From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs.

Qingshuai Chen,Kui Liu,Yaoqi Zhou,Bailing Zhou,Jihua Wang,Zanxia Cao,Ru Yu,Pingping Huang

doi:10.3389/fpls.2021.650926

Abstract

Long non-coding RNAs (lncRNAs) play a vital role in a variety of biological functions in plant growth and development. In this study, we provided an overview of the molecular mechanisms of lncRNAs in interacting with other biomolecules with an emphasis on those lncRNAs validated only by low-throughput experiments. LncRNAs function through playing multiple roles, including sponger for sequestering RNA or DNA, guider or decoy for recruiting or hijacking transcription factors or peptides, and scaffold for binding with chromatin modification complexes, as well as precursor of microRNAs or small interfering RNAs. These regulatory roles have been validated in several plant species with a comprehensive list of 73 lncRNA–molecule interaction pairs in 16 plant species found so far, suggesting their commonality in the plant kingdom. Such initial findings of a small number of functional plant lncRNAs represent the beginning of what is to come as lncRNAs with unknown functions were found in orders of magnitude more than proteins.

Highlights

Non-coding RNAs, transcribed in over 90% of eukaryotic genomes of fungi, plants, and animals (Chekanova et al, 2007), were initially thought as “dark matter” in transcripts because their expressions are low, the sequences are poorly conserved, and the protein-coding potentials are absent (Palazzo and Koonin, 2020)
Most Long non-coding RNAs (lncRNAs) are transcribed by RNA polymerase II (Pol II) or III (Pol III), and some could be produced by plant-specific RNA Pol IV and V (Wierzbicki et al, 2008)
PROMPT_1281 is a promoter upstream transcript (PROMPT) lncRNAs, which is sensitive to osmotic stress in Populus simonii, through binding with MYBs transcription factors to interrupt them from interacting with DNA and lead to an increase in the expression of target genes in cis and trans (Song Y. et al, 2019; Figure 5B)

Summary

Introduction

Non-coding RNAs (ncRNAs), transcribed in over 90% of eukaryotic genomes of fungi, plants, and animals (Chekanova et al, 2007), were initially thought as “dark matter” in transcripts because their expressions are low, the sequences are poorly conserved, and the protein-coding potentials are absent (Palazzo and Koonin, 2020). The long non-coding RNAs can interact with DNA to regulate gene transcriptions.

Results

Conclusion