(Q33742594)

29 July 2017

title

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae (English)

1 reference

29 July 2017

0 references

Saccharomyces cerevisiae

1 reference

Mallory A Freeberg

1

1 reference

29 July 2017

Ting Han

2

1 reference

29 July 2017

James J Moresco

3

1 reference

29 July 2017

Andy Kong

4

1 reference

29 July 2017

Yu-Cheng Yang

5

1 reference

29 July 2017

Zhi John Lu

6

1 reference

29 July 2017

John R Yates

7

1 reference

29 July 2017

John K Kim

8

1 reference

29 July 2017

language of work or name

1 reference

14 February 2013

1 reference

29 July 2017

1 reference

29 July 2017

volume

14

1 reference

29 July 2017

issue

2

1 reference

29 July 2017

page(s)

R13

1 reference

Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Adaptation to stress in yeast: to translate or not?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

YB-1 binds to CAUC motifs and stimulates exon inclusion by enhancing the recruitment of U2AF to weak polypyrimidine tracts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Insights into RNA biology from an atlas of mammalian mRNA-binding proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Safe keeping the message: mRNP complexes tweaking after transcription

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Gcn4p-mediated transcriptional repression of ribosomal protein genes under amino-acid starvation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Comprehensive comparative analysis of strand-specific RNA sequencing methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Robust heat shock induces eIF2alpha-phosphorylation-independent assembly of stress granules containing eIF3 and 40S ribosomal subunits in budding yeast, Saccharomyces cerevisiae.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

RNA granules: post-transcriptional and epigenetic modulators of gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

VARNA: Interactive drawing and editing of the RNA secondary structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Polysomes, P bodies and stress granules: states and fates of eukaryotic mRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

mRNA localization: gene expression in the spatial dimension

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Pre-mRNA processing reaches back to transcription and ahead to translation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

The transcriptional landscape of the yeast genome defined by RNA sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

RNA-binding proteins and post-transcriptional gene regulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Oxidative stress-activated zinc cluster protein Stb5 has dual activator/repressor functions required for pentose phosphate pathway regulation and NADPH production

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Stm1p, a ribosome-associated protein, is important for protein synthesis in Saccharomyces cerevisiae under nutritional stress conditions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

CLIP: a method for identifying protein-RNA interaction sites in living cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Repressors Nrg1 and Nrg2 regulate a set of stress-responsive genes in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

FMRP RNA targets: identification and validation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Fast and reliable prediction of noncoding RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Yeast Agp2p and Agp3p function as amino acid permeases in poor nutrient conditions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

CLIP identifies Nova-regulated RNA networks in the brain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Global analysis of protein expression in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Messenger-RNA-binding proteins and the messages they carry

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Glucose depletion rapidly inhibits translation initiation in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

The yeast inositol-sensitive upstream activating sequence, UASINO, responds to nitrogen availability

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

The Cln3 cyclin is down-regulated by translational repression and degradation during the G1 arrest caused by nitrogen deprivation in budding yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053964

Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

21 June 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2013-14-2-R13

Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2013-14-2-R13

ASH1 mRNA localization in yeast involves multiple secondary structural elementsand Ash1 protein translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2013-14-2-R13

Local RNA base pairing probabilities in large sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FGB-2013-14-2-R13

4-Thiouridine incorporation into the RNA of monkey kidney cells (CV-1) triggers near-UV light long-term inhibition of DNA, RNA and protein synthesis

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23409723

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structural elements required for the localization of ASH1 mRNA and of a green fluorescent protein reporter particle in vivo

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23409723

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

An extended RNA binding site for the yeast branch point-binding protein and the role of its zinc knuckle domains in RNA binding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23409723

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/GB-2013-14-2-R13

1 reference

Dimensions Publication ID

29 July 2017

0 references

1 reference

29 July 2017

1 reference