Global coordination of transcriptional control and mRNA decay during cellular differentiation

Abstract

We have systematically identified the targets of the Schizosaccharomyces pombe RNA-binding protein Meu5p, which is transiently induced during cellular differentiation. Meu5p-bound transcripts (>80) are expressed at low levels and have shorter half-lives in meu5 mutants, suggesting that Meu5p binding stabilizes its RNA targets.Most Meu5p targets are induced during differentiation by the activity of the Mei4p transcription factor. However, although most Mei4p targets display a sharp peak of expression, Meu5p targets are expressed for a longer period. In the absence of Meu5p, all Mei4p targets are expressed with similar kinetics (similar to non-Meu5p targets). Therefore, Meu5p determines the temporal profile of its targets.As the meu5 gene is itself a target of the transcription factor Mei4p, the RNA-binding protein Meu5p and their shared targets form a feed-forward loop (FFL), a network motif that is common in transcriptional networks.Our data highlight the importance of considering both transcriptional and posttranscriptional controls to understand dynamic changes in RNA levels, and provide insight into the structure of the regulatory networks that integrate transcription and RNA decay.

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

“…S4), compared with 12 min for Sc. As expected, the cDTA-derived Sp half-lives show a fair correlation with half-lives obtained by another nonperturbing metabolic labeling (Amorim et al 2010). Furthermore, reprocessing the data of Amorim et al (2010) with our cDTA algorithm, which takes into account the labeling bias and an additional parameter to correct for cell growth, increases the correlation to our results and leads to a median half-life of 50 min, in good agreement with an estimate of 59 min in our study (Supplemental Fig.…”

Functional characterization of Upf1 targets inSchizosaccharomyces pombe

“…36 For upf2 and upf3 mutants, we selected as differentially expressed those genes that showed differences of at least 1.5-fold in two independent biological replicates. RIpchip targets were identified as described 37 using custom-made scripts written in R. Upf1 targets identified by RIp-chip were not enriched in RNAs present in RIp-chip experiments using untagged strains or other RNA-binding proteins, 37 demonstrating the specificity of the protocol.…”

The influence of nuclear compartmentalisation on stochastic dynamics of self-repressing gene expression

“…We found values for mean mRNA levels (m), mean protein levels (p), mRNA decay rates (d 2 ) and protein decay rates (d 4 ) for 2390 different unique genes from experimental papers (Marguerat et al, 2012;Amorim et al, 2010;Christiano et al, 2014). These parameters and the correlations between them are displayed in Figure 7.…”

“…It is clear from this figure that there exists a strong correlation between mean mRNA and protein levels and weak correlation between the other parameters. (Marguerat et al, 2012;Amorim et al, 2010;Christiano et al, 2014). Histograms are shown on diagonal panels and scatter plots comparing parameters are shown on off-diagonal panels.…”

“…However, it is possible to see a few genes for which the protein decay rate is relatively slow and the correlation distance exceeds 0.2. Figure 8: Distance correlation (computed using equation (14)) comparing noise comparison results for slow protein degradation case and fast protein degradation with 2390 unique S. Pombe parameter sets (Marguerat et al, 2012;Amorim et al, 2010;Christiano et al, 2014). Black lines highlight distances of 0.2 for slow and fast protein degradation cases.…”