Literature DB >> 11142388

Nuclease protection of RNAs containing site-specific labels: a rapid method for mapping RNA-protein interactions.

P A Maroney1, C M Romfo, T W Nilsen.   

Abstract

This report describes a method that combines nuclease protection and site-specific labeling to determine sites and extents of RNA-protein interactions. The utility of the method is demonstrated by the analysis of the binding of factors to the 3' splice site region of a pre-mRNA labeled at three specific positions. This "reverse footprinting" technique should be widely applicable to a variety of questions concerning RNA-protein interactions.

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Year:  2000        PMID： 11142388      PMCID： PMC1370058          DOI： 10.1017/s1355838200001308

Source DB:  PubMed          Journal:  RNA        ISSN： 1355-8382            Impact factor:   4.942


  12 in total

1.  A tertiary interaction detected in a human U2-U6 snRNA complex assembled in vitro resembles a genetically proven interaction in yeast.

Authors:  S Valadkhan; J L Manley
Journal:  RNA       Date:  2000-02       Impact factor: 4.942

2.  Functional recognition of 5' splice site by U4/U6.U5 tri-snRNP defines a novel ATP-dependent step in early spliceosome assembly.

Authors:  P A Maroney; C M Romfo; T W Nilsen
Journal:  Mol Cell       Date:  2000-08       Impact factor: 17.970

3.  Site-specific modification of pre-mRNA: the 2'-hydroxyl groups at the splice sites.

Authors:  M J Moore; P A Sharp
Journal:  Science       Date:  1992-05-15       Impact factor: 47.728

4.  Trans splicing of nematode pre-messenger RNA in vitro.

Authors:  G J Hannon; P A Maroney; J A Denker; T W Nilsen
Journal:  Cell       Date:  1990-06-29       Impact factor: 41.582

5.  The position of site-directed cleavage of RNA using RNase H and 2'-O-methyl oligonucleotides is dependent on the enzyme source.

Authors:  J Lapham; Y T Yu; M D Shu; J A Steitz; D M Crothers
Journal:  RNA       Date:  1997-09       Impact factor: 4.942

6.  Functional recognition of the 3' splice site AG by the splicing factor U2AF35.

Authors:  S Wu; C M Romfo; T W Nilsen; M R Green
Journal:  Nature       Date:  1999-12-16       Impact factor: 49.962

7.  The 3' splice site of pre-messenger RNA is recognized by a small nuclear ribonucleoprotein.

Authors:  B Chabot; D L Black; D M LeMaster; J A Steitz
Journal:  Science       Date:  1985-12-20       Impact factor: 47.728

8.  The U1 small nuclear RNA-protein complex selectively binds a 5' splice site in vitro.

Authors:  S M Mount; I Pettersson; M Hinterberger; A Karmas; J A Steitz
Journal:  Cell       Date:  1983-06       Impact factor: 41.582

9.  Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates.

Authors:  J F Milligan; D R Groebe; G W Witherell; O C Uhlenbeck
Journal:  Nucleic Acids Res       Date:  1987-11-11       Impact factor: 16.971

10.  RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation.

Authors:  J Lapham; D M Crothers
Journal:  RNA       Date:  1996-03       Impact factor: 4.942
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  6 in total

1.  Spatial organization of protein-RNA interactions in the branch site-3' splice site region during pre-mRNA splicing in yeast.

Authors:  David S McPheeters; Peggy Muhlenkamp
Journal:  Mol Cell Biol       Date:  2003-06       Impact factor: 4.272

2.  Multiple roles for SR proteins in trans splicing.

Authors:  Suzanne Furuyama; James P Bruzik
Journal:  Mol Cell Biol       Date:  2002-08       Impact factor: 4.272

3.  Retroviral splicing suppressor sequesters a 3' splice site in a 50S aberrant splicing complex.

Authors:  Keith E Giles; Karen L Beemon
Journal:  Mol Cell Biol       Date:  2005-06       Impact factor: 4.272

4.  U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression.

Authors:  Shalini Sharma; Christophe Maris; Frédéric H-T Allain; Douglas L Black
Journal:  Mol Cell       Date:  2011-03-04       Impact factor: 17.970

5.  Dynamic regulation of alternative splicing by silencers that modulate 5' splice site competition.

Authors:  Yang Yu; Patricia A Maroney; John A Denker; Xiang H-F Zhang; Olexandr Dybkov; Reinhard Lührmann; Eckhard Jankowsky; Lawrence A Chasin; Timothy W Nilsen
Journal:  Cell       Date:  2008-12-26       Impact factor: 41.582

6.  FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.

Authors:  Jason G Underwood; Andrew V Uzilov; Sol Katzman; Courtney S Onodera; Jacob E Mainzer; David H Mathews; Todd M Lowe; Sofie R Salama; David Haussler
Journal:  Nat Methods       Date:  2010-11-07       Impact factor: 28.547
  6 in total

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