NDLI: Protein-RNA networks revealed through covalent RNA marks.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Lapointe, Christopher P. Wilinski, Daniel Saunders, Harriet A. J. Wickens, Marvin
Description	Country affiliation: United States Author Affiliation: Lapointe CP ( Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.); Wilinski D ( Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.); Saunders HA ( Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.); Wickens M ( Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.)
Abstract	Protein-RNA networks are ubiquitous and central in biological control. We present an approach termed RNA Tagging that enables the user to identify protein-RNA interactions in vivo by analyzing purified cellular RNA, without protein purification or cross-linking. An RNA-binding protein of interest is fused to an enzyme that adds uridines to the end of RNA. RNA targets bound by the chimeric protein in vivo are covalently marked with uridines and subsequently identified from extracted RNA via high-throughput sequencing. We used this approach to identify hundreds of RNAs bound by a Saccharomyces cerevisiae PUF protein, Puf3p. The results showed that although RNA-binding proteins productively bind specific RNAs to control their function, they also 'sample' RNAs without exerting a regulatory effect. We used the method to uncover hundreds of new and likely regulated targets for a protein without canonical RNA-binding domains, Bfr1p. RNA Tagging is well suited to detect and analyze protein-RNA networks in vivo.
File Format	HTM / HTML
ISSN	15487091
e-ISSN	15487105
DOI	10.1038/nmeth.3651
Journal	Nature Methods
Issue Number	12
Volume Number	12
Language	English
Publisher	Nature Publishing Group
Publisher Date	2015-12-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Clinical Laboratory Techniques Rna, Fungal Metabolism Rna, Messenger Rna-binding Proteins Repressor Proteins Saccharomyces Cerevisiae Proteins Saccharomyces Cerevisiae 3' Untranslated Regions Genetics Binding Sites Protein Binding Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Cell Biology Biochemistry Molecular Biology Biotechnology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast.

Transcript leader regions of two Saccharomyces cerevisiae mRNAs contain internal ribosome entry sites that function in living cells.

High-resolution mapping of transcription factor binding sites on native chromatin.

Techniques: Exploring protein-RNA interactions with RNA Tagging.

Multiple Myo4 motors enhance ASH1 mRNA transport in Saccharomyces cerevisiae

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.

Structural biology of poly(A) site definition.

Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site.

The transcriptional repressor activator protein Rap1p is a direct regulator of TATA-binding protein.

Protein-RNA networks revealed through covalent RNA marks.

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DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast.

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Techniques: Exploring protein-RNA interactions with RNA Tagging.

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