Noncoding RNA: from dark matter to bright star

Xue, Yuanchao; Chen, Runsheng; Qu, Liang‐Hu; Cao, Xiaofeng

doi:10.1007/s11427-020-1676-5

Cited by 33 publications

(15 citation statements)

References 63 publications

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“…MicroRNAs are master regulators of various cellular processes related to plant growth and development, via interactions with their targets at both transcriptional and posttranscriptional levels. Involvement of miRNAs in a variety of developmental processes has been studied in cotton (Ayubov et al, 2019) and summarized in other model plant systems (Xu et al, 2018;Xue et al, 2020). However, we believe that it is the first report to find the sequential and growth-stage specific expression of a large set of miRNAs during cotton ovule and fiber development in G. arboreum (Figure 1D).…”

Section: Discussionmentioning

confidence: 83%

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn2+ ion transporter capacity in cotton ovules

Wen

Huang

et al. 2021

Sci. China Life Sci.

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MicroRNAs (miRNAs) play critical roles in regulating gene expression in plants, yet their functions underlying cultivated diploid Gossypium arboreum cotton ovule development are largely unknown. Here, we acquired small RNA profiles from G. arboreum ovules and fibers collected at different growth stages, and identified 46 novel miRNAs that accounted for 23.7% of all miRNAs in G. arboreum reported in the latest plant sRNA database. Through analysis of 84 (including 38 conserved) differentially expressed G. arboreum miRNAs, we detected 215 putative protein-coding genes in 26 biological processes as their potential targets. A Malvaceae-specific novel miRNA named gar-miRN44 was found to likely regulate cotton ovule growth by targeting to a newly duplicated Zn 2+ ion transporter gene GaZIP1L. During cotton ovule development, gar-miRN44 transcript level decreased sharply after 10 to 15 days post-anthesis (DPA), while that of the GaZIP1L increased significantly, with a concomitant increase of Zn 2+ ion concentration in late ovule developmental stages. Molecular dynamics simulation and ion absorption analysis showed that GaZIP1L has stronger Zn 2+ ion binding ability than the original GaZIP1, indicating that the newly evolved GaZIP1L may be more suitable for maintaining high Zn 2+ ion transport capacity that is likely required for cotton ovule growth via enhanced cellulose synthase activities. Our systematic miRNA profiling in G. arboreum and characterization of gar-miRN44 not only contribute to the understanding of miRNA function in cotton, but also provide potential targets for plant breeding.gar-miRN44, Malvaceae, GaZIP1L, Zn 2+ ion transport, cotton ovule development

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Section: Discussionmentioning

confidence: 83%

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn2+ ion transporter capacity in cotton ovules

Wen

Huang

et al. 2021

Sci. China Life Sci.

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“…Noncoding RNAs (ncRNAs) that lack a protein-encoding function play key roles in the regulation of plant gene expression [43][44][45][46][47][48][49][50][51][52]. Based on their length, regulatory ncRNA could be separated into long ncRNAs (lncRNAs) and short ncRNAs such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) [43][44][45][46]. Generally, lncRNAs contain more than 200 nucleotides (nts), whereas miRNA contain 18-24 nts.…”

Section: Epigenetic Mechanisms Regulating Plant Gene Expressionmentioning

confidence: 99%

Concerto on Chromatin: Interplays of Different Epigenetic Mechanisms in Plant Development and Environmental Adaptation

Liu

Chang

2021

Plants

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Epigenetic mechanisms such as DNA methylation, histone post-translational modifications, chromatin remodeling, and noncoding RNAs, play important roles in regulating plant gene expression, which is involved in various biological processes including plant development and stress responses. Increasing evidence reveals that these different epigenetic mechanisms are highly interconnected, thereby contributing to the complexity of transcriptional reprogramming in plant development processes and responses to environmental stresses. Here, we provide an overview of recent advances in understanding the epigenetic regulation of plant gene expression and highlight the crosstalk among different epigenetic mechanisms in making plant developmental and stress-responsive decisions. Structural, physical, transcriptional and metabolic bases for these epigenetic interplays are discussed.

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“…The latter comprises “housekeeping ncRNA,” for example, ribosomal (r) RNAs and transfer (t) RNAs, and “regulatory RNAs,” for example, microRNAs (miRNAs or mIRs), small nucleolar RNAs (snoRNAs), and P-element–induced Wimpy testis (PIWI)-interacting RNAs (piRNAs) ( Djebali et al, 2012 )]. Research on regulatory RNAs has made considerable progress, and solid evidence of regulatory RNAs has been found in several biological pathways ( Xue et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Aberrantly Expressed Small Noncoding RNAome in Keloid Skin Tissue

Yin

Wang

2022

Front. Genet.

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The skin is an organ that protects against injury and infection but can be damaged easily. Wound healing is a subtle balance which, if broken, can lead to keloid formation. Small noncoding (nc) RNAs can be of “housekeeping,” for example, ribosomal RNAs and transfer RNAs, or “regulatory,” for example, microRNAs (miRNAs or miRs), small nucleolar RNAs (snoRNAs), and P-element–induced Wimpy testis (PIWI)-interacting RNA (piRNA) types. We examined five types of small ncRNAs [miR, piRNA, snoRNA, small nuclear (sn) RNA, and repeat-associated small interfering RNA (rasiRNA)] in keloid skin tissue (KST) using sequencing and real-time reverse transcription-quantitative polymerase chain reaction. All comparisons were made in relation to expression in normal skin tissue (obtained by abdominoplasty). The expression of three piRNAs was upregulated, and the expression of six piRNAs was downregulated in KST. The expression of 12 snoRNAs was upregulated, and the expression of two snoRNAs was downregulated in KST. The expression of two snRNAs was downregulated in KST. The expression of 18 miRs was upregulated, and the expression of three miRNAs was downregulated in KST. The expression of one rasiRNA was upregulated, and the expression of one rasiRNA was downregulated in KST. We revealed the differential expression of small ncRNAs in KST, which may aid the development of new treatment for keloids.

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Noncoding RNA: from dark matter to bright star

Cited by 33 publications

References 63 publications

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn2+ ion transporter capacity in cotton ovules

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn2+ ion transporter capacity in cotton ovules

Concerto on Chromatin: Interplays of Different Epigenetic Mechanisms in Plant Development and Environmental Adaptation

Aberrantly Expressed Small Noncoding RNAome in Keloid Skin Tissue

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