Functional classification of plant long noncoding RNAs: a transcript is known by the company it keeps

Lucero, Leandro; Ferrero, Lucía; Fonouni‐Farde, Camille; Ariel, Federico

doi:10.1111/nph.16903

Cited by 56 publications

(47 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Based on their genomic localization regarding other genes, lncRNAs are broadly grouped into different classes: (1) lincRNAs or long non-coding intergenic RNAs; (2) NAT lncRNAs or natural anti-sense lncRNAs; (3) intronic lncRNAs, located in the introns; and (4) sense lncRNAs [ 3 ]. LncRNAs have been identified in many plant species and their expression in response to various abiotic and biotic stresses has been investigated, although our knowledge about lncRNA functions is still very limited [ 4 , 5 , 6 , 7 , 8 , 9 ]. However, the catalogue of lncRNAs for some plants with complex polyploidy and repeat-rich genomes, including wheat ( Triticum aestivum L.), remains mainly underexplored [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

“…LncRNAs have been identified in many plant species and their expression in response to various abiotic and biotic stresses has been investigated, although our knowledge about lncRNA functions is still very limited [4][5][6][7][8][9]. However, the catalogue of lncRNAs for some plants with complex polyploidy and repeat-rich genomes, including wheat (Triticum aestivum L.), remains mainly underexplored [10].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

Kirov

Dudnikov

Merkulov³

et al. 2020

Plants

View full text Add to dashboard Cite

The intergenic space of plant genomes encodes many functionally important yet unexplored RNAs. The genomic loci encoding these RNAs are often considered “junk”, DNA as they are frequently associated with repeat-rich regions of the genome. The latter makes the annotations of these loci and the assembly of the corresponding transcripts using short RNAseq reads particularly challenging. Here, using long-read Nanopore direct RNA sequencing, we aimed to identify these “junk” RNA molecules, including long non-coding RNAs (lncRNAs) and transposon-derived transcripts expressed during early stages (10 days post anthesis) of seed development of triticale (AABBRR, 2n = 6x = 42), an interspecific hybrid between wheat and rye. Altogether, we found 796 lncRNAs and 20 LTR retrotransposon-related transcripts (RTE-RNAs) expressed at this stage, with most of them being previously unannotated and located in the intergenic as well as intronic regions. Sequence analysis of the lncRNAs provide evidence for the frequent exonization of Class I (retrotransposons) and class II (DNA transposons) transposon sequences and suggest direct influence of “junk” DNA on the structure and origin of lncRNAs. We show that the expression patterns of lncRNAs and RTE-related transcripts have high stage specificity. In turn, almost half of the lncRNAs located in Genomes A and B have the highest expression levels at 10–30 days post anthesis in wheat. Detailed analysis of the protein-coding potential of the RTE-RNAs showed that 75% of them carry open reading frames (ORFs) for a diverse set of GAG proteins, the main component of virus-like particles of LTR retrotransposons. We further experimentally demonstrated that some RTE-RNAs originate from autonomous LTR retrotransposons with ongoing transposition activity during early stages of triticale seed development. Overall, our results provide a framework for further exploration of the newly discovered lncRNAs and RTE-RNAs in functional and genome-wide association studies in triticale and wheat. Our study also demonstrates that Nanopore direct RNA sequencing is an indispensable tool for the elucidation of lncRNA and retrotransposon transcripts.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

Kirov

Dudnikov

Merkulov³

et al. 2020

Plants

View full text Add to dashboard Cite

show abstract

“…Based on their biogenesis and location, the lncRNAs can be classified into several subgroups [56], as described below.…”

Section: Long Non-coding Rnasmentioning

confidence: 99%

Non-Coding RNAs in Response to Drought Stress

Gelaw

Sanan-Mishra

2021

IJMS

View full text Add to dashboard Cite

Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.

show abstract

“…CircRNAs constitute a novel class of lncRNAs consisting in covalently closed molecules of single-stranded RNA, resulting from back-splicing, a non-canonical form of alternative splicing [14]. Alternatively, lncRNAs can be further categorized depending on their molecular functions and interactions with additional regulatory molecules such as proteins, DNA, or other RNAs [15,16].…”

Section: Introductionmentioning

confidence: 99%

Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations

Fonouni‐Farde

Ariel

Crespi

2021

ncRNA

Self Cite

View full text Add to dashboard Cite

The first reference to the “C-value paradox” reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.

show abstract

Functional classification of plant long noncoding RNAs: a transcript is known by the company it keeps

Cited by 56 publications

References 86 publications

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

Non-Coding RNAs in Response to Drought Stress

Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations

Contact Info

Product

Resources

About