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<p>Long non-coding RNAs (lncRNAs) are ≥ 200 nucleotides, non-protein-coding transcripts and regulate developmental processes. In the present study, a natural antisense (NAT) -lncRNA was functionally characterized to understand its role in filament elongation. The NAT-lncRNA transcribes from antisense strand overlapping with <i>SAUR61</i> transcript by 263&#xa0;bp. <i>SAUR61</i> is part of <i>SAUR63</i> sub-clade with members organised as tandemly arrayed gene (TAG) cluster in <i>Arabidopsis thaliana</i> with high sequence similarity. The lncRNA thus hypothetically could regulate members of TAG in <i>cis</i>- and <i>trans,</i> which was validated upon expression analysis. Analysis of transcriptional regulation showed near-ubiquitous reporter activity driven by <i>NAT</i><sub><i>SAUR61</i></sub> promoter in cotyledons, hypocotyl and seedling roots. In mature plants, GUS activity was observed in leaf lamina and veins, trichomes, stem; sepals, androecium (filaments, anthers, and pollen grains), gynoecium (style); and, at the tip and base of developing siliques. Gibberellic acid was found to be a negative transcriptional regulator. Artificial miRNA mediated downregulation of <i>NAT</i><sub><i>SAUR61</i></sub> resulted in up-regulation of steady-state levels of transcript of <i>SAUR63</i> cluster, reduced root length in seedlings, and secondary thickening in anther leading to early dehiscence and release of functional pollen. Most significantly, downregulation of <i>NAT</i><sub><i>SAUR61</i></sub> led to elongated stamens which over-grows and deposits copious amount of pollen on stigma. In contrast, constitutive overexpression of <i>NAT</i><sub><i>SAUR61</i></sub> resulted in down-regulation of transcript levels of <i>SAUR63</i> cluster, increased root length of seedlings and secondary thickenings in anther, leading to lack of dehiscence and release of functional pollen grains. The stamen length was significantly shortened and is an additional cause of failure of pollination. Ovule development was affected in amiRNA-<i>NAT</i><sub><i>SAUR61</i></sub>, whereas it was normal in <i>NAT</i><sub><i>SAUR61</i>-oex</sub> lines. As a result, siliques were aborted in both cases but for different reasons. The study is thus a first report of <i>cis</i>- and <i>trans</i>- regulation of <i>SAUR63</i> sub-clade through a <i>NAT-lncRNA</i>. <i>NAT</i><sub><i>SAUR61</i></sub> maintains homeostasis of <i>SAUR63</i> clade transcripts, and is major regulator of stamen and root length. In future, detailed functional analysis is required to understand the mechanistic basis of the <i>NAT-lncRNA</i> action and explore the potential of delineating and manipulating two significant traits—root and stamen for crop improvement. </p>

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A Natural Antisense Long Non-Coding RNA, NATSAUR61, Acts as a Regulator of Tandemly Arrayed Genes of SAUR63 Sub-Clade and Controls Filament Elongation in Arabidopsis thaliana

  • 期刊论文

  • 发表日期：

    2026年5月12日

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  • Richa Shukla,
  • Ekta Pokhriyal,
  • Sandip Das

摘要

Long non-coding RNAs (lncRNAs) are ≥ 200 nucleotides, non-protein-coding transcripts and regulate developmental processes. In the present study, a natural antisense (NAT) -lncRNA was functionally characterized to understand its role in filament elongation. The NAT-lncRNA transcribes from antisense strand overlapping with SAUR61 transcript by 263 bp. SAUR61 is part of SAUR63 sub-clade with members organised as tandemly arrayed gene (TAG) cluster in Arabidopsis thaliana with high sequence similarity. The lncRNA thus hypothetically could regulate members of TAG in cis- and trans, which was validated upon expression analysis. Analysis of transcriptional regulation showed near-ubiquitous reporter activity driven by NATSAUR61 promoter in cotyledons, hypocotyl and seedling roots. In mature plants, GUS activity was observed in leaf lamina and veins, trichomes, stem; sepals, androecium (filaments, anthers, and pollen grains), gynoecium (style); and, at the tip and base of developing siliques. Gibberellic acid was found to be a negative transcriptional regulator. Artificial miRNA mediated downregulation of NATSAUR61 resulted in up-regulation of steady-state levels of transcript of SAUR63 cluster, reduced root length in seedlings, and secondary thickening in anther leading to early dehiscence and release of functional pollen. Most significantly, downregulation of NATSAUR61 led to elongated stamens which over-grows and deposits copious amount of pollen on stigma. In contrast, constitutive overexpression of NATSAUR61 resulted in down-regulation of transcript levels of SAUR63 cluster, increased root length of seedlings and secondary thickenings in anther, leading to lack of dehiscence and release of functional pollen grains. The stamen length was significantly shortened and is an additional cause of failure of pollination. Ovule development was affected in amiRNA-NATSAUR61, whereas it was normal in NATSAUR61-oex lines. As a result, siliques were aborted in both cases but for different reasons. The study is thus a first report of cis- and trans- regulation of SAUR63 sub-clade through a NAT-lncRNA. NATSAUR61 maintains homeostasis of SAUR63 clade transcripts, and is major regulator of stamen and root length. In future, detailed functional analysis is required to understand the mechanistic basis of the NAT-lncRNA action and explore the potential of delineating and manipulating two significant traits—root and stamen for crop improvement.