentosa, novel mutations and correlation between human and yeast phenotypes.

Towns KV, Kipioti A, Long V, McKibbin M, Maubaret C, Vaclavik V, Ehsani P, Springell K, Kamal M, Ramesar RS, Mackey DA, Moore AT, Mukhopadhyay R, Webster AR, Black GC, O'Sullivan J, Bhattacharya SS, Pierce EA, Beggs JD, Inglehearn CF.

Hum Mutat. 2010 May;31(5):E1361-76. doi: 10.1002/humu.21236.


Processivity and coupling in messenger RNA transcription.

Aitken S, Robert MC, Alexander RD, Goryanin I, Bertrand E, Beggs JD.

PLoS One. 2010 Jan 28;5(1):e8845. doi: 10.1371/journal.pone.0008845.


Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome.

Grainger RJ, Barrass JD, Jacquier A, Rain JC, Beggs JD.

RNA. 2009 Dec;15(12):2161-73. doi: 10.1261/rna.1908309. Epub 2009 Oct 23.


Interaction of yeast eIF4G with spliceosome components: implications in pre-mRNA processing events.

Kafasla P, Barrass JD, Thompson E, Fromont-Racine M, Jacquier A, Beggs JD, Lewis J.

RNA Biol. 2009 Nov-Dec;6(5):563-74. Epub 2009 Nov 18.


Analysis of Lsm1p and Lsm8p domains in the cellular localization of Lsm complexes in budding yeast.

Reijns MA, Auchynnikava T, Beggs JD.

FEBS J. 2009 Jul;276(13):3602-17. doi: 10.1111/j.1742-4658.2009.07080.x. Epub 2009 May 20.


Mutations in the U5 snRNA result in altered splicing of subsets of pre-mRNAs and reduced stability of Prp8.

Kershaw CJ, Barrass JD, Beggs JD, O'Keefe RT.

RNA. 2009 Jul;15(7):1292-304. doi: 10.1261/rna.1347409. Epub 2009 May 15.


A role for Q/N-rich aggregation-prone regions in P-body localization.

Reijns MA, Alexander RD, Spiller MP, Beggs JD.

J Cell Sci. 2008 Aug 1;121(Pt 15):2463-72. doi: 10.1242/jcs.024976. Epub 2008 Jul 8.


Requirements for nuclear localization of the Lsm2-8p complex and competition between nuclear and cytoplasmic Lsm complexes.

Spiller MP, Reijns MA, Beggs JD.

J Cell Sci. 2007 Dec 15;120(Pt 24):4310-20. Epub 2007 Nov 20.


prp8 mutations that cause human retinitis pigmentosa lead to a U5 snRNP maturation defect in yeast.

Boon KL, Grainger RJ, Ehsani P, Barrass JD, Auchynnikava T, Inglehearn CF, Beggs JD.

Nat Struct Mol Biol. 2007 Nov;14(11):1077-83. Epub 2007 Oct 14.


The Lsm2-8 complex determines nuclear localization of the spliceosomal U6 snRNA.

Spiller MP, Boon KL, Reijns MA, Beggs JD.

Nucleic Acids Res. 2007;35(3):923-9. Epub 2007 Jan 23.


Yeast ntr1/spp382 mediates prp43 function in postspliceosomes.

Boon KL, Auchynnikava T, Edwalds-Gilbert G, Barrass JD, Droop AP, Dez C, Beggs JD.

Mol Cell Biol. 2006 Aug;26(16):6016-23.


Prp8p dissection reveals domain structure and protein interaction sites.

Boon KL, Norman CM, Grainger RJ, Newman AJ, Beggs JD.

RNA. 2006 Feb;12(2):198-205. Epub 2005 Dec 22.


Crosstalk between RNA metabolic pathways: an RNOMICS approach.

Beggs JD, Tollervey D.

Nat Rev Mol Cell Biol. 2005 May;6(5):423-9. Review.


Lsm proteins and RNA processing.

Beggs JD.

Biochem Soc Trans. 2005 Jun;33(Pt 3):433-8. Review.


Prp8 protein: at the heart of the spliceosome.

Grainger RJ, Beggs JD.

RNA. 2005 May;11(5):533-57. Review.


Interaction between a G-patch protein and a spliceosomal DEXD/H-box ATPase that is critical for splicing.

Silverman EJ, Maeda A, Wei J, Smith P, Beggs JD, Lin RJ.

Mol Cell Biol. 2004 Dec;24(23):10101-10.


Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex.

Kufel J, Bousquet-Antonelli C, Beggs JD, Tollervey D.

Mol Cell Biol. 2004 Nov;24(21):9646-57.


Lsm proteins promote regeneration of pre-mRNA splicing activity.

Verdone L, Galardi S, Page D, Beggs JD.

Curr Biol. 2004 Aug 24;14(16):1487-91.


Splicing goes global.

Barrass JD, Beggs JD.

Trends Genet. 2003 Jun;19(6):295-8. Review.


Identification and characterization of Prp45p and Prp46p, essential pre-mRNA splicing factors.

Albers M, Diment A, Muraru M, Russell CS, Beggs JD.

RNA. 2003 Jan;9(1):138-50.


Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p.

Kufel J, Allmang C, Verdone L, Beggs JD, Tollervey D.

Mol Cell Biol. 2002 Jul;22(14):5248-56.


Vac14 controls PtdIns(3,5)P(2) synthesis and Fab1-dependent protein trafficking to the multivesicular body.

Dove SK, McEwen RK, Mayes A, Hughes DC, Beggs JD, Michell RH.

Curr Biol. 2002 Jun 4;12(11):885-93.

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