Regulation of Human mRNA Turnover

mRNA turnover plays a critical role in regulation of gene expression. With the long-term goal of understanding how mRNA decay is regulated in gene expression and disease, our lab focuses on dissecting the human cellular mRNA decay machineries.

mRNA Decay in Human Cells

Correct regulation of gene expression is essential for the growth and development of an organism. The expression of genes in the cell is to a large extent controlled at the level of mRNA accumulation. One way by which the level of a specific mRNA can be regulated is by controlling its rate of decay. The accurate regulation of mRNA turnover is a pre-requisite for sustained life, and mis-regulation of mRNA decay is associated with a range of human diseases. However, despite its importance in gene expression, the mechanism and regulation of human mRNA decay is currently poorly understood.

Many mRNAs encoding proto-oncogenes, interleukins and transcription factors contain destabilizing AU-rich elements (AREs) in their 3' untranslated regions (UTRs). Specific cell signals can transiently stabilize these mRNAs and thereby upregulate protein expression by orders of magnitude. Mis-regulation of ARE-mediated mRNA decay can lead to transformation of human cells, leading to tumor growth.

Another mRNA decay pathway, termed nonsense-mediated decay (NMD), targets mRNAs that have acquired premature translation termination codons due to failure in mRNA processing or to genetic mutation. This pathway is believed to render recessive many human genetic diseases, such as beta-thalasemia, marfans syndrome, cystic fibrosis etc, by degrading mRNAs that originate from the mutant alleles with premature termination codons. NMD also plays an important role in regulating mRNA levels from normal genes.

Eukaryotic mRNAs are protected at their 5' and 3' ends by the cap and poly(A) tail. The limiting step in decay of most mRNAs is the removal of these elements. In Saccharomyces cerevisiae, mRNAs are predominantly degraded by initial removal of the poly(A) tail, by deadenylation, followed by decapping and 5'-3' and 3'-5' exonucleolytic decay. Many of the enzyme complexes involved in these processes have been identified by genetic screens. In contrast, very little is known about human mRNA decay factors.

Current Lab Projects

Our laboratory focuses on several aspects of mRNA decay regulation in human cells, described below.

1) Regulation of ARE-mediated mRNA Decay:

An important signal for rapid mRNA turnover in mammalian cells is the AU-rich element (ARE), which is found in the 3'UTR of many unstable mRNAs. Importantly, while such mRNAs are normally rapidly degraded, specific cell signals can trigger mRNA stabilization and result in protein production. For example, ARE-mediated decay plays a prominent role in the regulation of mRNAs that encode proto-oncogenes, interleukins and cytokines. The ARE-binding protein TTP is an activator of ARE-mediated decay in human cells. TTP contains two CCCH-type zinc finger domains that are necessary and sufficient for ARE binding. In addition, two paralogs of TTP involved in ARE-mediated decay are BRF-1 and BRF-2. To understand how the TTP-family of ARE-binding proteins activate mRNA decay, we are investigating how they communicate with enzymes involved in mRNA decay. This should provide a first step to understanding the mechanism by which ARE-mediated decay can be regulated at the molecular level, to modulate gene expression.

2) The Mechanism of Nonsense-Mediated Decay:

Eukaryotic cells have evolved mechanisms to ensure the fidelity of gene expression. One such mechanism, called mRNA surveillance, ensures that only mRNAs with full coding potential are available for translation in the cytoplasm. This process detects mRNAs with truncated open reading frames and subjects them to nonsense-mediated mRNA decay (NMD). NMD thus prevents the synthesis of potentially deleterious truncated proteins and is responsible for rendering a large fraction of human disease mutations recessive. We, and others, previously identified human proteins involved in NMD, named hUpf1, hUpf2 and hUpf3. NMD depends on active translation, and the translation release factors, eRF1 and eRF3, interact with the hUpf proteins. In mammals, a premature termination codon is detected when present in the mRNA more than 50 nucleotides upstream of the last splice junction. We, and others, previously demonstrated that a multi-protein exon-junction complex (EJC), which is deposited upstream of exon-exon junctions after pre-mRNA splicing, communicates with the terminating ribosome via the hUpf proteins to identify the premature termination codons. We are currently conducting experiments to understand how the EJC communicates with the hUpf proteins and the terminating ribosome.

3) Deadenylation in Human mRNA Decay:

Deadenylation is believed to be an important rate-limiting step in mRNA decay. However, very little is known about deadenylases in human cells. Based on sequence similarity to a yeast deadenylase complex, we have identified ten putative human deadenylases. We are currently trying to establish the role of the deadenylases in the ARE- and nonsense-mediated decay pathways (see above).

4) Decapping in Human mRNA Decay :

Another important process in mRNA decay is decapping. We identified a human decapping complex that contains at least two proteins, hDcp1 and hDcp2, and we showed that the hDcp2 protein possesses catalytic activity (Lykke-Andersen, MCB, 2002). We affinity purified the decapping complex from a human cell line, and identified three new proteins in the complex. We are currently testing the importance of these novel proteins in mRNA decapping and decay.

Publications

Lardelli RM; Schaffer AE; Eggens VR; Zaki MS; Grainger S; Sathe S; Van Nostrand EL; Schlachetzki Z; Rosti B; Akizu N; Scott E; Silhavy JL; Heckman LD; Rosti RO; Dikoglu E; Gregor A; Guemez-Gamboa A; Musaev D; Mande R; Widjaja A; Shaw TL; Markmiller S; Marin-Valencia I; Davies JH; de Meirleir L; Kayserili H; Altunoglu U; Freckmann ML; Warwick L; Chitayat D; Blaser S; Çağlayan AO; Bilguvar K; Per H; Fagerberg C; Christesen HT; Kibaek M; Aldinger KA; Manchester D; Matsumoto N; Muramatsu K; Saitsu H; Shiina M; Ogata K; Foulds N; Dobyns WB; Chi NC; Traver D; Spaccini L; Bova SM; Gabriel SB; Gunel M; Valente EM; Nassogne MC; Bennett EJ; Yeo GW; Baas F; Lykke-Andersen J; Gleeson JG (2017) Biallelic mutations in the 3' exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing. 0:0-0 [pubmed]

Durand S; Franks TM; Lykke-Andersen J (2016) Hyperphosphorylation amplifies UPF1 activity to resolve stalls in nonsense-mediated mRNA decay. Nat Commun 7:12434-None [pubmed]

Arribas-Layton M; Dennis J; Bennett EJ; Damgaard CK; Lykke-Andersen J (2016) The C-Terminal RGG Domain of Human Lsm4 Promotes Processing Body Formation Stimulated by Arginine Dimethylation. Mol. Cell. Biol. 36:2226-2235 [pubmed]

Fu R; Olsen MT; Webb K; Bennett EJ; Lykke-Andersen J (2016) Recruitment of the 4EHP-GYF2 cap-binding complex to tetraproline motifs of tristetraprolin promotes repression and degradation of mRNAs with AU-rich elements. RNA 22:373-382 [pubmed]

Toma KG; Rebbapragada I; Durand S; Lykke-Andersen J (2015) Identification of elements in human long 3' UTRs that inhibit nonsense-mediated decay. RNA 21:887-897 [pubmed]

Lee SR; Pratt GA; Martinez FJ; Yeo GW; Lykke-Andersen J (2015) Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity. Mol. Cell 59:413-425 [pubmed]

Erickson SL; Corpuz EO; Maloy JP; Fillman C; Webb K; Bennett EJ; Lykke-Andersen J (2015) Competition between Decapping Complex Formation and Ubiquitin-Mediated Proteasomal Degradation Controls Human Dcp2 Decapping Activity. Mol. Cell. Biol. 35:2144-2153 [pubmed]

Lykke-Andersen J; Bennett EJ (2014) Protecting the proteome: Eukaryotic cotranslational quality control pathways. J. Cell Biol. 204:467-476 [pubmed]

Reznik B; Clement SL; Lykke-Andersen J (2014) hnRNP F complexes with tristetraprolin and stimulates ARE-mRNA decay. PLoS ONE 9:e100992-None [pubmed]

Arribas-Layton M; Wu D; Lykke-Andersen J; Song H (2013) Structural and functional control of the eukaryotic mRNA decapping machinery. Biochim. Biophys. Acta 1829:580-589 [pubmed]

Durand S; Lykke-Andersen J (2013) Nonsense-mediated mRNA decay occurs during eIF4F-dependent translation in human cells. Nat. Struct. Mol. Biol. 20:702-709 [pubmed]

Lee SR; Lykke-Andersen J (2013) Emerging roles for ribonucleoprotein modification and remodeling in controlling RNA fate. Trends Cell Biol. 23:504-510 [pubmed]

Damgaard CK; Lykke-Andersen J (2013) Regulation of ARE-mRNA Stability by Cellular Signaling: Implications for Human Cancer. Cancer Treat. Res. 158:153-180 [pubmed]

Erickson SL; Lykke-Andersen J (2011) Cytoplasmic mRNP granules at a glance. J. Cell. Sci. 124:293-297 [pubmed]

Clement SL; Scheckel C; Stoecklin G; Lykke-Andersen J (2011) Phosphorylation of tristetraprolin by MK2 impairs AU-rich element mRNA decay by preventing deadenylase recruitment. Mol. Cell. Biol. 31:256-266 [pubmed]

Durand S; Lykke-Andersen J (2011) SnapShot: Nonsense-mediated mRNA decay. Cell 145:324-324.e2 [pubmed]

Damgaard CK; Lykke-Andersen J (2011) Translational coregulation of 5'TOP mRNAs by TIA-1 and TIAR. Genes Dev. 25:2057-2068 [pubmed]

Franks TM; Singh G; Lykke-Andersen J (2010) Upf1 ATPase-dependent mRNP disassembly is required for completion of nonsense- mediated mRNA decay. Cell 143:938-950 [pubmed]

Reznik B; Lykke-Andersen J (2010) Regulated and quality-control mRNA turnover pathways in eukaryotes. Biochem. Soc. Trans. 38:1506-1510 [pubmed]

Rebbapragada I; Lykke-Andersen J (2009) Execution of nonsense-mediated mRNA decay: what defines a substrate? Curr. Opin. Cell Biol. 21:394-402 [pubmed]

Clement SL; Lykke-Andersen J (2008) A tethering approach to study proteins that activate mRNA turnover in human cells. Methods Mol. Biol. 419:121-133 [pubmed]

Singh G; Rebbapragada I; Lykke-Andersen J (2008) A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay. PLoS Biol. 6:e111-None [pubmed]

Wagner E; Clement SL; Lykke-Andersen J (2007) An unconventional human Ccr4-Caf1 deadenylase complex in nuclear cajal bodies. Mol. Cell. Biol. 27:1686-1695 [pubmed]

Franks TM; Lykke-Andersen J (2007) TTP and BRF proteins nucleate processing body formation to silence mRNAs with AU-rich elements. Genes Dev. 21:719-735 [pubmed]

Singh G; Jakob S; Kleedehn MG; Lykke-Andersen J (2007) Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm. Mol. Cell 27:780-792 [pubmed]

Clement SL; Lykke-Andersen J (2006) No mercy for messages that mess with the ribosome. Nat. Struct. Mol. Biol. 13:299-301 [pubmed]

Fillman C; Lykke-Andersen J (2005) RNA decapping inside and outside of processing bodies. Curr. Opin. Cell Biol. 17:326-331 [pubmed]

Weischenfeldt J; Lykke-Andersen J; Porse B (2005) Messenger RNA surveillance: neutralizing natural nonsense. Curr. Biol. 15:R559-62 [pubmed]

Lykke-Andersen J; Wagner E (2005) Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1. Genes Dev. 19:351-361 [pubmed]

Kedersha N; Stoecklin G; Ayodele M; Yacono P; Lykke-Andersen J; Fritzler MJ; Scheuner D; Kaufman RJ; Golan DE; Anderson P (2005) Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. J. Cell Biol. 169:871-884 [pubmed]

Fenger-Grøn M; Fillman C; Norrild B; Lykke-Andersen J (2005) Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. Mol. Cell 20:905-915 [pubmed]

Lykke-Andersen J (2004) Making structural sense of nonsense-mediated decay. Nat. Struct. Mol. Biol. 11:305-306 [pubmed]

Singh G; Lykke-Andersen J (2003) New insights into the formation of active nonsense-mediated decay complexes. Trends Biochem. Sci. 28:464-466 [pubmed]

Wagner E; Lykke-Andersen J (2002) mRNA surveillance: the perfect persist. J. Cell. Sci. 115:3033-3038 [pubmed]

Lykke-Andersen J (2002) Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol. Cell. Biol. 22:8114-8121 [pubmed]

Lykke-Andersen J (2001) mRNA quality control: Marking the message for life or death. Curr. Biol. 11:88-91 [pubmed]

Lykke-Andersen J; Shu MD; Steitz JA (2001) Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science 293:1836-1839 [pubmed]

Lykke-Andersen J; Shu MD; Steitz JA (2000) Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. Cell 103:1121-1131 [pubmed]