Regulation of Plant microRNA Biogenesis

Grabowska, Aleksandra; Bhat, Susheel Sagar; Smoczynska, Aleksandra; Bielewicz, Dawid; Jarmołowski, Artur; Kulinska, Zofia Szweykowska

doi:10.1007/978-3-030-35772-6_1

Cited by 5 publications

(5 citation statements)

References 125 publications

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“…Except for miR398 and miR408 , we did not observe a positive relationship between the accumulation rate of certain mature miRNAs (by RNA-seq) with the estimated precursors (by RT-qPCR). This result is in coincidence with the demonstration of a frequent inconsistency between the expression of MIR genes and the abundance of mature miRNAs in plants exposed to stress conditions ( Barciszewska-Pacak et al, 2015 ; Bustamante et al, 2018 ; Choi et al, 2020 ), which suggest the existence of an additional regulatory layer downstream transcriptional activity to control miRNA accumulation ( Szweykowska-Kulinska and Jarmolowski, 2018 ; Manavella et al, 2019 ; Grabowska et al, 2020 ). It has been demonstrated that CHROMATIN REMODELING FACTOR 2 ( CHR2 ) acts as an ATP-dependent RNA helicase that remodels the structure of the miRNA precursors and inhibits their processing in A. thaliana ( Wang et al, 2018 ).…”

Section: Discussionsupporting

confidence: 77%

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network

et al. 2021

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Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress combinations, most interactions were negative, suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling pieces of evidence that the response to combined stresses cannot be easily predicted from the study individual stresses.

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Section: Discussionsupporting

confidence: 77%

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network

et al. 2021

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“…Small RNA sequencing data of WT barley plant shoots and roots in the control and nitrogen excess stress used in this study were previously published by Grabowska et al (2020) and deposited in the GO database under accession number GSE145799. Small RNA libraries from the shoots and roots of pep444c‐332.10 plants were prepared as described in Grabowska et al (2020). Samples were sequenced on an Illumina platform (Genesupport SA, Switzerland).…”

Section: Methodsmentioning

confidence: 99%

PEP444c encoded within the MIR444c gene regulates microRNA444c accumulation in barley

Chojnacka,

Smoczynska,

Bielewicz

et al. 2023

Physiologia Plantarum

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MicroRNAs are small, noncoding RNA molecules that regulate the expression of their target genes. The MIR444 gene family is present exclusively in monocotyledons, and microRNAs444 from this family have been shown to target certain MADS‐box transcription factors in rice and barley. We identified three barley MIR444 (MIR444a/b/c) genes and comprehensively characterised their structure and the processing pattern of the primary transcripts (pri‐miRNAs444). Pri‐microRNAs444 undergo extensive alternative splicing, generating functional and nonfunctional pri‐miRNA444 isoforms. We show that barley pri‐miRNAs444 contain numerous open reading frames (ORFs) whose transcripts associate with ribosomes. Using specific antibodies, we provide evidence that selected ORFs encoding PEP444a within MIR444a and PEP444c within MIR444c are expressed in barley plants. Moreover, we demonstrate that CRISPR‐associated endonuclease 9 (Cas9)‐mediated mutagenesis of the PEP444c‐encoding sequence results in a decreased level of PEP444 transcript in barley shoots and roots and a 5‐fold reduced level of mature microRNA444c in roots. Our observations suggest that PEP444c encoded by the MIR444c gene is involved in microRNA444c biogenesis in barley.

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“…Small RNA sequencing data of WT barley plant shoots and roots in the control and nitrogen excess stress used in this study were previously published by Grabowska et al (2020) and deposited in the GO database under accession number GSE145799. Small RNA libraries from the shoots and roots of pep444c-332.10 plants were prepared as described in Grabowska et al (2020). Samples were sequenced on an Illumina platform (Genesupport SA, Switzerland).…”

Section: Small Rna Library Preparationmentioning

confidence: 99%

PEP444c encoded within theMIR444cgene regulates microRNA444c accumulation in barley

Chojnacka

Smoczynska

Bielewicz

et al. 2023

Preprint

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MicroRNAs are small, non-coding RNA molecules that regulate expression of their target genes. The MIR444 gene family is present exclusively in monocotyledons, and microRNAs444 from this family have been shown to target certain MADS-box transcription factors in rice and barley. We identified three barley MIR444 (MIR444a/b/c) genes and comprehensively characterized their structure and the processing pattern of the primary transcripts (pri-miRNAs444). Pri-microRNAs444 undergo extensive alternative splicing, by which functional and non-functional pri-miRNA444 isoforms are generated. We show that barley pri-miRNAs444 contain numerous open reading frames (ORFs) whose transcripts associate with ribosomes. Using specific antibodies, we provide evidence that selected ORFs encoding PEP444a within MIR444a and PEP444c within MIR444c are expressed in barley plants. Moreover, we demonstrate that CRISPR-associated endonuclease 9 (Cas9)-mediated mutagenesis of the PEP444c encoding sequence results in a decreased level of PEP444 transcript in barley shoots and roots, and a 5-fold reduced level of mature microRNA444c in roots. Taken together, our observations suggest that PEP444c encoded by the MIR444c gene is involved in microRNA444c biogenesis in barley.

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Regulation of Plant microRNA Biogenesis

Cited by 5 publications

References 125 publications

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network

PEP444c encoded within the MIR444c gene regulates microRNA444c accumulation in barley

PEP444c encoded within theMIR444cgene regulates microRNA444c accumulation in barley

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