MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are abundant endogenous small RNAs (smRNAs... more MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are abundant endogenous small RNAs (smRNAs) that control transcript expression through posttranscriptional gene silencing. Here, we show that concomitant loss of XRN4/EIN5, a 5 0 -3 0 exoribonuclease, and ABH1/CBP80, a subunit of the mRNA cap binding complex, results in Arabidopsis plants manifesting myriad developmental defects. We find that ABH1/CBP80 is necessary to obtain proper mature miRNA levels, which suggests this protein affects the miRNA-mediated RNA silencing pathway. Additionally, we show that XRN4/EIN5 affects the levels of a smRNA class that is processed from both sense and antisense strands of $130 endogenous transcripts that apparently are converted to double-stranded RNA (dsRNA) and subsequently processed. We find that the parent transcripts of these smRNAs accumulate in an uncapped form upon loss of XRN4/EIN5, which suggests that uncapped endogenous transcripts can become smRNA biogenesis substrates. Overall, our results reveal unexpected connections between RNA metabolism and silencing pathways.
Academia Molecular Biology and Genomics, May 6, 2024
The disciplines of molecular biology and genomics are intimately linked, whereby the heart of gen... more The disciplines of molecular biology and genomics are intimately linked, whereby the heart of genomics studies are driven by molecular biology techniques. Furthermore, the insights of a genomics inquiry need to be validated and further explored using focused molecular biology-driven experimental programs. Thus, both disciplines are closely related and a dedicated journal delivering the top research in these areas would be of prime relevance to foster the scientific knowledge. To address this gap, we introduce Academia Molecular Biology and Genomics, aiming to publish the highest quality Research Articles, Brief Research Reports, Brief Communications, Perspectives, Opinions, Technical Notes, Mini, full and Systematic Reviews, in-depth Protocols and other, across the varied areas of Genomics and Molecular Biology related research. Through this journal, we provide a deep and varied resource for all Molecular Biology and Genomics related researchers for publishing and knowledge consolidation. In addition to basic research findings and review articles, our focus on technical advances and protocols will allow researchers to share their important new analysis tools and techniques for widespread adoption. In this way, our journal aims to foster interdisciplinary collaboration and the exchange of ideas among researchers working in different areas of genomics, with the goal of advancing our understanding of the structure, function, and evolution of genomes and their implications for biology, medicine, agriculture, and new technologies.
MicroRNAs (miRNAs) are essential for regulation of gene expression. Though numerous miRNAs have b... more MicroRNAs (miRNAs) are essential for regulation of gene expression. Though numerous miRNAs have been identified by high-throughput sequencing, few precursor miRNAs (pre-miRNAs) are experimentally validated. Here we report a strategy for constructing high-throughput sequencing libraries enriched for full-length pre-miRNAs. We find widespread and extensive uridylation of Argonaute (Ago)-bound pre-miRNAs, which is primarily catalyzed by two terminal uridylyltransferases: TUT7 and TUT4. Uridylation by TUT7/4 not only polishes pre-miRNA 3' ends, but also facilitates their degradation by the exosome, preventing clogging of Ago with defective species. We show that the exosome exploits distinct substrate preferences of DIS3 and RRP6, its two catalytic subunits, to distinguish productive from defective pre-miRNAs. Furthermore, we identify a positive feedback loop formed by the exosome and TUT7/4 in triggering uridylation and degradation of Ago-bound pre-miRNAs. Our study reveals a pre-mi...
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are abundant endogenous small RNAs (smRNAs... more MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are abundant endogenous small RNAs (smRNAs) that control transcript expression through posttranscriptional gene silencing. Here, we show that concomitant loss of XRN4/EIN5, a 5 0 -3 0 exoribonuclease, and ABH1/CBP80, a subunit of the mRNA cap binding complex, results in Arabidopsis plants manifesting myriad developmental defects. We find that ABH1/CBP80 is necessary to obtain proper mature miRNA levels, which suggests this protein affects the miRNA-mediated RNA silencing pathway. Additionally, we show that XRN4/EIN5 affects the levels of a smRNA class that is processed from both sense and antisense strands of $130 endogenous transcripts that apparently are converted to double-stranded RNA (dsRNA) and subsequently processed. We find that the parent transcripts of these smRNAs accumulate in an uncapped form upon loss of XRN4/EIN5, which suggests that uncapped endogenous transcripts can become smRNA biogenesis substrates. Overall, our results reveal unexpected connections between RNA metabolism and silencing pathways.
Academia Molecular Biology and Genomics, May 6, 2024
The disciplines of molecular biology and genomics are intimately linked, whereby the heart of gen... more The disciplines of molecular biology and genomics are intimately linked, whereby the heart of genomics studies are driven by molecular biology techniques. Furthermore, the insights of a genomics inquiry need to be validated and further explored using focused molecular biology-driven experimental programs. Thus, both disciplines are closely related and a dedicated journal delivering the top research in these areas would be of prime relevance to foster the scientific knowledge. To address this gap, we introduce Academia Molecular Biology and Genomics, aiming to publish the highest quality Research Articles, Brief Research Reports, Brief Communications, Perspectives, Opinions, Technical Notes, Mini, full and Systematic Reviews, in-depth Protocols and other, across the varied areas of Genomics and Molecular Biology related research. Through this journal, we provide a deep and varied resource for all Molecular Biology and Genomics related researchers for publishing and knowledge consolidation. In addition to basic research findings and review articles, our focus on technical advances and protocols will allow researchers to share their important new analysis tools and techniques for widespread adoption. In this way, our journal aims to foster interdisciplinary collaboration and the exchange of ideas among researchers working in different areas of genomics, with the goal of advancing our understanding of the structure, function, and evolution of genomes and their implications for biology, medicine, agriculture, and new technologies.
MicroRNAs (miRNAs) are essential for regulation of gene expression. Though numerous miRNAs have b... more MicroRNAs (miRNAs) are essential for regulation of gene expression. Though numerous miRNAs have been identified by high-throughput sequencing, few precursor miRNAs (pre-miRNAs) are experimentally validated. Here we report a strategy for constructing high-throughput sequencing libraries enriched for full-length pre-miRNAs. We find widespread and extensive uridylation of Argonaute (Ago)-bound pre-miRNAs, which is primarily catalyzed by two terminal uridylyltransferases: TUT7 and TUT4. Uridylation by TUT7/4 not only polishes pre-miRNA 3' ends, but also facilitates their degradation by the exosome, preventing clogging of Ago with defective species. We show that the exosome exploits distinct substrate preferences of DIS3 and RRP6, its two catalytic subunits, to distinguish productive from defective pre-miRNAs. Furthermore, we identify a positive feedback loop formed by the exosome and TUT7/4 in triggering uridylation and degradation of Ago-bound pre-miRNAs. Our study reveals a pre-mi...
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Papers by Brian Gregory