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Items: 1 to 50 of 126

1.

Erratum: Electrophoretic Mobility Shift Assays for RNA-Protein Complexes.

Rio DC.

Cold Spring Harb Protoc. 2018 Oct 1;2018(10):pdb.err106104. doi: 10.1101/pdb.err106104. No abstract available.

PMID:
30275071
2.

JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns.

Wang Q, Rio DC.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8181-E8190. doi: 10.1073/pnas.1806018115. Epub 2018 Aug 13.

3.

Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5.

Lee YJ, Wang Q, Rio DC.

Genes Dev. 2018 Aug 1;32(15-16):1060-1074. doi: 10.1101/gad.316034.118. Epub 2018 Jul 24.

4.

Striking circadian neuron diversity and cycling of Drosophila alternative splicing.

Wang Q, Abruzzi KC, Rosbash M, Rio DC.

Elife. 2018 Jun 4;7. pii: e35618. doi: 10.7554/eLife.35618.

5.

piRNA-mediated regulation of transposon alternative splicing in the soma and germ line.

Teixeira FK, Okuniewska M, Malone CD, Coux RX, Rio DC, Lehmann R.

Nature. 2017 Dec 14;552(7684):268-272. doi: 10.1038/nature25018. Epub 2017 Dec 6.

6.

Drosophila IRBP bZIP heterodimer binds P-element DNA and affects hybrid dysgenesis.

Francis MJ, Roche S, Cho MJ, Beall E, Min B, Panganiban RP, Rio DC.

Proc Natl Acad Sci U S A. 2016 Nov 15;113(46):13003-13008. Epub 2016 Oct 31.

7.

The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.

Wang Q, Taliaferro JM, Klibaite U, Hilgers V, Shaevitz JW, Rio DC.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):5269-74. doi: 10.1073/pnas.1600936113. Epub 2016 Apr 25.

8.

Biochemical identification of new proteins involved in splicing repression at the Drosophila P-element exonic splicing silencer.

Horan L, Yasuhara JC, Kohlstaedt LA, Rio DC.

Genes Dev. 2015 Nov 1;29(21):2298-311. doi: 10.1101/gad.268847.115.

9.

An Efficient Method for Electroporation of Small Interfering RNAs into ENCODE Project Tier 1 GM12878 and K562 Cell Lines.

Muller RY, Hammond MC, Rio DC, Lee YJ.

J Biomol Tech. 2015 Dec;26(4):142-9. doi: 10.7171/jbt.15-2604-003. Epub 2015 Oct 29.

10.

P Transposable Elements in Drosophila and other Eukaryotic Organisms.

Majumdar S, Rio DC.

Microbiol Spectr. 2015 Apr;3(2):MDNA3-0004-2014. doi: 10.1128/microbiolspec.MDNA3-0004-2014. Review.

11.

Mechanisms and Regulation of Alternative Pre-mRNA Splicing.

Lee Y, Rio DC.

Annu Rev Biochem. 2015;84:291-323. doi: 10.1146/annurev-biochem-060614-034316. Epub 2015 Mar 12. Review.

12.

Northern blots: capillary transfer of RNA from agarose gels and filter hybridization using standard stringency conditions.

Rio DC.

Cold Spring Harb Protoc. 2015 Mar 2;2015(3):306-13. doi: 10.1101/pdb.prot081018.

PMID:
25734063
13.

Denaturation and electrophoresis of RNA with glyoxal.

Rio DC.

Cold Spring Harb Protoc. 2015 Feb 2;2015(2):223-6. doi: 10.1101/pdb.prot081000.

PMID:
25646499
14.

Denaturation and electrophoresis of RNA with formaldehyde.

Rio DC.

Cold Spring Harb Protoc. 2015 Feb 2;2015(2):219-22. doi: 10.1101/pdb.prot080994.

PMID:
25646498
15.

Reverse transcription-polymerase chain reaction.

Rio DC.

Cold Spring Harb Protoc. 2014 Nov 3;2014(11):1207-16. doi: 10.1101/pdb.prot080887.

PMID:
25368309
16.

In vitro splicing reactions in Drosophila Kc nuclear extracts.

Rio DC.

Cold Spring Harb Protoc. 2014 Aug 1;2014(8):887-90. doi: 10.1101/pdb.prot080853.

PMID:
25086019
17.

Preparation of Drosophila Kc cell nuclear extracts for in vitro splicing.

Rio DC.

Cold Spring Harb Protoc. 2014 Aug 1;2014(8):891-5. doi: 10.1101/pdb.prot080846.

PMID:
25086018
18.

Northern blots for small RNAs and microRNAs.

Rio DC.

Cold Spring Harb Protoc. 2014 Jul 1;2014(7):793-7. doi: 10.1101/pdb.prot080838.

PMID:
24987143
19.

3'-End labeling of RNA with yeast Poly(A) polymerase and 3'-deoxyadenosine 5'-[α-32P]triphosphate.

Rio DC.

Cold Spring Harb Protoc. 2014 Jun 2;2014(6):687-9. doi: 10.1101/pdb.prot080770.

PMID:
24890209
20.

5'-end labeling of RNA with [γ-32P]ATP and T4 polynucleotide kinase.

Rio DC.

Cold Spring Harb Protoc. 2014 Apr 1;2014(4):441-3. doi: 10.1101/pdb.prot080739.

PMID:
24692496
21.

Electrophoretic mobility shift assays for RNA-protein complexes.

Rio DC.

Cold Spring Harb Protoc. 2014 Apr 1;2014(4):435-40. doi: 10.1101/pdb.prot080721. Erratum in: Cold Spring Harb Protoc. 2018 Oct 1;2018(10):pdb.err106104.

PMID:
24692495
22.

Large-scale immunopurification of ribonucleoprotein complexes from Drosophila nucleoplasmic extracts for tiling microarrays.

Rio DC.

Cold Spring Harb Protoc. 2014 Mar 1;2014(3):299-303. doi: 10.1101/pdb.prot080705.

PMID:
24591694
23.

Preparation of ribonucleoprotein-enriched nucleoplasmic extracts from Drosophila cells.

Rio DC.

Cold Spring Harb Protoc. 2014 Mar 1;2014(3):295-8. doi: 10.1101/pdb.prot080697.

PMID:
24591693
24.

Ultraviolet photochemical cross-linking to detect RNA-binding proteins.

Rio DC.

Cold Spring Harb Protoc. 2013 Dec 1;2013(12):1178-81. doi: 10.1101/pdb.prot079418.

PMID:
24298030
25.

High-yield synthesis of RNA using T7 RNA polymerase and plasmid DNA or oligonucleotide templates.

Nilsen TW, Rio DC, Ares M Jr.

Cold Spring Harb Protoc. 2013 Nov 1;2013(11). pii: pdb.prot078535. doi: 10.1101/pdb.prot078535.

PMID:
24184762
26.

Expression and purification of active recombinant T7 RNA polymerase from E. coli.

Rio DC.

Cold Spring Harb Protoc. 2013 Nov 1;2013(11). pii: pdb.prot078527. doi: 10.1101/pdb.prot078527.

PMID:
24184761
27.

The Drosophila splicing factor PSI is phosphorylated by casein kinase II and tousled-like kinase.

Taliaferro JM, Marwha D, Aspden JL, Mavrici D, Cheng NE, Kohlstaedt LA, Rio DC.

PLoS One. 2013;8(2):e56401. doi: 10.1371/journal.pone.0056401. Epub 2013 Feb 20.

28.

Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression.

Taliaferro JM, Aspden JL, Bradley T, Marwha D, Blanchette M, Rio DC.

Genes Dev. 2013 Feb 15;27(4):378-89. doi: 10.1101/gad.210708.112. Epub 2013 Feb 7.

29.

The human THAP9 gene encodes an active P-element DNA transposase.

Majumdar S, Singh A, Rio DC.

Science. 2013 Jan 25;339(6118):446-8. doi: 10.1126/science.1231789.

30.

In vitro transcription of labeled RNA: synthesis, capping, and substitution.

Nilsen TW, Rio DC.

Cold Spring Harb Protoc. 2012 Nov 1;2012(11):1181-6. doi: 10.1101/pdb.prot072066.

PMID:
23118360
31.

Filter-binding assay for analysis of RNA-protein interactions.

Rio DC.

Cold Spring Harb Protoc. 2012 Oct 1;2012(10):1078-81. doi: 10.1101/pdb.prot071449.

PMID:
23028069
32.

A segmental genomic duplication generates a functional intron.

Hellsten U, Aspden JL, Rio DC, Rokhsar DS.

Nat Commun. 2011 Aug 30;2:454. doi: 10.1038/ncomms1461.

33.

Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans.

Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE.

RNA. 2011 Oct;17(10):1884-94. doi: 10.1261/rna.2696311. Epub 2011 Aug 24.

34.

Evolution of a tissue-specific splicing network.

Taliaferro JM, Alvarez N, Green RE, Blanchette M, Rio DC.

Genes Dev. 2011 Mar 15;25(6):608-20. doi: 10.1101/gad.2009011.

35.

Distinct regulatory programs establish widespread sex-specific alternative splicing in Drosophila melanogaster.

Hartmann B, Castelo R, Miñana B, Peden E, Blanchette M, Rio DC, Singh R, Valcárcel J.

RNA. 2011 Mar;17(3):453-68. doi: 10.1261/rna.2460411. Epub 2011 Jan 13.

36.

An SF1 affinity model to identify branch point sequences in human introns.

Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD.

Nucleic Acids Res. 2011 Mar;39(6):2344-56. doi: 10.1093/nar/gkq1046. Epub 2010 Nov 10.

37.
38.

Enrichment of poly(A)+ mRNA using immobilized oligo(dT).

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jul 1;2010(7):pdb.prot5454. doi: 10.1101/pdb.prot5454.

PMID:
20647358
39.

Guidelines for the use of RNA purification kits.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jul 1;2010(7):pdb.ip79. doi: 10.1101/pdb.ip79.

PMID:
20647349
40.

Determining the yield and quality of purified RNA.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.top82. doi: 10.1101/pdb.top82.

PMID:
20516190
41.

Nondenaturing agarose gel electrophoresis of RNA.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5445. doi: 10.1101/pdb.prot5445.

PMID:
20516183
42.

Polyacrylamide gel electrophoresis of RNA.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5444. doi: 10.1101/pdb.prot5444.

PMID:
20516182
43.

Removal of DNA from RNA.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5443. doi: 10.1101/pdb.prot5443.

PMID:
20516181
44.

Removal of ribosomal subunits (and rRNA) from cytoplasmic extracts before solubilization with SDS and deproteinization.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5442. doi: 10.1101/pdb.prot5442.

PMID:
20516180
45.

Preparation of cytoplasmic and nuclear RNA from tissue culture cells.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5441. doi: 10.1101/pdb.prot5441.

PMID:
20516179
46.

Ethanol precipitation of RNA and the use of carriers.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5440. doi: 10.1101/pdb.prot5440.

PMID:
20516178
47.

Purification of RNA using TRIzol (TRI reagent).

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5439. doi: 10.1101/pdb.prot5439.

PMID:
20516177
48.

Purification of RNA by SDS solubilization and phenol extraction.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5438. doi: 10.1101/pdb.prot5438.

PMID:
20516176
49.

THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.

Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC.

Nat Struct Mol Biol. 2010 Jan;17(1):117-23. doi: 10.1038/nsmb.1742. Epub 2009 Dec 13.

50.

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila.

Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE.

PLoS Genet. 2009 Jun;5(6):e1000525. doi: 10.1371/journal.pgen.1000525. Epub 2009 Jun 19.

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