(Q34842023)

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Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels

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Europe PubMed Central

4 August 2017

Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels (English)

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4 August 2017

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5 June 2020

Jurgen R. Haanstra

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Barbara Marleen Bakker

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Mark Ryten

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Dorothea Droll

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Valentin Färber

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Clemetine Merce

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Christine Clayton

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15 September 2014

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Molecular Microbiology

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307-326

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5 June 2020

describes a project that uses

object named as

DESeq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

Depletion of the Trypanosome Pumilio domain protein PUF2 or of some other essential proteins causes transcriptome changes related to coding region length

1 reference

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8 July 2018

Trypanosome MKT1 and the RNA-binding protein ZC3H11: interactions and potential roles in post-transcriptional regulatory networks

1 reference

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8 July 2018

Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

The CAF1-NOT complex of trypanosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

mRNA quality control goes transcriptional.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

The regulation of trypanosome gene expression by RNA-binding proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Global identification of conserved post-transcriptional regulatory programs in trypanosomatids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

The roles of 3'-exoribonucleases and the exosome in trypanosome mRNA degradation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Pyrimidine biosynthesis is not an essential function for Trypanosoma brucei bloodstream forms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Complex degradation processes lead to non-exponential decay patterns and age-dependent decay rates of messenger RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Trypanosome CNOT10 is essential for the integrity of the NOT deadenylase complex and for degradation of many mRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Pyrimidine salvage in Trypanosoma brucei bloodstream forms and the trypanocidal action of halogenated pyrimidines

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Extensive degradation of RNA precursors by the exosome in wild-type cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Transcription-associated quality control of mRNP.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

The control of elongation by the yeast Ccr4-not complex

1 reference

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8 July 2018

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

1 reference

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8 July 2018

Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Depletion of trypanosome CTR9 leads to gene expression defects

1 reference

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8 July 2018

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

1 reference

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8 July 2018

Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Dual targeting of isoleucyl-tRNA synthetase in Trypanosoma brucei is mediated through alternative trans-splicing

1 reference

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8 July 2018

Nuclear quality control of RNA polymerase II transcripts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Posttranscriptional control and the role of RNA-binding proteins in gene regulation in trypanosomatid protozoan parasites

1 reference

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8 July 2018

The role of the 5'-3' exoribonuclease XRNA in transcriptome-wide mRNA degradation

1 reference

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8 July 2018

Gene expression in Trypanosoma brucei: lessons from high-throughput RNA sequencing

1 reference

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8 July 2018

Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Global quantification of mammalian gene expression control

1 reference

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8 July 2018

Trans-splicing in trypanosomes: machinery and its impact on the parasite transcriptome

1 reference

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8 July 2018

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Nascent transcript sequencing visualizes transcription at nucleotide resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Cell biology of the trypanosome genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Differential expression analysis for sequence count data

1 reference

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8 July 2018

The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution

1 reference

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8 July 2018

Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development

1 reference

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8 July 2018

Trans-acting proteins regulating mRNA maturation, stability and translation in trypanosomatids

1 reference

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8 July 2018

The silicon trypanosome.

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8 July 2018

Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites

1 reference

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8 July 2018

Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Genome-wide computational identification of functional RNA elements in Trypanosoma brucei

1 reference

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8 July 2018

The role of deadenylation in the degradation of unstable mRNAs in trypanosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Transcriptionally active TFIIH of the early-diverged eukaryote Trypanosoma brucei harbors two novel core subunits but not a cyclin-activating kinase complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Multiple roles for polypyrimidine tract binding (PTB) proteins in trypanosome RNA metabolism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Identification and characterization of nuclear non-canonical poly(A) polymerases from Trypanosoma brucei

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Heat shock causes a decrease in polysomes and the appearance of stress granules in trypanosomes independently of eIF2(alpha) phosphorylation at Thr169

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

The RNA-binding protein TbDRBD3 regulates the stability of a specific subset of mRNAs in trypanosomes

1 reference

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8 July 2018

A role for Caf1 in mRNA deadenylation and decay in trypanosomes and human cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Trypanosome MTR4 is involved in rRNA processing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

In vivo dynamics of RNA polymerase II transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Roles of a Trypanosoma brucei 5'->3' exoribonuclease homolog in mRNA degradation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

COPASI--a COmplex PAthway SImulator

1 reference

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8 July 2018

Post-transcriptional control of nuclear-encoded cytochrome oxidase subunits in Trypanosoma brucei: evidence for genome-wide conservation of life-cycle stage-specific regulatory elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Energy metabolism of trypanosomatids: adaptation to available carbon sources

1 reference

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8 July 2018

Microarray detection of novel nuclear RNA substrates for the exosome.

1 reference

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8 July 2018

Gene transcription in trypanosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Systematic study of sequence motifs for RNA trans splicing in Trypanosoma brucei

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Tagging a T. brucei RRNA locus improves stable transfection efficiency and circumvents inducible expression position effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Developmentally regulated instability of the GPI-PLC mRNA is dependent on a short-lived protein factor

1 reference

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8 July 2018

Endocytosis, membrane recycling and sorting of GPI-anchored proteins: Trypanosoma brucei as a model system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Exploration of essential gene functions via titratable promoter alleles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

A role for the exosome in the in vivo degradation of unstable mRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Sequence elements in both the intergenic space and the 3' untranslated region of the Crithidia fasciculata KAP3 gene are required for cell cycle regulation of KAP3 mRNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Degradation of the unstable EP1 mRNA in Trypanosoma brucei involves initial destruction of the 3'-untranslated region

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Mechanisms of developmental regulation in Trypanosoma brucei: a polypyrimidine tract in the 3'-untranslated region of a surface protein mRNA affects RNA abundance and translation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Temporal order of RNA-processing reactions in trypanosomes: rapid trans splicing precedes polyadenylation of newly synthesized tubulin transcripts

1 reference

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8 July 2018

Differential response to RNA trans-splicing signals within the phosphoglycerate kinase gene cluster in Trypanosoma brucei

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Intergenic regions between tandem gp63 genes influence the differential expression of gp63 RNAs in Leishmania chagasi promastigotes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

Maturation of polycistronic pre-mRNA in Trypanosoma brucei: analysis of trans splicing and poly(A) addition at nascent RNA transcripts from the hsp70 locus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4285177

8 July 2018

The stage-regulated expression of Leishmania mexicana CPB cysteine proteases is mediated by an intercistronic sequence element

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

The Trypanosoma brucei mitochondrial ATP synthase is developmentally regulated at the level of transcript stability.

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

Trypanosome alternative oxidase is regulated post-transcriptionally at the level of RNA stability.

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome.

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

Regulated expression of glycosomal phosphoglycerate kinase in Trypanosoma brucei.

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

Cycloheximide-mediated accumulation of transcripts from a procyclin expression site depends on the intergenic region.

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

Proline metabolism in procyclic Trypanosoma brucei is down-regulated in the presence of glucose

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

Transcriptome-wide analysis of exosome targets

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

1 reference

https://api.crossref.org/works/10.1111%2FMMI.12764

21 January 2018

Identifiers

10.1111/MMI.12764

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25145465%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25145465%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25145465%20AND%20SRC:MED&resulttype=core&format=json

5 June 2020

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