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lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Multidimensional analysis of long noncoding RNAs function in Solanaceae plants.

Wenjing Yang1,2, Quanzi Bai1, Xuan Zhang1

  • 1CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.

The New Phytologist
|June 2, 2025
PubMed
Summary

This study identifies and characterizes over 113,000 long noncoding RNA (lncRNA) genes across seven Solanaceae species. The findings provide a foundational resource for exploring plant lncRNA functions in development and stress responses.

Keywords:
LncRNAsSolanaceaeepigenomesfruit ripeningfunctional annotation

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Transcriptomics

Background:

  • Long noncoding RNAs (lncRNAs) are increasingly recognized as key regulators in plant biology.
  • Functional annotation of lncRNAs in the Solanaceae family remains limited despite progress in identification.

Purpose of the Study:

  • To systematically identify and characterize lncRNAs across seven Solanaceae species.
  • To provide a comprehensive resource for functional annotation and discovery of plant lncRNAs.

Main Methods:

  • Large-scale strand-specific RNA sequencing (ssRNA-seq) was employed for uniform lncRNA identification.
  • Analysis included sequence, conservation, expression profiles, epigenetic signals, and genetic mutants.
  • Bioinformatic approaches were used for functional prediction and comparative analysis with protein-coding genes.

Main Results:

  • Approximately 113,700 lncRNA genes were identified and characterized.
  • In tomato, 97.4% of lncRNAs received basic annotation, with 25.7% predicted for roles in stress, development, and metabolism.
  • Unique characteristics of lncRNAs compared to protein-coding genes were highlighted, and 1158 lncRNAs were linked to fruit development and ripening.

Conclusions:

  • This study establishes a comprehensive framework for lncRNA functional research in Solanaceae.
  • The curated dataset serves as a valuable resource for understanding lncRNA roles in plant processes.
  • The findings facilitate the discovery of novel lncRNA functions in plants.