From specific to global analysis of posttranscriptional regulation in eukaryotes: posttranscriptional regulatory networks (Q38057686)

27 August 2017

title

From specific to global analysis of posttranscriptional regulation in eukaryotes: posttranscriptional regulatory networks (English)

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27 August 2017

1

Sarath Chandra Janga

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language of work or name

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3 November 2012

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Briefings in functional genomics

27 August 2017

published in

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27 August 2017

volume

11

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27 August 2017

issue

6

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27 August 2017

page(s)

505-521

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Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli.

27 August 2017

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The RNA infrastructure: dark matter of the eukaryotic cell?

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Integrating post-transcriptional regulation into the embryonic stem cell gene regulatory network

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Coordinated posttranscriptional mRNA population dynamics during T-cell activation

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Gene regulation by RNA binding proteins and microRNAs in angiogenesis

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

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

21 January 2018

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CLIP identifies Nova-regulated RNA networks in the brain

21 January 2018

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

21 January 2018

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iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

21 January 2018

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RNA-binding proteins in human genetic disease

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Cell-specific RNA-binding proteins in human disease

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Emerging roles of RNA and RNA-binding protein network in cancer cells

21 January 2018

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A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation.

21 January 2018

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Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction

21 January 2018

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SVM based prediction of RNA-binding proteins using binding residues and evolutionary information.

21 January 2018

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Predicting DNA- and RNA-binding proteins from sequences with kernel methods

21 January 2018

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Protein function annotation from sequence: prediction of residues interacting with RNA.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.

21 January 2018

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Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling

21 January 2018

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Regulation of gene expression by a metabolic enzyme

21 January 2018

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21 January 2018

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Global analysis of protein activities using proteome chips

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A protocol for PAIR: PNA-assisted identification of RNA binding proteins in living cells

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

In vivo identification of ribonucleoprotein-RNA interactions

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Role of the mouse ank gene in control of tissue calcification and arthritis

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Analysis of subcellularly localized mRNAs using in situ hybridization, mRNA amplification, and expression profiling

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A three-hybrid system to detect RNA-protein interactions in vivo

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Identification of RNA-protein interaction networks using PAR-CLIP

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

SERF: in vitro election of random RNA fragments to identify protein binding sites within large RNAs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A translational repression assay procedure (TRAP) for RNA-protein interactions in vivo

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Identifying mRNAs bound by RNA-binding proteins using affinity purification and differential display

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Target RNA motif and target mRNAs of the Quaking STAR protein

21 January 2018

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

21 January 2018

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RaPID: an aptamer-based mRNA affinity purification technique for the identification of RNA and protein factors present in ribonucleoprotein complexes

21 January 2018

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Unbiased RNA-protein interaction screen by quantitative proteomics.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

The role of structural disorder in the function of RNA and protein chaperones

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A one-hybrid system for detecting RNA-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

TGF-β induces the expression of the adaptor Ndfip1 to silence IL-4 production during iTreg cell differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

An RNA map predicting Nova-dependent splicing regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Nascent transcript sequencing visualizes transcription at nucleotide resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A novel role for shuttling SR proteins in mRNA translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

SR proteins in vertical integration of gene expression from transcription to RNA processing to translation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Identification and characterization of srp1, a gene of fission yeast encoding a RNA binding domain and a RS domain typical of SR splicing factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Defining a neuron: neuronal ELAV proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

TAP, the human homolog of Mex67p, mediates CTE-dependent RNA export from the nucleus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

The RNA Modification Database, RNAMDB: 2011 update

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Grand challenge commentary: RNA epigenetics?

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

RNA editing in plant organelles: machinery, physiological function and evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Systematic discovery of structural elements governing stability of mammalian messenger RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Genome-wide analysis of mRNA decay patterns during early Drosophila development

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A universal framework for regulatory element discovery across all genomes and data types

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

MEME SUITE: tools for motif discovery and searching

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Detecting microRNA binding and siRNA off-target effects from expression data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Fast gapped-read alignment with Bowtie 2

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

TopHat: discovering splice junctions with RNA-Seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Fast and SNP-tolerant detection of complex variants and splicing in short reads

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Fast mapping of short sequences with mismatches, insertions and deletions using index structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Post-transcriptional operons and regulons co-ordinating gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Analysis of turnover and translation regulatory RNA-binding protein expression through binding to cognate mRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Exploration of biological network centralities with CentiBiN.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Network biology: understanding the cell's functional organization

21 January 2018

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https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

MicroRNAs: target recognition and regulatory functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Most mammalian mRNAs are conserved targets of microRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

MicroRNA expression profiles classify human cancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

MicroRNA regulation by RNA-binding proteins and its implications for cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Genomic analyses of the RNA-binding protein Hu antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Functional interplay between RNA-binding protein HuR and microRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Relief of microRNA-mediated translational repression in human cells subjected to stress

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

The let-7 target gene mouse lin-41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBFGP%2FELS046

21 January 2018

Identifiers

DOI

10.1093/BFGP/ELS046

1 reference

27 August 2017

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