Update on functional analysis of long non-coding RNAs in common crops

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: May 30, 2024

With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes extensively investigated animals, there has considerably less research on plant lncRNAs. Nevertheless, multiple studies major crops showed lncRNAs involved crucial processes, growth and development, reproduction, stress responses. This review summarizes progress lncRNA roles several crops, presents key strategies for exploring discusses current challenges future prospects. The insights provided this will enhance our comprehension of functions with potential implications improving crop genetics breeding.

Language: Английский

---

Transposable Elements Contribute to the Regulation of Long Noncoding RNAs in Drosophila melanogaster

Insects, Journal Year: 2024, Volume and Issue: 15(12), P. 950 - 950

Published: Nov. 30, 2024

Background: Transposable elements (TEs) and noncoding sequences are major components of the genome, yet their functional contributions to long RNAs (lncRNAs) not well understood. Although many lncRNAs originating from TEs (TE-lncRNAs) have been identified across various organisms, characteristics regulatory roles, particularly in insects, remain largely unexplored. This study integrated multi-omics data investigate TE-lncRNAs D. melanogaster, focusing on influence transposons different omics levels. Results: We 16,118 overlapping with lncRNA that constitute 2119 (40.4% all lncRNAs) using 256 public RNA-seq samples 15 lncRNA-seq Drosophila S2 cells treated heavy metals. Of these, 67.2% contain more than one TE. The LTR/Gypsy family was most common transposon insertion. Transposons preferred insert into promoters, transcription starting sites, intronic regions, especially chromosome ends. Compared lncRNAs, showed longer lengths, a lower conservation, levels but higher specificity expression. Multi-omics analysis revealed positive correlations between insertions chromatin openness at pre-transcriptional level. Notably, total 516 provided transcriptional factor binding sites through insertions. network key rewired by transposons, potentially recruiting other factors exert functions under metal stress. Additionally, 99 were associated m6A methylation modification 115 candidate small open reading frames Conclusions: Our demonstrated contribute regulation lncRNAs. only promote also facilitate post-transcriptional epigenetic regulation.

Language: Английский

---

The long noncoding RNAs lnc10 and lnc11 regulating flavonoid biosynthesis in Ginkgo biloba

Plant Science, Journal Year: 2023, Volume and Issue: 339, P. 111948 - 111948

Published: Dec. 12, 2023

Language: Английский

---

Deciphering shared attributes of plant long non-coding RNAs through a comparative computational approach

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Sept. 12, 2023

Abstract Over the past decade, long non-coding RNA (lncRNA), which lacks protein-coding potential, has emerged as an essential regulator of genome. The present study examined 13,599 lncRNAs in Arabidopsis thaliana , 11,565 Oryza sativa and 32,397 Zea mays for their characteristic features explored associated genomic epigenomic features. We found were distributed throughout chromosomes Helitron family transposable elements (TEs) enriched, while terminal inverted repeat depleted lncRNA transcribing regions. Our analyses determined that regions show rare or weak signals most epigenetic marks except H3K9me2 cytosine methylation all three plant species. LncRNAs showed preferential localization nucleus cytoplasm; however, distribution ratio cytoplasm varies among studied identified several conserved endogenous target mimic sites plants. 233, 301, 273 unique miRNAs, potentially targeting A. O. Z. respectively. revealed interact with lncRNAs, genes are involved a diverse array biological molecular processes. miRNA-targeted displayed strong affinity transcription factors, including ERF BBR-BPC, mutually plants, advocating functions. Overall, exhibit characteristics govern growth development

Language: Английский

---

Genome-Wide Identification and Characterization of lncRNAs in sunflower endosperm

Research Square (Research Square), Journal Year: 2022, Volume and Issue: unknown

Published: Aug. 19, 2022

Abstract Background: Long non-coding RNAs (lncRNAs), as important regulators, play roles in plant growth and development. The expression epigenetic regulation of lncRNAs remain uncharacterized generally seeds, especially the transient endosperm dicotyledons. Results: In this study, we identified 11,840 candidate 12 day-after-pollination sunflower by analyzing RNA-seq data. These were evenly distributed all chromosomes had specific features that distinct from mRNAs including tissue-specificity expression, shorter fewer exons. By GO analysis protein coding genes showing strong correlation with lncRNAs, revealed these potential function many biological processes seed Additionally, genome-wide DNA methylation analyses level at transcription start sites was negatively correlated gene levels lncRNAs. Finally, 36 imprinted 32 maternally expressed four paternally CG CHG context, upstream body regions slightly lower than embryo tissues, which indicated maternal demethylation potentially induce bias endosperm. Conclusion: Our findings not only characterized on a scale development endosperm, but also provide novel insights into parental effects dicotyledonous seeds.

Language: Английский

---