Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA)

Schwalb, Björn; Schulz, Daniel; Sun, Mai; Zacher, Benedikt; Dümcke, Sebastian; Martin, Dietmar E.; Cramer, Patrick; Tresch, Achim

doi:10.1093/bioinformatics/bts052

Cited by 30 publications

(28 citation statements)

References 7 publications

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“…For example, as the transcription of a gene increases, so does its decay rate in a compensatory response called buffering (3,10). The factors and pathways involved in this process are starting to be identified, but the mechanism of this phenomenon is not known.…”

Section: Discussionmentioning

confidence: 99%

The Rpb4/7 Module of RNA Polymerase II Is Required for Carbon Catabolite Repressor Protein 4-Negative on TATA (Ccr4-Not) Complex to Promote Elongation

Babbarwal

Reese

2014

Journal of Biological Chemistry

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Background: mRNA transcription and decay are coordinated processes. Results: The Rpb4/7 module of RNA polymerase II is required for the transcription and mRNA decay factor Ccr4-Not to associate with elongation complexes. Conclusion: Association between these two entities is required for Ccr4-Not to promote transcription elongation. Significance: Our work provides molecular insights into how transcription and mRNA decay are linked.

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Section: Discussionmentioning

confidence: 99%

The Rpb4/7 Module of RNA Polymerase II Is Required for Carbon Catabolite Repressor Protein 4-Negative on TATA (Ccr4-Not) Complex to Promote Elongation

Babbarwal

Reese

2014

Journal of Biological Chemistry

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“…Data Analysis-Analysis of data from cDTA was carried out as described (1) using R/Bioconductor and the DTA package (27). Because we used a mixture of S. cerevisiae and S. pombe cells, we used a custom probe annotation environment (cdf) to exclude cross-hybridization probes from our analyses.…”

Section: Methodsmentioning

confidence: 99%

Rpb4 Subunit Functions Mainly in mRNA Synthesis by RNA Polymerase II

Schulz

Pirkl

Lehmann

et al. 2014

Journal of Biological Chemistry

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Background:The RNA polymerase II (Pol II) subunit Rpb4 was reported to function in mRNA degradation. Results: Rpb4 deletion causes defects in mRNA synthesis and compensatory changes in mRNA degradation. Covalent attachment of Rpb4 to the Pol II core largely restores mRNA metabolism. Conclusion: Rpb4 is an integral part of Pol II and functions mainly in Pol II transcription. Significance: Rpb4 functions mainly in transcription.

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“…Given our labeling time, the differences of both approaches are negligible. The whole analysis workflow has been carried out using the open source R/Bioconductor package DTA (Schwalb et al 2012). …”

Section: Cdta Data Analysismentioning

confidence: 99%

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

Sun

Schwalb²,

Schulz³

et al. 2012

Genome Res.

288

377

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To monitor eukaryotic mRNA metabolism, we developed comparative dynamic transcriptome analysis (cDTA). cDTA provides absolute rates of mRNA synthesis and decay in Saccharomyces cerevisiae (Sc) cells with the use of Schizosaccharomyces pombe (Sp) as an internal standard. cDTA uses nonperturbing metabolic labeling that supersedes conventional methods for mRNA turnover analysis. cDTA reveals that Sc and Sp transcripts that encode orthologous proteins have similar synthesis rates, whereas decay rates are fivefold lower in Sp, resulting in similar mRNA concentrations despite the larger Sp cell volume. cDTA of Sc mutants reveals that a eukaryote can buffer mRNA levels. Impairing transcription with a point mutation in RNA polymerase (Pol) II causes decreased mRNA synthesis rates as expected, but also decreased decay rates. Impairing mRNA degradation by deleting deadenylase subunits of the Ccr4-Not complex causes decreased decay rates as expected, but also decreased synthesis rates. Extended kinetic modeling reveals mutual feedback between mRNA synthesis and degradation that may be achieved by a factor that inhibits synthesis and enhances degradation.

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Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA)

Cited by 30 publications

References 7 publications

The Rpb4/7 Module of RNA Polymerase II Is Required for Carbon Catabolite Repressor Protein 4-Negative on TATA (Ccr4-Not) Complex to Promote Elongation

The Rpb4/7 Module of RNA Polymerase II Is Required for Carbon Catabolite Repressor Protein 4-Negative on TATA (Ccr4-Not) Complex to Promote Elongation

Rpb4 Subunit Functions Mainly in mRNA Synthesis by RNA Polymerase II

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

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