Dynamically regulated transcription factors are encoded by highly unstable mRNAs in theDrosophilalarval brain

Abstract

The level of each RNA species depends on the balance between its rates of production and decay. Although previous studies have measured RNA decay across the genome in tissue culture and single-celled organisms, few experiments have been performed in intact complex tissues and organs. It is therefore unclear whether the determinants of RNA decay found in cultured cells are preserved in an intact tissue, and whether they differ between neighboring cell types and are regulated during development. To address these questions, we measured RNA synthesis and decay rates genome wide via metabolic labeling of whole culturedDrosophilalarval brains using 4-thiouridine. Our analysis revealed that decay rates span a range of more than 100-fold, and that RNA stability is linked to gene function, with mRNAs encoding transcription factors being much less stable than mRNAs involved in core metabolic functions. Surprisingly, among transcription factor mRNAs there was a clear demarcation between more widely used transcription factors and those that are expressed only transiently during development. mRNAs encoding transient transcription factors are among the least stable in the brain. These mRNAs are characterized by epigenetic silencing in most cell types, as shown by their enrichment with the histone modification H3K27me3. Our data suggests the presence of an mRNA destabilizing mechanism targeted to these transiently expressed transcription factors to allow their levels to be regulated rapidly with high precision. Our study also demonstrates a general method for measuring mRNA transcription and decay rates in intact organs or tissues, offering insights into the role of mRNA stability in the regulation of complex developmental programs.

Imp and Sypin vivotemporal RNA interactomes uncover networks of temporal regulators ofDrosophilabrain development

“…To characterise a further example, we calculated the RNA half-life of a late-born neuron marker jim in syp KO L3 brains. We calculated jim RNA half-life from smFISH images by relating single molecule counts of nascent and mature mRNAs (Figure S4D-E) (Halpern and Itzkovitz, 2016; Mueller et al, 2013), which yielded a value comparable to an orthogonal metabolic labelling method (Thompson et al, 2023). Here, we found significant destabilisation of jim in syp KO brains (Figure 4D and S4F), suggesting that Syp is crucial for the correct post-transcriptional regulation of jim .…”

Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing

“… 7 Second, RNA levels of TFs are unstable with short half-lives and thus may not correlate with protein levels in every circumstance. 34 Any hypotheses generated from these analyses must be further functionally validated. Here, we provide evidence in support of the hypothesis that the POU motif family members contribute to cholangiocarcinogenesis using in vitro knockout experiments of POU2F1, but further work is needed to fully understand this mechanism of action.…”