RNA Lifecycle Interactive Diagram

Messenger RNA (mRNA) is a large family of molecules responsible for transferring genetic information stored in DNA to the cell through its translation into functional proteins. The multi-stage “life-cycle” of mRNA—from transcription to translation and degradation—is regulated by a diverse array of RNA binding proteins (RBPs) that influence every aspect of proper and essential gene expression.

Gene expression begins with transcription, the process of creating an mRNA copy of a DNA template. To initiate this process, transcription factors and co-activators bind to DNA gene regulatory elements—promoter regions and enhancer sequences—which signal the recruitment of RNA polymerase II to form the RNA transcription complex. RNA polymerase then separates the strands of the DNA helix and synthesizes a pre-mRNA copy of the template strand by joining complementary RNA nucleotides in a 5’ to 3’ fashion.

During transcription, pre-mRNAs are assembled into ribonucleoprotein (RNP) complexes for editing and processing. These steps, which include 5’ mRNA capping, adenosine to inosine editing, m6A modification, pseudouridylation, splicing, 3’ processing, and polyadenylation, collectively ensure the stability of the mRNA transcript, regulate nuclear export, and promote efficient translation by the ribosome. Each stage requires the association and activity of distinct sets of RBPs and enzymes and is surveilled by nuclear mechanisms to prevent processing errors and safeguard gene expression. Ultimately, these events lead to the production of an export-competent mRNP that translocates through the nuclear pore to the cytoplasm, guided by the interactions of key RBPs, including NXF1, XPO1, and PHAX.

In the cytoplasm, mature RNPs interact with additional RBPs, called initiation factors, which bind to the 5’ cap and 5’ untranslated region to elicit the formation of the translation initiation complex. This multiprotein machinery facilitates the interaction between individual mRNAs and the 40S ribosomal subunit that scans the transcript for the start codon, followed by recruitment of the 60S ribosomal subunit and the start of amino acid chain elongation. Translation is further influenced by the exon-junction complex (EJC) found on mature RNPs. The EJC, which consists of RBPs including CASC3, MAGOH, RBM8A, EIF4A3, and PYM1, acts as a molecular signature of exon splicing events during mRNA processing and confers a translational enhancement; although, the exact EJC mechanism remains unresolved.

The fate of mRNAs in the cytoplasm may alternatively be influenced by RBPs that direct gene silencing via RNA interference (RNAi) or decay via mRNA surveillance mechanisms. In RNAi, small non-coding RNAs processed by Dicer target specific mRNAs and direct their enzymatic degradation by the RNA-induced silencing complex (RISC). In parallel, the fidelity of mRNA molecules is ensured by surveillance mechanisms, including nonsense-mediated decay (NMD). NMD is a conserved mechanism that detects and eliminates mRNA transcripts containing premature stop codons, thus preventing the translation of truncated proteins with dominant negative or harmful gain of function mutations. NMD can be activated in response to the presence of an EJC signal downstream of the termination codon on an RNP during translation, or in an EJC-independent fashion, regulated in part by the length of the 3’ untranslated portion of the mRNA.

As the key intermediary of gene expression, mRNA processing and translation are essential for cellular function and health. Accordingly, mutations in RBPs that lead to defects in these events have been implicated in a growing list of human diseases, including neurodegeneration and cancer, and are currently being investigated as promising targets for therapeutic intervention.

Selected Reviews:

• Gerstberger S, Hafner M, Tuschl T. A census of human RNA-binding proteins. Nat Rev Genet. 2014;15(12):829-45.
• Singh G, Pratt G, Yeo GW, Moore MJ. The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion. Annu Rev Biochem. 2015;84:325-54.
• Björk P, Wieslander L. Integration of mRNP formation and export. Cell Mol Life Sci. 2017;74(16):2875-2897.
• Le hir H, Saulière J, Wang Z. The exon junction complex as a node of post-transcriptional networks. Nat Rev Mol Cell Biol. 2016;17(1):41-54.
• Rana TM. Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol. 2007;8(1):23-36.
• Dreyfuss G, Kim VN, Kataoka N. Messenger-RNA-binding proteins and the messages they carry. Nat Rev Mol Cell Biol. 2002;3(3):195-205.
• Lykke-andersen S, Jensen TH. Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes. Nat Rev Mol Cell Biol. 2015;16(11):665-77.
• Chang YF, Imam JS, Wilkinson MF. The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem. 2007;76:51-74.
• Nussbacher JK, Batra R, Lagier-tourenne C, Yeo GW. RNA-binding proteins in neurodegeneration: Seq and you shall receive. Trends Neurosci. 2015;38(4):226-36.
• Kapeli K, Martinez FJ, Yeo GW. Genetic mutations in RNA-binding proteins and their roles in ALS. Hum Genet. 2017;136(9):1193-1214.
• Lukong KE, Chang KW, Khandjian EW, Richard S. RNA-binding proteins in human genetic disease. Trends Genet. 2008;24(8):416-25.

We would like to thank Dr. Kristopher Brannan, Department of Cellular and Molecular Medicine, University of California, San Diego, for reviewing this diagram.

Created January 2020.