Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data (Q30729776)

20 August 2017

Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data (English)

1 reference

20 August 2017

Cheng-Yu Hou

1

1 reference

20 August 2017

Ming-Tsung Wu

2

1 reference

20 August 2017

Shin-Hua Lu

3

1 reference

20 August 2017

Yue-Ie Hsing

4

1 reference

20 August 2017

Ho-Ming Chen

5

1 reference

20 August 2017

language of work or name

English

0 references

publication date

10 January 2014

1 reference

20 August 2017

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20 August 2017

15

1 reference

20 August 2017

15

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-15

20 August 2017

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cites work

A compendium of RNA-binding motifs for decoding gene regulation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Cloning and characterization of maize miRNAs involved in responses to nitrogen deficiency

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Short non-coding RNA fragments accumulating in chloroplasts: footprints of RNA binding proteins?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Smad proteins bind a conserved RNA sequence to promote microRNA maturation by Drosha

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Transcriptome-wide identification of microRNA targets in rice

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Rice MicroRNA effector complexes and targets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Molecular characterization of Arabidopsis thaliana PUF proteins--binding specificity and target candidates

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Small RNAs derived from snoRNAs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

MEME SUITE: tools for motif discovery and searching

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Site-specific binding of a PPR protein defines and stabilizes 5' and 3' mRNA termini in chloroplasts

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Small silencing RNAs: an expanding universe

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Deadenylation is a widespread effect of miRNA regulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

The highways and byways of mRNA decay

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

RNA-quality control by the exosome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Crystal structure of Argonaute and its implications for RISC slicer activity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Evidence that polyadenylation factor CPSF-73 is the mRNA 3' processing endonuclease.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

The expanding snoRNA world

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Modular recognition of RNA by a human pumilio-homology domain

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Biogenesis of small nucleolar ribonucleoproteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Exosome-mediated recognition and degradation of mRNAs lacking a termination codon

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

An mRNA surveillance mechanism that eliminates transcripts lacking termination codons

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

PUM2, a novel murine puf protein, and its consensus RNA-binding site

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Identification of a regulated pathway for nuclear pre-mRNA turnover.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

The Pumilio RNA-binding domain is also a translational regulator.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Direct binding of Smad3 and Smad4 to critical TGF beta-inducible elements in the promoter of human plasminogen activator inhibitor-type 1 gene

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Processing of the precursors to small nucleolar RNAs and rRNAs requires common components

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Mechanism and regulation of mRNA polyadenylation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

Cleavage and polyadenylation factor CPF specifically interacts with the pre-mRNA 3' processing signal AAUAAA

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898255

AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets

14 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-15

A link between RNA metabolism and silencing affecting Arabidopsis development.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-15

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-15

Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-15

Global identification of miRNAs and targets in Populus euphratica under salt stress

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24405808

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-15-15

1 reference

Dimensions Publication ID

20 August 2017

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-15

Fatcat ID

release_odg55vric5frrnapnfi5ik6ci4

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/odg55vric5frrnapnfi5ik6ci4

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

20 August 2017

1 reference