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Items: 1 to 20 of 128

1.

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae.

Freeberg MA, Han T, Moresco JJ, Kong A, Yang YC, Lu ZJ, Yates JR, Kim JK.

Genome Biol. 2013 Feb 14;14(2):R13. doi: 10.1186/gb-2013-14-2-r13.

2.

Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Bioinformatic Analysis.

Freeberg MA, Kim JK.

Methods Mol Biol. 2016;1361:91-104. doi: 10.1007/978-1-4939-3079-1_6.

PMID:
26483018
3.

Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Experimental Procedures.

Han T, Kim JK.

Methods Mol Biol. 2016;1361:77-90. doi: 10.1007/978-1-4939-3079-1_5.

PMID:
26483017
4.

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae.

Yang Y, Umetsu J, Lu ZJ.

Sci China Life Sci. 2014 Jan;57(1):22-35. doi: 10.1007/s11427-013-4583-0. Epub 2013 Dec 26.

PMID:
24369346
5.

PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T.

J Vis Exp. 2010 Jul 2;(41). pii: 2034. doi: 10.3791/2034.

6.

In silico characterization and prediction of global protein-mRNA interactions in yeast.

Pancaldi V, Bähler J.

Nucleic Acids Res. 2011 Aug;39(14):5826-36. doi: 10.1093/nar/gkr160. Epub 2011 Apr 1.

7.

Differential protein occupancy profiling of the mRNA transcriptome.

Schueler M, Munschauer M, Gregersen LH, Finzel A, Loewer A, Chen W, Landthaler M, Dieterich C.

Genome Biol. 2014 Jan 13;15(1):R15. doi: 10.1186/gb-2014-15-1-r15.

8.

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.

Riordan DP, Herschlag D, Brown PO.

Nucleic Acids Res. 2011 Mar;39(4):1501-9. doi: 10.1093/nar/gkq920. Epub 2010 Oct 18.

9.

Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast.

Jackson JS Jr, Houshmandi SS, Lopez Leban F, Olivas WM.

RNA. 2004 Oct;10(10):1625-36. Epub 2004 Aug 30.

10.

Target selection by natural and redesigned PUF proteins.

Porter DF, Koh YY, VanVeller B, Raines RT, Wickens M.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15868-73. doi: 10.1073/pnas.1508501112. Epub 2015 Dec 14.

11.

Identification of RNA-protein interaction networks using PAR-CLIP.

Ascano M, Hafner M, Cekan P, Gerstberger S, Tuschl T.

Wiley Interdiscip Rev RNA. 2012 Mar-Apr;3(2):159-77. doi: 10.1002/wrna.1103. Epub 2011 Dec 27. Review.

12.

Protein-RNA networks revealed through covalent RNA marks.

Lapointe CP, Wilinski D, Saunders HA, Wickens M.

Nat Methods. 2015 Dec;12(12):1163-70. doi: 10.1038/nmeth.3651. Epub 2015 Nov 2.

13.

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.

Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO.

PLoS Biol. 2008 Oct 28;6(10):e255. doi: 10.1371/journal.pbio.0060255.

14.

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast.

Webb S, Hector RD, Kudla G, Granneman S.

Genome Biol. 2014 Jan 7;15(1):R8. doi: 10.1186/gb-2014-15-1-r8.

15.

PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.

Danan C, Manickavel S, Hafner M.

Methods Mol Biol. 2016;1358:153-73. doi: 10.1007/978-1-4939-3067-8_10.

16.

The elongation factor eEF3 (Yef3) interacts with mRNA in a translation independent manner.

Samra N, Atir-Lande A, Pnueli L, Arava Y.

BMC Mol Biol. 2015 Sep 24;16:17. doi: 10.1186/s12867-015-0045-5.

17.

High-resolution profiling of protein occupancy on polyadenylated RNA transcripts.

Munschauer M, Schueler M, Dieterich C, Landthaler M.

Methods. 2014 Feb;65(3):302-9. doi: 10.1016/j.ymeth.2013.09.017. Epub 2013 Oct 1.

18.

CLIPdb: a CLIP-seq database for protein-RNA interactions.

Yang YC, Di C, Hu B, Zhou M, Liu Y, Song N, Li Y, Umetsu J, Lu ZJ.

BMC Genomics. 2015 Feb 5;16:51. doi: 10.1186/s12864-015-1273-2.

19.

Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.

Holmes RK, Tuck AC, Zhu C, Dunn-Davies HR, Kudla G, Clauder-Munster S, Granneman S, Steinmetz LM, Guthrie C, Tollervey D.

PLoS Genet. 2015 Dec 22;11(12):e1005735. doi: 10.1371/journal.pgen.1005735. eCollection 2015 Dec.

20.

Coordinating expression of RNA binding proteins with their mRNA targets.

Jiang H, Xu L, Wang Z, Keene J, Gu Z.

Sci Rep. 2014 Nov 24;4:7175. doi: 10.1038/srep07175.

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