Gene-specific transcript buffering revealed by perturbation of coactivator complexes
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ABSTRACT:
PROVIDER: PRJNA1232156 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32577059.fastq.gz | Fastqsanger.gz | |||
| SRR32577060.fastq.gz | Fastqsanger.gz | |||
| SRR32577061.fastq.gz | Fastqsanger.gz | |||
| SRR32577062.fastq.gz | Fastqsanger.gz | |||
| SRR32577063.fastq.gz | Fastqsanger.gz |
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Project description:Transcript buffering entails reciprocal modulation of mRNA synthesis and degradation to maintain stable RNA levels under varying cellular conditions. Current models depict a global connection between mRNA synthesis and degradation, but underlying mechanisms remain unclear. Here we show that changes in RNA metabolism following depletion of TIP60/KAT5, the acetyltransferase subunit of the NuA4 transcriptional coactivator complex, reveal that transcript buffering occurs at a gene-specific level. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling in mouse embryonic stem cells, we demonstrate that transcriptional changes caused by TIP60 depletion are offset by corresponding changes in RNA nuclear export and cytoplasmic stability, indicating gene-specific buffering. Disruption of the unrelated ATAC coactivator complex also causes gene-specific transcript buffering. We propose that cells dynamically adjust RNA splicing, export, and degradation in response to individual RNA synthesis alterations, thereby sustaining cellular homeostasis.
2025-03-10 | GSE291187 | GEO
Project description:Transcript buffering entails reciprocal modulation of mRNA synthesis and degradation to maintain stable RNA levels under varying cellular conditions. Current models depict a global connection between mRNA synthesis and degradation, but underlying mechanisms remain unclear. Here, we show that changes in RNA metabolism following depletion of TIP60/KAT5, the acetyltransferase subunit of the NuA4 transcriptional coactivator complex, reveal that transcript buffering occurs at a gene-specific level. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesized transcript fractions with biophysical modeling in mouse embryonic stem cells, we demonstrate that transcriptional changes caused by TIP60 depletion are offset by corresponding changes in RNA nuclear export and cytoplasmic stability, indicating gene-specific buffering. Disruption of the unrelated ATAC coactivator complex also causes gene-specific transcript buffering. We propose that cells dynamically adjust RNA splicing, export, and degradation in response to individual RNA synthesis alterations, thereby sustaining cellular homeostasis.
| S-EPMC11922027 | biostudies-literature
Project description:The rates of mRNA synthesis and degradation determine cellular mRNA levels and can be monitored by comparative Dynamic Transcriptome Analysis (cDTA) that uses non-perturbing metabolic RNA labeling. Here we present cDTA data for 46 yeast strains lacking genes involved in mRNA degradation and metabolism. In these strains, changes in mRNA degradation rates are generally compensated by changes in mRNA synthesis rates, resulting in a buffering of mRNA levels. We show that buffering of mRNA levels requires the RNA exonuclease Xrn1. The buffering is rapidly established when mRNA synthesis is impaired, but is delayed when mRNA degradation is impaired, apparently due to Xrn1-dependent transcription repressor induction. Cluster analysis of the data defines the general mRNA degradation machinery, reveals different substrate preferences for the two mRNA deadenylase complexes Ccr4-Not and Pan2-Pan3, and unveils an interwoven cellular mRNA surveillance network. For this purpose, cDTA was carried out as described in Sun et.al. Genome Res. 2012 (DOI:10.1101/gr.130161.111). S. cerevisiae cultures were grown at 30¡ãC in 50 ml aliquots of YPD medium. S. pombe cultures were grown at 32¡ãC in YES medium. For inhibitor perturbation, BY4741 cells (OD600=0.1) were inoculated from a saturated overnight culture in two 100 ml aliquots of YPD liquid medium, incubated at 30¡ãC and grown to early-log phase (OD600=0.8). Cells were labeled for 6 minutes (sample 0 min). Then cycloheximide was added and cells were labeled for 10 minutes and 60 minutes. Cells were harvested and treated as described in Sun et.al. Genome Res. 2012 (DOI:10.1101/gr.130161.111). 1,10-Phenanthroline was added to the culture to a final concentration of 25 _g/ml as described (Dori-Bachash et al., 2012), and labeled for 6 minutes after 18 minutes treatment. Cells were treated as above. For the anchor-away analysis, S. cerevisiae cells (OD600=0.1) were cultured in two 200 ml aliquots of YPD containing 1_g/ml rapamycin and incubated at 30¡ãC untill OD600 reached 0.8. Due to the instability of rapamycin, we added 1_g/ml rapamycin every two hours. Then a 20 ml sample was taken and labeled with 4sU. The cells were then treated as described in Sun et.al. Genome Res. 2012 (DOI:10.1101/gr.130161.111).
2013-10-18 | E-MTAB-1525 | biostudies-arrayexpress
Project description:ABSTRACT. Many cellular functions are ensured by the activity of multimolecular complexes and homeostatic mechanisms ensure their stoichiometric assembly. Disruption of individual complex components can perturb this process and induce local adaptive responses. In addition to cell-autonomous effects, such surveillance systems are also active at the organismal level: cellular stress in one tissue can be sensed systemically and lead to adaptive responses in other tissues during aging and disease, as found for muscle-to-central nervous system (CNS) stress signaling, Here, we have examined the local and systemic stress responses induced by the genetic perturbation of distinct molecular complexes, i.e. the sarcomere, mitochondrial complex I, proteasome, and VCP (valosin-containing protein) complex. Surprisingly, we find that a conserved stress response is induced locally in muscle and systemically following the muscle-specific RNAi for components of these diverse multimolecular complexes. These local and systemic responses are centered on the transcriptional induction of proteases and peptidases, many of which can degrade an aggregation-prone model protein, huntingtin-polyQ. The myokine Amyrel is a possible mediator of this muscle-to-CNS signaling because it was previously found to be triggered by proteasome stress in muscle and to regulate protease expression in the CNS. In agreement with this model, here we find that Amyrel expression is induced by perturbation of diverse multimolecular complexes. Moreover, Amyrel induction in muscle reduces pathogenic huntingtin-polyQ aggregates in the retina. These findings therefore suggest that Amyrel contributes to reshaping CNS proteostasis in response to perturbation of multimolecular complexes in skeletal muscle. Altogether, our study provides insight into a muscle-to-CNS systemic response that conveys the status of multimolecular complexes of skeletal muscle.
2025-10-22 | GSE299453 | GEO
Project description:RNA buffering upon transcriptional distorsion
| PRJNA1112890 | ENA
Project description:Translational buffering refers to the regulation of ribosome occupancy to offset the effects of transcriptional variation. While previous work reported translational buffering in a limited set of conditions, it remains unknown whether this is an intrinsic property of specific genes across a large number of different cell types. To identify genes exhibiting this phenomenon on a global scale and across different experimental conditions, we uniformly analyzed 1515 matched ribosome profiling and RNA-seq datasets from human and mouse tissues or cell lines. This resource enabled us to determine the set of genes exhibiting translational buffering by comparative analysis of variation at ribosome occupancy and the RNA levels across cell types and the relationship between mRNA abundance and translation efficiency. We demonstrate that translational buffering is a conserved property of genes using homologous gene pairs from humans and mice. Genes exhibiting translational buffering have lower variation in protein abundance in cancer cell lines, primary human tissues and mouse samples. Moreover, we observed that translationally buffered genes are more likely to be haploinsufficient and triplosensitive suggesting a demand for stringent dosage limits in these genes. We hypothesized two models of translational buffering, namely “differential accessibility model” and “change in translation initiation rate model”. Our experiment suggests that some transcripts conform to the former and others align with the alternate model. Overall, our work broadens the catalog of genes subjected to translational buffering, underscores the characteristics of genes that demonstrate this phenomenon and additionally provides an insight into the rationale driving this effect.
2025-06-24 | GSE297442 | GEO
Project description:The change in abundance of individual mRNAs as cells differentiate through neurodevelopmental stages is generally attributed to transcription level alterations while the potential contribution of mRNA half-life is commonly overlooked. While some genes are regulated solely by transcription, others may be regulated by mRNA half-life only, or genes with changed transcription rates could be buffered by compensating half-life decreases or even boosted by amplifying half-life increases. In addition, during neurodevelopment there is widespread 3ʹUTR lengthening that could be shaped by differential shifts in the stability of transcript isoforms. Here we measure transcription rate and mRNA half-life changes during induced Pluripotent Stem Cell-derived neuronal development using RATE-seq at the resolution of gene isoforms. We found that during transitions to progenitor and neuron stages, transcript buffering occurs in up to half of all genes. Half-life only changes are observed in as many genes as transcription rate only changes, and almost 10% of genes exhibit transcript boosting. Global mRNA half-life decreases two-fold in neurons relative to iPSCs. The observed mRNA destabilization differentially affects gene isoforms and contributes to 3ʹUTR lengthening. Small RNA sequencing further captured an increase in microRNA copy number per cell. We propose that mRNA destabilization and 3ʹUTR lengthening are driven in part by an increase in microRNA load. Our findings identify mRNA stability mechanisms in human neurodevelopment that regulate gene and isoform level abundance and provide a precedent for similar post-transcriptional regulatory events as other tissues develop.
2023-09-01 | GSE212990 | GEO
Project description:Differences in gene regulation between human and closely related species influence phenotypes that are distinctly human. While gene regulation is a multi-step process, the majority of research concerning divergence in gene regulation among primates has focused on transcription. To gain a comprehensive view of gene regulation, we surveyed genome-wide ribosome occupancy, which reflects levels of protein translation, in lymphoblastoid cell lines derived from human, chimpanzee and rhesus macaque. We further integrated mRNA and protein level measurements collected from matching cell lines. We find that, in addition to transcriptional regulation, the major factor determining protein level divergence between human and closely related species is post-translational buffering. Inter-species divergence in transcription is generally propagated to the level of protein translation. In contrast, gene expression divergence is often attenuated post-translationally, potentially mediated through post-translational modifications. Results from our analysis indicate that post-translational buffering is a conserved mechanism that led to relaxation of selective constraint on transcript levels in humans.
2018-05-10 | GSE71808 | GEO
Project description:Transcript buffering and 3ʹUTR lengthening are shaped during human neurodevelopment by shifts in mRNA stability and microRNA load
| PRJNA878683 | ENA
Project description:To understand the precise mechanism that guide the formation of multisubunit complexes is of key importance. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here we demonstrate that the distinct modules of ATAC (ADA Two A Containing) and SAGA (SPT ADA GCN5 Acetyltransferase), two lysine acetyl transferase-containing transcription coactivator complexes, assemble co-translationally in the cytoplasm of mammalian cells. Fully assembled SAGA complex forms in the cytoplasm of mammalian cells and cytoplasmic SAGA acetylates non-histones proteins, before imported in the nucleus. In contrast, ATAC has no cytoplasmic functions as it cannot be detected in the cytoplasm of mammalian cells. However, fully assembled endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related co-activators, ATAC and SAGA, assemble by using co-translational pathways, but their subcellular localization, cytoplasmic detectability and functions are distinct.
2023-09-27 | PXD038695 | Pride