Uridylated Histone mRNA Degradation Intermediates Bind SLBP and 3′hEXO Individually and Together

ABSTRACT mRNA in the yeast Saccharomyces cerevisiae is primarily degraded through a pathway that is stimulated by removal of the mRNA cap structure. Here we report that a mutation in the SPB8(YJL124c) gene, initially identified as a suppressor mutation of a poly(A)-binding protein (PAB1) gene deletion, stabilizes the mRNA cap structure. Specifically, we find that thespb8-2 mutation results in the accumulation of capped, poly(A)-deficient mRNAs. The presence of this mutation also allows for the detection of mRNA species trimmed from the 3′ end. These data show that this Sm-like protein family member is involved in the process of mRNA decapping, and they provide an example of 3′-5′ mRNA degradation intermediates in yeast.

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dTIS11 Protein-dependent Polysomal Deadenylation Is the Key Step in AU-rich Element-mediated mRNA Decay in Drosophila Cells

Journal of Biological Chemistry ◽

10.1074/jbc.m112.356188 ◽

2012 ◽

Vol 287 (42) ◽

pp. 35527-35538 ◽

Cited By ~ 15

Author(s):

Caroline Vindry ◽

Aurélien Lauwers ◽

David Hutin ◽

Romuald Soin ◽

Corinne Wauquier ◽

...

Keyword(s):

Antimicrobial Peptide ◽

Molecular Mechanism ◽

Mrna Decay ◽

Degradation Process ◽

Mrna Degradation ◽

Decay Process ◽

Human Protein ◽

P Bodies ◽

Drosophila Cells ◽

Degradation Intermediates

The destabilization of AU-rich element (ARE)-containing mRNAs mediated by proteins of the TIS11 family is conserved among eukaryotes including Drosophila. Previous studies have demonstrated that Tristetraprolin, a human protein of the TIS11 family, induces the degradation of ARE-containing mRNAs through a large variety of mechanisms including deadenylation, decapping, and P-body targeting. We have previously shown that the degradation of the mRNA encoding the antimicrobial peptide Cecropin A1 (CecA1) is controlled by the TIS11 protein (dTIS11) in Drosophila cells. In this study, we used CecA1 mRNA as a model to investigate the molecular mechanism of dTIS11-mediated mRNA decay. We observed that during the biphasic deadenylation and decay process of this mRNA, dTIS11 enhances deadenylation performed by the CCR4-CAF-NOT complex while the mRNA is still associated with ribosomes. Sequencing of mRNA degradation intermediates revealed that the complete deadenylation of the mRNA triggers its decapping and decay in both the 5′-3′ and the 3′-5′ directions. Contrary to the observations made for its mammalian homologs, overexpression of dTIS11 does not promote the localization of ARE-containing mRNAs in P-bodies but rather decreases the accumulation of CecA1 mRNA in these structures by enhancing the degradation process. Therefore, our results suggest that proteins of the TIS11 family may have acquired additional functions in the course of evolution from invertebrates to mammals.

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Re-polyadenylation occurs predominantly on maternal mRNA degradation intermediates during mammalian oocyte-to-embryo transition

10.1101/2021.08.29.458080 ◽

2021 ◽

Author(s):

Yusheng Liu ◽

Yiwei Zhang ◽

Hu Nie ◽

Zhonghua Liu ◽

Jiaqiang Wang ◽

...

Keyword(s):

Transcriptional Regulation ◽

Mrna Degradation ◽

Mammalian Oocyte ◽

Maternal Mrna ◽

Early Embryos ◽

Specific Regulation ◽

And Function ◽

Post Transcriptional Regulation ◽

Degradation Intermediates ◽

Polyadenylated Mrna

The nascent mRNA transcribed in the nucleus is cleaved and polyadenylated before it is transported to the cytoplasm for translation. Polyadenylation can also occur in the cytoplasm for post-transcriptional regulation, especially in neurons, oocytes and early embryos. Recently, we revealed transcriptome-wide maternal mRNA cytoplasmic re-polyadenylation during the mammalian oocyte-to-embryo transition (OET). However, the mechanism of re-polyadenylation during mammalian OET, including the sites to be re-polyadenylated and the enzymes involved, is still poorly understood. Here, by analyzing the PAIso-seq1 and PAIso-seq2 poly(A) inclusive transcriptome data during OET in mice, rats, pigs, and humans, we reveal conserved re-polyadenylation of mRNA degradation intermediates. These re-polyadenylated mRNA degradation intermediates account for over half of the polyadenylated mRNA during OET in all four species. We find that mRNA degradation intermediates for re-polyadenylation are generated through Btg4-mediated deadenylation in both mouse and human. Interestingly, the poly(A) tails on the re-polyadenylated mRNA degradation intermediates are of different lengths and contain different levels of non-A residues compared to regular polyadenylation sites, suggesting specific regulation and function of these poly(A) tails in mammalian OET. Together, our findings reveal the maternal mRNA degradation intermediates as substrates for conserved cytoplasmic dominant re-polyadenylation during mammalian OET, and uncover the mechanism of production of these mRNA degradation intermediates. These findings provide new insights into mRNA post-transcriptional regulation, and a new direction for the study of mammalian OET.

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Nuclear Pre-mRNA Decapping and 5′ Degradation in Yeast Require the Lsm2-8p Complex

Molecular and Cellular Biology ◽

10.1128/mcb.24.21.9646-9657.2004 ◽

2004 ◽

Vol 24 (21) ◽

pp. 9646-9657 ◽

Cited By ~ 46

Author(s):

Joanna Kufel ◽

Cecile Bousquet-Antonelli ◽

Jean D. Beggs ◽

David Tollervey

Keyword(s):

Heat Shock ◽

Mrna Export ◽

Mrna Degradation ◽

Mrna Decapping ◽

Nuclear Rna ◽

Mrna Analysis ◽

Degradation Intermediates

ABSTRACT Previous analyses have identified related cytoplasmic Lsm1-7p and nuclear Lsm2-8p complexes. Here we report that mature heat shock and MET mRNAs that are trapped in the nucleus due to a block in mRNA export were strongly stabilized in strains lacking Lsm6p or the nucleus-specific Lsm8p protein but not by the absence of the cytoplasmic Lsm1p. These nucleus-restricted mRNAs remain polyadenylated until their degradation, indicating that nuclear mRNA degradation does not involve the incremental deadenylation that is a key feature of cytoplasmic turnover. Lsm8p can be UV cross-linked to nuclear poly(A)+ RNA, indicating that an Lsm2-8p complex interacts directly with nucleus-restricted mRNA. Analysis of pre-mRNAs that contain intronic snoRNAs indicates that their 5′ degradation is specifically inhibited in strains lacking any of the Lsm2-8p proteins but Lsm1p. Nucleus-restricted mRNAs and pre-mRNA degradation intermediates that accumulate in lsm mutants remain 5′ capped. We conclude that the Lsm2-8p complex normally targets nuclear RNA substrates for decapping.

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Changes in mRNA Degradation Efficiencies under Varying Conditions Are Regulated by Multiple Determinants in Arabidopsis thaliana

Plant and Cell Physiology ◽

10.1093/pcp/pcaa147 ◽

2020 ◽

Author(s):

Daishin Ueno ◽

Maki Mikami ◽

Shotaro Yamasaki ◽

Miho Kaneko ◽

Takafumi Mukuta ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Developmental Stages ◽

Cultured Cells ◽

Growth Conditions ◽

Mrna Degradation ◽

Translation Efficiency ◽

Sequence Motifs ◽

Mrna Accumulation ◽

Mrna Length ◽

Degradation Intermediates

Abstract Multiple mechanisms are involved in gene expression, with mRNA degradation being critical for the control of mRNA accumulation. In plants, although some trans-acting factors and motif sequences have been identified in deadenylation-dependent mRNA degradation, endonucleolytic cleavage-dependent mRNA degradation has not been studied in detail. Previously, we developed truncated RNA-end sequencing (TREseq) in Arabidopsis thaliana and detected G-rich sequence motifs around 5′ degradation intermediates. However, it remained to be elucidated whether degradation efficiencies of 5′ degradation intermediates in A. thaliana vary among growth conditions and developmental stages. To address this issue, we conducted TREseq of cultured cells under heat stress and at three developmental stages (seedlings, expanding leaves and expanded leaves) and compared 5′ degradation intermediates data among the samples. Although some 5′ degradation intermediates had almost identical degradation efficiencies, others differed among conditions. We focused on the genes and sites whose degradation efficiencies differed. Changes in degradation efficiencies at the gene and site levels revealed an effect on mRNA accumulation in all comparisons. These changes in degradation efficiencies involved multiple determinants, including mRNA length and translation efficiency. These results suggest that several determinants govern the efficiency of mRNA degradation in plants, helping the organism to adapt to varying conditions by controlling mRNA accumulation.

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Detection of mRNA degradation intermediates in tissues using the 3′-end poly(A)-tailing polymerase chain reaction method

Analytical Biochemistry ◽

10.1016/j.ab.2004.08.023 ◽

2004 ◽

Vol 335 (1) ◽

pp. 58-65 ◽

Cited By ~ 4

Author(s):

Andy Eberding ◽

Vicki Rehaume ◽

Chow H. Lee

Keyword(s):

Polymerase Chain Reaction ◽

Polymerase Chain Reaction Method ◽

Mrna Degradation ◽

Chain Reaction ◽

Reaction Method ◽

Polymerase Chain ◽

Degradation Intermediates

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Degradation intermediates as an indicator of mRNA and cell metabolism

10.1101/2021.08.29.458069 ◽

2021 ◽

Author(s):

Yusheng Liu ◽

Yiwei Zhang ◽

Hu Nie ◽

Falong Lu ◽

Jiaqiang Wang

Keyword(s):

Degradation Rate ◽

Cultured Cells ◽

Cell Metabolism ◽

Single Cells ◽

Mrna Degradation ◽

Rate Analysis ◽

Mouse Tissues ◽

Degradation Intermediates ◽

Mrna Degradation Rate

Traditional mRNA degradation rate measurements involves complex experimental design with RNA labeling or transcription blocking together with sampling at multiple timepoints. These experimental requirements limit the application of transcriptome-wide mRNA degradation rate analysis mainly in cultured cells, but rarely in in vivo samples. Therefore, a direct and simple strategy needs to be developed to study mRNA degradation rate. Here, we defined mRNA degradation intermediates as transcripts where decay is about to occur or has partially occurred in the 3′-untranslated regions after poly(A) tail deadenylation, and found that the proportion of mRNA degradation intermediates is a very simple and convenient indicator for evaluating the degradation rate of mRNA in mouse and human cell lines. In addition, we showed that a higher proportion of mRNA degradation intermediates is correlated with faster cell cycle and higher turnover rate of mouse tissues. Further, we validated that in mouse maturing oocytes where transcription is silent, the proportion of mRNA degradation intermediates is positively correlated with the mRNA degradation rate. Together, these results demonstrate that degradation intermediates can function as a good indicator of mRNA, cell, and tissue metabolism, and can be easily assayed by total RNA 3′-end sequencing from a single bulk cell sample without the need for drug treatment or multi-timepoint sampling. This finding is of great potential for studies on mRNA degradation rate at the molecular, cellular, or organic level, including samples or systems that cannot be assayed with previous methods. In addition, further application of the findings into single cells will likely greatly aid the identification and study of rare cells with unique cellular metabolism dynamics such as tissue stem cells and tumor cells.

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