Codon choice directs constitutive mRNA levels in trypanosomes

Nascimento, Janaína de Freitas; Kelly, Steven; Sunter, Jack D.; Carrington, Mark

doi:10.7554/elife.32467

Cited by 67 publications

(62 citation statements)

References 80 publications

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“…Correlation of different transcriptome analyses12,21,[25][26][27] and this study (3x oligo capture). Pearson coefficients were calculated based on the relative abundance of transcripts, excluding rRNA transcripts.…”

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confidence: 77%

“…The ribo(-) kit and different poly(A) RNA-seq datasets derived from previous studies were downloaded from NCBI SRA (accession number: SRP042959 12 ) and EBI ENA (accession numbers: PRJEB8747 21 ; PRJNA287144 25 ; PRJEB22797 26 ; PRJEB14403 27 ). For correlation analyses, transcripts per million were calculated for each dataset in the non-alignment-based mode with SALMON 28 using the transcriptome of T. brucei Lister 427 (release 36, downloaded from TriTrypDB 18 as reference and normalized to the total number of transcripts excluding the number of rRNA transcripts.…”

Section: Comparison Of Ribo(-) and Poly(a) Rna-seq Analysismentioning

confidence: 99%

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Efficient and specific oligo-based depletion of rRNA

Kraus

Brink

Siegel

2019

Preprint

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In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA or other highly abundant transcripts is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences.In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects.By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.

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mentioning

confidence: 77%

Section: Comparison Of Ribo(-) and Poly(a) Rna-seq Analysismentioning

confidence: 99%

Efficient and specific oligo-based depletion of rRNA

Kraus

Brink

Siegel

2019

Preprint

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show abstract

“…It is also important to make the distinction that common and rare codons do not necessarily imply optimal and non-optimal codons. At present, codon optimality-mediated decay has been extensively studied and established particularly in Saccharomyces cerevisiae as well as other model organisms such as Schizosaccharomyces pombe, Drosophila melanogaster, Danio rerio, Escherichia coli, Trypanosoma brucei, and Neurospora crassa [21][22][23][24][25][26][27]. At present, the molecular mechanisms of this system of codon optimality in humans are under intense scrutiny [28, preprint: 29].…”

Section: Introductionmentioning

confidence: 99%

Codon bias confers stability to humanmRNAs

et al. 2019

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Codon bias has been implicated as one of the major factors contributing to mRNA stability in several model organisms. However, the molecular mechanisms of codon bias on mRNA stability remain unclear in humans. Here, we show that human cells possess a mechanism to modulate RNA stability through a unique codon bias. Bioinformatics analysis showed that codons could be clustered into two distinct groups-codons with G or C at the third base position (GC3) and codons with either A or T at the third base position (AT3): the former stabilizing while the latter destabilizing mRNA. Quantification of codon bias showed that increased GC3-content entails proportionately higher GC-content. Through bioinformatics, ribosome profiling, and in vitro analysis, we show that decoupling the effects of codon bias reveals two modes of mRNA regulation, one GC3-and one GC-content dependent. Employing an immunoprecipitation-based strategy, we identify ILF2 and ILF3 as RNA-binding proteins that differentially regulate global mRNA abundances based on codon bias. Our results demonstrate that codon bias is a two-pronged system that governs mRNA abundance.

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“…Interestingly, the codon usage also has a major impact on gene expression (de Freitas Nascimento et al. ) since it can control the mRNA stability and ribosome occupancy (Jeacock et al. ).…”

Section: Discussionmentioning

confidence: 99%

The Trypanosoma brucei RNA‐Binding Protein TbRRM1 is Involved in the Transcription of a Subset of RNA Pol II‐Dependent Genes

Bañuelos

Levy

Níttolo

et al. 2019

J Eukaryotic Microbiology

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It has been long thought that RNA Polymerase (Pol) II transcriptional regulation does not operate in trypanosomes. However, recent reports have suggested that these organisms could regulate RNA Pol II transcription by epigenetic mechanisms. In this paper, we investigated the role of TbRRM1 in transcriptional regulation of RNA Pol II‐dependent genes by focusing both in genes located in a particular polycistronic transcription unit (PTU) and in the monocistronic units of the SL‐RNA genes. We showed that TbRRM1 is recruited throughout the PTU, with a higher presence on genes than intergenic regions. However, its depletion leads both to the decrease of nascent RNA and to chromatin compaction only of regions located distal to the main transcription start site. These findings suggest that TbRRM1 facilitates the RNA Pol II transcriptional elongation step by collaborating to maintain an open chromatin state in particular regions of the genome. Interestingly, the SL‐RNA genes do not recruit TbRRM1 and, after TbRRM1 knockdown, nascent SL‐RNAs accumulate while the chromatin state of these regions remains unchanged. Although it was previously suggested that TbRRM1 could regulate RNA Pol II‐driven genes, we provide here the first experimental evidence which involves TbRRM1 to transcriptional regulation.

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Codon choice directs constitutive mRNA levels in trypanosomes

Cited by 67 publications

References 80 publications

Efficient and specific oligo-based depletion of rRNA

Efficient and specific oligo-based depletion of rRNA

Codon bias confers stability to humanmRNAs

The Trypanosoma brucei RNA‐Binding Protein TbRRM1 is Involved in the Transcription of a Subset of RNA Pol II‐Dependent Genes

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