Dynamic mRNA stability changes buffer transcriptional activation during neuronal differentiation and are regulated by RNA binding proteins

Abstract

The steady state levels of mRNA are outcomes of a finely tuned interplay between RNA transcription and decay. Therefore, the modulation of RNA stability is generally assumed to influence RNA abundance in a positive direction. However, the correlation between mRNA transcription, translation and stability remains elusive. Here, we employed a newly developed simplified mRNA stability profiling technique to explore the role of mRNA stability in SH-SY5Y neuronal differentiation model. Transcriptome-wide mRNA stability analysis revealed neural-specific RNA stability kinetics, including stabilization of transcripts encoding regulators of neuronal morphogenesis and function and destabilization of mitochondrial electron transport and redox homeostasis. When we further examined the relationship between transcription, translation and mRNA stability, a bidirectional regulation of RNA stability was revealed, wherein mRNA stability could either exert the buffering effect on gene products or change in a same direction as transcription. Motif analysis unveiled SAMD4A as a major regulator of the dynamic changes in mRNA stability observed during differentiation. Knockdown of SAMD4A impaired neuronal differentiation and influenced the response to oxidative stress. Mechanistically, SAMD4A was found to alter the stability of several mRNAs to which it binds. Meanwhile, a dimorphic pattern of the correlation between gene expression and SAMD4A-regulated mRNA stability was observed, suggesting dynamic regulation mRNA stability during the neuronal differentiation guided by SAMD4A. The novel insights into the interplay between mRNA stability and cellular behaviors provide a foundation for understanding neurodevelopmental processes and neurodegenerative disorders and highlights dynamic mRNA stability as an important layer of gene expression regulation.

Angiogenin regulates mitochondrial stress and function via tRNA-derived fragments generation and impacting tRNA modifications

“…Ribo-seq data analysis was conducted as previously reported 44,73 . In brief, Seqprep was used to remove adapters and low-quality reads.…”

“…Ribosome profiling was conducted in accordance with our prior work 73 , adapting a protocol with minor adjustments as outlined by 74 . Subsequent to sample collection, ribosome foot-printing involved the addition of 1.25 U/μL RNase I (NEB Cat# M0243L) to 500 μL clarified lysate, followed by 45 minutes incubation at RT on a rotator mixer.…”

tRNA modifications inform tissue specific mRNA translation and codon optimization

“…Ribosome profiling was performed as we previously reported (57), which was based on another protocol with few modifications (58). Ribosome foot-printing was performed on samples collected as mentioned above by adding 1.25 U/μl RNase I (NEB, #M0243L) to 500 μl clarified lysate and incubating samples on a rotator mixer for 45 min at room temperature.…”