Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay.

In both prokaryotes and eukaryotes, nonsense mutations in a gene can enhance the decay rate or reduce the abundance of the mRNA transcribed from that gene, and we call this process nonsense-mediated mRNA decay. We have been investigating the cis-acting sequences involved in this decay pathway. Previous experiments have demonstrated that, in addition to a nonsense codon, specific sequences 3' of a nonsense mutation, which have been defined as downstream elements, are required for mRNA destabilization. The results presented here identify a sequence motif (TGYYGATGYYYYY, where Y stands for either T or C) that can predict regions in genes that, when positioned 3' of a nonsense codon, promote rapid decay of its mRNA. Sequences harboring two copies of the motif from five regions in the PGK1, ADE3, and HIS4 genes were able to function as downstream elements. In addition, four copies of this motif can function as an independent downstream element. The sequences flanking the motif played a more significant role in modulating its activity when fewer copies of the sequence motif were present. Our results indicate the sequences 5' of the motif can modulate its activity by maintaining a certain distance between the sequence motif and the termination codon. We also suggest that the sequences 3' of the motif modulate the activity of the downstream element by forming RNA secondary structures. Consistent with this view, a stem-loop structure positioned 3' of the sequence motif can enhance the activity of the downstream element. This sequence motif is one of the few elements that have been identified that can predict regions in genes that can be involved in mRNA turnover. The role of these sequences in mRNA decay is discussed.

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Characterization of cis-acting sequences and decay intermediates involved in nonsense-mediated mRNA turnover.

Molecular and Cellular Biology ◽

10.1128/mcb.15.2.809 ◽

1995 ◽

Vol 15 (2) ◽

pp. 809-823 ◽

Cited By ~ 81

Author(s):

K W Hagan ◽

M J Ruiz-Echevarria ◽

Y Quan ◽

S W Peltz

Keyword(s):

Mrna Decay ◽

General Characteristic ◽

Mrna Turnover ◽

Coding Region ◽

Yeast Saccharomyces Cerevisiae ◽

Nonsense Mutations ◽

Cis Acting ◽

Nonsense Mediated Mrna Decay ◽

Translational Termination

Several lines of evidence indicate that the processes of mRNA turnover and translation are intimately linked and that understanding this relationship is critical to elucidating the mechanism of mRNA decay. One clear example of this relationship is the observation that nonsense mutations can accelerate the decay of mRNAs in a process that we term nonsense-mediated mRNA decay. The experiments described here demonstrate that in the yeast Saccharomyces cerevisiae premature translational termination within the initial two-thirds of the PGK1 coding region accelerates decay of that transcript regardless of which of the stop codons is used. Nonsense mutations within the last quarter of the coding region have no effect on PGK1 mRNA decay. The sequences required for nonsense-mediated mRNA decay include a termination codon and specific sequences 3' to the nonsense mutation. Translation of two-thirds of the PGK1 coding region inactivates the nonsense-mediated mRNA decay pathway. This observation explains why carboxyl-terminal nonsense mutations are resistant to accelerated decay. Characterization of the decay of nonsense-containing HIS4 transcripts yielded results mirroring those described above, suggesting that the sequence requirements described for the PGK1 transcript are likely to be a general characteristic of this decay pathway. In addition, an analysis of the decay intermediates of nonsense-containing mRNAs indicates that nonsense-mediated mRNA decay flows through a pathway similar to that described for a class of wild-type transcripts. The initial cleavage event occurs near the 5' terminus of the nonsense-containing transcript and is followed by 5'-->3' exonucleolytic digestion. A model for nonsense-mediated mRNA decay based on these results is discussed.

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Nonsense-mediated mRNA decay and development: shoot the messenger to survive?

Biochemical Society Transactions ◽

10.1042/bst0381500 ◽

2010 ◽

Vol 38 (6) ◽

pp. 1500-1505 ◽

Cited By ~ 10

Author(s):

Marta Vicente-Crespo ◽

Isabel M. Palacios

Keyword(s):

Mrna Decay ◽

Physiological Role ◽

Cellular Growth ◽

Nonsense Mutations ◽

Rna Surveillance ◽

Animal Development ◽

Nonsense Mediated Mrna Decay ◽

Surveillance Mechanism ◽

Shed Light

NMD (nonsense-mediated mRNA decay) is a surveillance mechanism that degrades transcripts containing nonsense mutations, preventing the translation of potentially harmful truncated proteins. Although the mechanistic details of NMD are gradually being understood, the physiological role of this RNA surveillance pathway still remains largely unknown. The core NMD genes Upf1 (up-frameshift suppressor 1) and Upf2 are essential for animal viability in the fruitfly, mouse and zebrafish. These findings may reflect an important role for NMD during animal development. Alternatively, the lethal phenotypes of upf1 and upf2 mutants might be due to their function in NMD-independent processes. In the present paper, we describe the phenotypes observed when the NMD factors are mutated in various organisms, and discuss findings that might shed light on the function of NMD in cellular growth and development of an organism.

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Identification and in Silico Characterization of Novel and Conserved MicroRNAs in Methyl Jasmonate-Stimulated Scots Pine (Pinus sylvestris L.) Needles

Forests ◽

10.3390/f11040384 ◽

2020 ◽

Vol 11 (4) ◽

pp. 384

Author(s):

Baiba Krivmane ◽

Ilze Šņepste ◽

Vilnis Šķipars ◽

Igor Yakovlev ◽

Carl Gunnar Fossdal ◽

...

Keyword(s):

Methyl Jasmonate ◽

Scots Pine ◽

Target Genes ◽

Regulation Of Gene Expression ◽

Stem Loop ◽

Protein Coding ◽

Stem Loop Structure ◽

In Silico Characterization ◽

Potential Precursor

MicroRNAs (miRNAs) are non-protein coding RNAs of ~20–24 nucleotides in length that play an important role in many biological and metabolic processes, including the regulation of gene expression, plant growth and developmental processes, as well as responses to stress and pathogens. The aim of this study was to identify and characterize novel and conserved microRNAs expressed in methyl jasmonate-treated Scots pine needles. In addition, potential precursor sequences and target genes of the identified miRNAs were determined by alignment to the Pinus unigene set. Potential precursor sequences were identified using the miRAtool, conserved miRNA precursors were also tested for the ability to form the required stem-loop structure, and the minimal folding free energy indexes were calculated. By comparison with miRBase, 4975 annotated sequences were identified and assigned to 173 miRNA groups, belonging to a total of 60 conserved miRNA families. A total of 1029 potential novel miRNAs, grouped into 34 families were found, and 46 predicted precursor sequences were identified. A total of 136 potential target genes targeted by 28 families were identified. The majority of previously reported highly conserved plant miRNAs were identified in this study, as well as some conserved miRNAs previously reported to be monocot specific. No conserved dicot-specific miRNAs were identified. A number of potential gymnosperm or conifer specific miRNAs were found, shared among a range of conifer species.

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Terminal uridyltransferase 7 regulates TLR4-triggered inflammation by controlling Regnase-1 mRNA uridylation and degradation

Nature Communications ◽

10.1038/s41467-021-24177-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Chia-Ching Lin ◽

Yi-Ru Shen ◽

Chi-Chih Chang ◽

Xiang-Yi Guo ◽

Yun-Yun Young ◽

...

Keyword(s):

Posttranscriptional Regulation ◽

Inflammatory Responses ◽

Rna Stability ◽

Innate Immune ◽

Stem Loop ◽

Stem Loop Structure ◽

Tlr4 Activation ◽

Harmful Effects ◽

Different Levels

AbstractDifferent levels of regulatory mechanisms, including posttranscriptional regulation, are needed to elaborately regulate inflammatory responses to prevent harmful effects. Terminal uridyltransferase 7 (TUT7) controls RNA stability by adding uridines to its 3′ ends, but its function in innate immune response remains obscure. Here we reveal that TLR4 activation induces TUT7, which in turn selectively regulates the production of a subset of cytokines, including Interleukin 6 (IL-6). TUT7 regulates IL-6 expression by controlling ribonuclease Regnase-1 mRNA (encoded by Zc3h12a gene) stability. Mechanistically, TLR4 activation causes TUT7 to bind directly to the stem-loop structure on Zc3h12a 3′-UTR, thereby promotes Zc3h12a uridylation and degradation. Zc3h12a from LPS-treated TUT7-sufficient macrophages possesses increased oligo-uridylated ends with shorter poly(A) tails, whereas oligo-uridylated Zc3h12a is significantly reduced in Tut7-/- cells after TLR4 activation. Together, our findings reveal the functional role of TUT7 in sculpting TLR4-driven responses by modulating mRNA stability of a selected set of inflammatory mediators.

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Nonsense-mediated mRNA decay was demonstrated in two hypofibrinogenemias caused by heterozygous nonsense mutations of FGG, Shizuoka III and Kanazawa II

Thrombosis Research ◽

10.1016/j.thromres.2013.08.010 ◽

2013 ◽

Vol 132 (4) ◽

pp. 465-470 ◽

Cited By ~ 7

Author(s):

Keisuke Soya ◽

Yuka Takezawa ◽

Nobuo Okumura ◽

Fumiko Terasawa

Keyword(s):

Mrna Decay ◽

Nonsense Mutations ◽

Nonsense Mediated Mrna Decay

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sRNA STnc150 is involved in virulence regulation of Salmonella Typhimurium by targeting fimA mRNA

FEMS Microbiology Letters ◽

10.1093/femsle/fnab124 ◽

2021 ◽

Vol 368 (18) ◽

Author(s):

Jing Li ◽

Na Li ◽

Chengcheng Ning ◽

Yun Guo ◽

Chunhui Ji ◽

...

Keyword(s):

Salmonella Typhimurium ◽

Target Genes ◽

Reporter System ◽

Stem Loop ◽

Viral Loads ◽

Virulence Regulation ◽

Stem Loop Structure ◽

Complementary Strain

ABSTRACT Small RNAs (sRNAs) are essential virulent regulators in Salmonella typhimurium (STM). To explore the role of sRNA STnc150 in regulating STM virulence, we constructed a STnc150 deletion strain (ΔSTnc150) and its complementary strain (ΔSTnc150/C). Then, we compared their characteristics to their original parent strain experimentally, identified the target genes of STnc150 and determined the expression levels of target genes. The results showed that the ΔSTnc150 strain exhibited delayed biofilm formation, enhanced adhesion to macrophages, significantly reduced LD50, increased liver and spleen viral loads and more vital pathological damaging ability than its parent and complementary strains. Further, bioinformatics combined with the bacterial dual plasmid reporter system confirmed that the bases 72–88 of STnc150 locating at the secondary stem-loop structure of the STnc150 are complementary with the bases 1–19 in the 5′-terminal of fimA mRNA of the type 1 fimbriae subunit. Western blot analysis showed that fimA protein level was increased in STnc150 strain compared with its parent and complementary strains. Together, this study suggested that STnc150 can down-regulate STM fimA expression at the translation level, which provided insights into the regulatory mechanisms of sRNAs in virulence of STM.

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A UPF1 variant drives conditional remodeling of nonsense-mediated mRNA decay

10.1101/2021.01.27.428318 ◽

2021 ◽

Author(s):

Sarah E. Fritz ◽

Soumya Ranganathan ◽

J. Robert Hogg

Keyword(s):

Gene Expression ◽

Mrna Decay ◽

Gene Expression Regulation ◽

Translation Termination ◽

Translational Repression ◽

The Core ◽

Human Genes ◽

Rna Quality Control ◽

Nonsense Mediated Mrna Decay

AbstractThe nonsense-mediated mRNA decay (NMD) pathway monitors translation termination to degrade transcripts with premature stop codons and regulate thousands of human genes. Due to the major role of NMD in RNA quality control and gene expression regulation, it is important to understand how the pathway responds to changing cellular conditions. Here we show that an alternative mammalian-specific isoform of the core NMD factor UPF1, termed UPF1LL, enables condition-dependent remodeling of NMD specificity. UPF1LL associates more stably with potential NMD target mRNAs than the major UPF1SL isoform, expanding the scope of NMD to include many transcripts normally immune to the pathway. Unexpectedly, the enhanced persistence of UPF1LL on mRNAs supports induction of NMD in response to rare translation termination events. Thus, while canonical NMD is abolished by translational repression, UPF1LL activity is enhanced, providing a mechanism to rapidly rewire NMD specificity in response to cellular stress.

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Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics

Cancers ◽

10.3390/cancers12030765 ◽

2020 ◽

Vol 12 (3) ◽

pp. 765 ◽

Cited By ~ 4

Author(s):

Kamila Pawlicka ◽

Umesh Kalathiya ◽

Javier Alfaro

Keyword(s):

Messenger Rna ◽

Mrna Decay ◽

Tumour Progression ◽

Transcript Abundance ◽

Tumour Suppressor Genes ◽

Nonsense Mediated Mrna Decay ◽

The Many ◽

Cycle Regulation ◽

Fine Tune

Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a surveillance pathway used by cells to control the quality mRNAs and to fine-tune transcript abundance. NMD plays an important role in cell cycle regulation, cell viability, DNA damage response, while also serving as a barrier to virus infection. Disturbance of this control mechanism caused by genetic mutations or dys-regulation of the NMD pathway can lead to pathologies, including neurological disorders, immune diseases and cancers. The role of NMD in cancer development is complex, acting as both a promoter and a barrier to tumour progression. Cancer cells can exploit NMD for the downregulation of key tumour suppressor genes, or tumours adjust NMD activity to adapt to an aggressive immune microenvironment. The latter case might provide an avenue for therapeutic intervention as NMD inhibition has been shown to lead to the production of neoantigens that stimulate an immune system attack on tumours. For this reason, understanding the biology and co-option pathways of NMD is important for the development of novel therapeutic agents. Inhibitors, whose design can make use of the many structures available for NMD study, will play a crucial role in characterizing and providing diverse therapeutic options for this pathway in cancer and other diseases.

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