Expression and processing of polycistronic artificial microRNAs and trans‐acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana

Lunardon, Alice; Muiruri, Kariuki Samwel; Axtell, Michael J.

doi:10.1111/tpj.15221

Cited by 18 publications

(7 citation statements)

References 80 publications

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“…7b ). This is in line with a recent report indicating that polycistronic 5′-hairpins are processed more efficiently than 3′-hairpins 71 . Interestingly, in the case of MIR842/MIR846 duet, the second miRNA but not the first, shows signs of co-transcriptional processing (Extended Data Fig.…”

Section: Resultssupporting

confidence: 93%

R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants

et al. 2022

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In most organisms, the maturation of nascent RNAs is coupled to transcription. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNA genes (MIRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs coupled to transcription. We found that the entire biogenesis occurs co-transcriptionally for pri-miRNAs processed from the loop of the hairpin but requires a second nucleoplasmic step for those processed from the base. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops, formed near the transcription start site region of MIRNAs, promote co-transcriptional pri-miRNA processing. Furthermore, our results suggest the neofunctionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.

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Section: Resultssupporting

confidence: 93%

R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants

et al. 2022

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“…Remarkably, when we analyzed polycistronic miRNA duets encoded by a single transcript, we observed that the miRNA hairpin located adjacent to an R-loop was processed co-transcriptionally more efficiently or even the only one showing signs of co-transcriptional processing (Figure 6F). This goes in line with a recent report indicating that polycistronic 5’ hairpins are processed more efficiently than 3’ hairpins (Lunardon et al, 2021). It also reinforces the hypothesis that R-loops between nascent pri-miRNAs and its encoding loci anchor and stabilize the molecule allowing the co-transcriptional processing.…”

Section: Resultssupporting

confidence: 93%

R-Loops between nascent pri-miRNAs and the encoding loci promote co-transcriptional processing of miRNAs in plants

Gonzalo

Tossolini

Gulanicz

et al. 2021

Preprint

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In most organisms, the maturation of nascent RNAs is coupled to transcription, undergoing many processing steps co-transcriptionally. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNAs (miRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we show that plant miRNA biogenesis is coupled to transcription in a process that relies on the formation of DNA:RNA hybrids (R-loops) between the nascent transcript and the encoding loci. We used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs co-transcriptionally. We found that the entire biogenesis occurs coupled to transcription for pri-miRNAs processed from the loop but requires a second nucleoplasmic step for those processed from the base of the hairpin. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops between the 5'-end single-stranded arm of the pri-miRNAs and the encoding loci anchor the transcript, promoting co-transcriptional processing. Our data demonstrate the coupling of transcription and miRNA processing in plants and discovered an unexpected function for R-loops promoting RNA processing. Furthermore, our results suggest the neo-functionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.

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“…The continuous cycle between the host and vector due to their circulative pathway affects prospective agricultural output all over the world. ToLCV particles enter the salivary glands of viruliferous flies while they feed on phloem sap and are then discharged into plants [99].…”

Section: Virus-vector Interactionmentioning

confidence: 99%

Leaf Curl Disease a Significant Constraint in the Production of Tomato: Impact, Challenges, and Management

Chintapalli¹,

Rayalcheruvu²

2022

Tomato - From Cultivation to Processing Technology

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Insect-borne plant viruses cause huge yield loss in the world’s most important crops. Understanding viral transmission mechanisms involves defining plant virus receptors inside their insect vectors. Tomato leaf curl virus (ToLCV) is the most devastating virus for worldwide tomato production. Understanding the biology of ToLCV and devising management techniques are critical in combating this global threat. Researchers are looking into using advanced technologies to detect plant viruses quickly and handle them properly for long-term agriculture. This review’s main goal is to highlight management solutions for effectively combating ToLCV outbreaks and worldwide spread. Resistance genes for plant viruses in agriculture have been identified using morphological, biochemical, and molecular markers from the ancient to the present era. Such techniques are extremely basic. Traditional virus identification methodologies should be integrated with current and advanced tools for efficient virus improvement in crops. This review’s main goal is to highlight management solutions for effectively combating ToLCV outbreaks and worldwide spread. For this aim, we focus on the impact of ToLCV on the world’s agriculture and the significance of recent advances in our comprehension of its interactions with its host and vector. Another important topic is the role of mutations and recombination in shaping the ToLCV genome’s evolution and regional distribution.

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Expression and processing of polycistronic artificial microRNAs and trans‐acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana

Cited by 18 publications

References 80 publications

R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants

R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants

R-Loops between nascent pri-miRNAs and the encoding loci promote co-transcriptional processing of miRNAs in plants

Leaf Curl Disease a Significant Constraint in the Production of Tomato: Impact, Challenges, and Management

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