Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification DOI Creative Commons

Xue-Chan Tian,

Zhao-Yang Chen, Shuai Nie

et al.

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(4)

Published: Feb. 8, 2024

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions regulating plant growth, root development, seed dormancy, the identification of lncRNAs remains a challenge due to scarcity specific extensively tested methods. Most mainstream machine learning-based methods used for lncRNA were initially developed using human or other animal datasets, accuracy effectiveness predicting have not been fully evaluated exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, LncFinder, datasets compared performance with prediction tools CPC2, CNCI, RNAplonc, LncADeep. Retraining these models significantly improved performance, two LncFinder-plant CPAT-plant, alongside ensemble, emerged most suitable identification. This underscores importance model retraining tackling challenges associated Finally, pipeline (Plant-LncPipe) that incorporates an ensemble best-performing covers entire data analysis process, reads mapping, transcript assembly, identification, classification, origin, efficient plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.

Language: Английский

NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants DOI Creative Commons
Lianhe Zhao, Jiajia Wang, Yanyan Li

et al.

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 49(D1), P. D165 - D171

Published: Oct. 22, 2020

Abstract NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. NONCODEV6 dedicated to providing the full scope lncRNAs across plants The number has increased from 548 640 644 510 since last update 2017. human 172 216 173 112. mouse 131 697 974. plant 94 697. relationship between cancer were updated with transcriptome sequencing profiles. Three important new features also introduced NONCODEV6: (i) lncRNA-disease relationships, cancer; (ii) lncRNA annotations tissue expression profiles predicted function five common plants; iii) conservation at transcript level for 23 species. accessible through http://www.noncode.org/.

Language: Английский

Citations

243
Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation DOI Creative Commons
Uday Chand Jha, Harsh Nayyar,

Rintu Jha

et al.

BMC Plant Biology, Journal Year: 2020, Volume and Issue: 20(1)

Published: Oct. 12, 2020

Abstract Background The immobile nature of plants means that they can be frequently confronted by various biotic and abiotic stresses during their lifecycle. Among the stresses, water stress, temperature extremities, salinity, heavy metal toxicity are major challenging overall plant growth. Plants have evolved complex molecular mechanisms to adapt under given stresses. Long non-coding RNAs (lncRNAs)—a diverse class contain > 200 nucleotides(nt)—play an essential role in adaptation Results LncRNAs play a significant as ‘biological regulators’ for developmental processes stress responses animals at transcription, post-transcription, epigenetic level, targeting stress-responsive mRNAs, regulatory gene(s) encoding transcription factors, numerous microRNAs (miRNAs) regulate expression different genes. However, mechanistic lncRNAs possible target contributing response adaptation, remain largely unknown. Here, we review types found species, with focus on understanding contribute tolerance plants. We start discussing biogenesis, type function, phylogenetic relationships, sequence conservation lncRNAs. Next, controlling including drought, heat, cold, toxicity, nutrient deficiency, relevant examples from species. Lastly, briefly discuss lncRNA databases bioinformatics predicting structural functional annotation novel Conclusions Understanding intricate is its infancy. availability comprehensive atlas across whole genomes crop plants, coupled responses, will enable us use potential biomarkers tailoring stress-tolerant future.

Language: Английский

Citations

154
Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption DOI Creative Commons
Hong Yang,

Yuting Cui,

Yanrong Feng

et al.

Cells, Journal Year: 2023, Volume and Issue: 12(5), P. 729 - 729

Published: Feb. 24, 2023

Abiotic stresses triggered by climate change and human activity cause substantial agricultural environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, regulation of transcription translation. Over the past decade, a large body literature has revealed various regulatory roles long non-coding RNAs (lncRNAs) their irreplaceable functions adaptation. LncRNAs are recognized class ncRNAs that longer than 200 nucleotides, influencing variety biological processes. In this review, we mainly focused on recent progress lncRNAs, outlining features, evolution, lncRNAs drought, low or high temperature, salt, heavy metal stress. The approaches characterize function how they regulate responses were further reviewed. Moreover, discuss accumulating discoveries regarding memory well. present review provides updated information directions for us potential future.

Language: Английский

Citations

49
Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs DOI Creative Commons
Kyle Palos, Liang Yu, Caylyn E Railey

et al.

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(6), P. 1762 - 1786

Published: Feb. 4, 2023

Abstract Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to variety regulatory processes. Functionally characterized lncRNAs play critical roles plants, ranging from regulating flowering controlling lateral root formation. However, findings the past decade have revealed thousands present plant transcriptomes, characterization has lagged far behind identification. In this setting, distinguishing function noise is challenging. community been at forefront discovery lncRNA biology, providing many functional mechanistic insights increased our understanding gene class. review, we examine key discoveries made biology over two half decades. We describe how pregenomics era informed efforts identify functionally characterize subsequent provide an overview archetypes into which fit speculate on new avenues research may uncover yet more archetypes. Finally, review discusses challenges facing field some exciting molecular computational approaches help inform comparative analyses.

Language: Английский

Citations

44
Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice DOI
Yuanyuan Zhong, Yonggui Luo, Jinliang Sun

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(6), P. 2117 - 2139

Published: Feb. 12, 2024

Plants have evolved complex mechanisms to adapt harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that sensitive low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for engineering achieve greater tolerance. In this study, we constructed rice pan-transcriptome and characterized transcriptional regulatory landscape in response stress. We performed Iso-Seq RNA-Seq of 11 cultivars subjected time-course treatment. Our analyses revealed alternative splicing-regulated gene expression plays significant role the response. Moreover, identified CATALASE C (OsCATC) Os03g0701200 as candidate genes enhanced Importantly, uncovered central roles 2 serine-arginine-rich proteins OsRS33 OsRS2Z38 analysis tolerance resequencing data from diverse collection 165 suggested may be key selection japonica domestication adaptation, associated with adaptive evolution rice. This study systematically investigated distribution, dynamic changes, splicing under Overall, our work generates rich resource broad implications understanding genetic basis plants.

Language: Английский

Citations

18
PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs DOI Creative Commons
Jingjing Jin, Peng Lü, Yalong Xu

et al.

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 49(D1), P. D1489 - D1495

Published: Oct. 3, 2020

Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with little or no protein coding potential. The expanding list of lncRNAs and accumulating evidence their functions in plants have necessitated the creation a comprehensive database for lncRNA research. However, currently available plant databases some deficiencies, including lack data from model plants, uneven annotation standards, visualization expression patterns, absence epigenetic information. To overcome these problems, we upgraded our Plant RNA Database (PLncDB, http://plncdb.tobaccodb.org/), which was based on uniform pipeline. PLncDB V2.0 contains 1 246 372 80 species 13 834 RNA-Seq datasets, integrating information four other resources EVLncRNAs, RNAcentral etc. Expression patterns signals can be visualized using multiple tools (JBrowse, eFP Browser EPexplorer). Targets regulatory networks also provided function exploration. In addition, is hierarchical user-friendly has five built-in search engines. We believe useful community mining studies provides resource data-driven research plants.

Language: Английский

Citations

120
Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage DOI

Xiaoming Song,

Jingjing Hu, Tong Wu

et al.

Horticulture Research, Journal Year: 2021, Volume and Issue: 8(1)

Published: March 1, 2021

Language: Английский

Citations

49
A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants DOI Creative Commons
Igor Fesenko, Svetlana A. Shabalina, Anna Mamaeva

et al.

Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 49(18), P. 10328 - 10346

Published: Sept. 17, 2021

Abstract Pervasive transcription of eukaryotic genomes results in expression long non-coding RNAs (lncRNAs) most which are poorly conserved evolution and appear to be non-functional. However, some lncRNAs have been shown perform specific functions, particular, regulation. Thousands small open reading frames (smORFs, <100 codons) located on potentially might translated into peptides or microproteins. We report a comprehensive analysis the conservation evolutionary trajectories lncRNAs-smORFs from moss Physcomitrium patens across transcriptomes 479 plant species. Although thousands smORFs subject substantial purifying selection, majority young could represent major pool for functional innovation. Using nanopore RNA sequencing, we show that, average, transcriptional level is higher than that non-conserved smORFs. Proteomic confirmed translation 82 novel species-specific Numerous containing low complexity regions (LCRs) transmembrane domains were identified, biological functions selected LCR-smORF demonstrated experimentally. Thus, microproteins encoded by major, functionally diverse component proteome.

Language: Английский

Citations

49
The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis DOI Creative Commons
Holly R. Pinkney, Brandon M. Wright, Sarah D. Diermeier

et al.

Non-Coding RNA, Journal Year: 2020, Volume and Issue: 6(4), P. 49 - 49

Published: Dec. 16, 2020

Long non-coding RNAs (lncRNAs) are a rapidly expanding field of research, with many new transcripts identified each year. However, only small subset lncRNAs has been characterized functionally thus far. To aid investigating the mechanisms action by which act, bioinformatic tools and databases invaluable. Here, we review selection computational for in silico analysis lncRNAs, including tissue-specific expression, protein coding potential, subcellular localization, structural conformation, interaction partners. The assembled lncRNA toolkit is aimed primarily at experimental researchers as useful starting point to guide wet-lab experiments, mainly containing multi-functional, user-friendly interfaces. With more available, it will be essential provide continuous updates maintain availability key software future.

Language: Английский

Citations

46
Decoding LncRNAs DOI Open Access
Lidia Borkiewicz, Joanna Kałafut,

Karolina Dudziak

et al.

Cancers, Journal Year: 2021, Volume and Issue: 13(11), P. 2643 - 2643

Published: May 27, 2021

Non-coding RNAs (ncRNAs) have been considered as unimportant additions to the transcriptome. Yet, in light of numerous studies, it has become clear that ncRNAs play important roles development, health and disease. Long-ignored, long non-coding (lncRNAs), made more than 200 nucleotides gained attention due their involvement drivers or suppressors a myriad tumours. The detailed understanding some functions, structures interactomes result interdisciplinary efforts, many cases, new methods need be created adapted characterise these molecules. Unlike most reviews on lncRNAs, we summarize achievements lncRNA studies by taking into consideration approaches for identification interactomes, structural arrangements. We also provide information about recent data lncRNAs diseases present applications molecules, especially medicine.

Language: Английский

Citations

36