Long Noncoding RNAs in Plants

Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Download Full-text

Long noncoding RNAs in biology and hematopoiesis

Blood ◽

10.1182/blood-2013-03-456111 ◽

2013 ◽

Vol 121 (24) ◽

pp. 4842-4846 ◽

Cited By ~ 28

Author(s):

Vikram R. Paralkar ◽

Mitchell J. Weiss

Keyword(s):

Gene Expression ◽

Transcriptome Sequencing ◽

Protein Localization ◽

Noncoding Rnas ◽

Cell Types ◽

Long Noncoding Rnas ◽

Protein Coding ◽

Regulate Gene Expression ◽

Multiple Processes ◽

Coding Potential

Abstract Genome and transcriptome sequencing have revealed a rich assortment of noncoding RNAs in eukaryote cells, including long noncoding RNAs (lncRNAs), which regulate gene expression independent of protein coding potential. LncRNAs modulate protein coding gene expression in many cell types by regulating multiple processes, including epigenetic control of transcription, mRNA stability, and protein localization. Although little is known about lncRNAs in hematopoiesis, they are likely to exert widespread roles in this process.

Download Full-text

Long Noncoding RNAs and Human Liver Disease

Annual Review of Pathology Mechanisms of Disease ◽

10.1146/annurev-pathol-042320-115255 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Johanna K. DiStefano ◽

Glenn S. Gerhard

Keyword(s):

Liver Disease ◽

Biological Significance ◽

Noncoding Rnas ◽

Classification Systems ◽

Long Noncoding Rnas ◽

Annual Review ◽

Publication Date ◽

Cholestatic Liver Disease ◽

Diverse Range ◽

Number Of Publications

Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome, exhibit a diverse range of biological functions, and exert effects through a variety of mechanisms. The sheer number of lncRNAs in the human genome has raised important questions about their potential biological significance and roles in human health and disease. Technological and computational advances have enabled functional annotation of a large number of lncRNAs. Though the number of publications related to lncRNAs has escalated in recent years, relatively few have focused on those involved in hepatic physiology and pathology. We provide an overview of evolving lncRNA classification systems and characteristics and highlight important advances in our understanding of the contribution of lncRNAs to liver disease, with a focus on nonalcoholic steatohepatitis, hepatocellular carcinoma, and cholestatic liver disease. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Download Full-text

When Long Noncoding Becomes Protein Coding

Molecular and Cellular Biology ◽

10.1128/mcb.00528-19 ◽

2020 ◽

Vol 40 (6) ◽

Cited By ~ 14

Author(s):

Corrine Corrina R. Hartford ◽

Ashish Lal

Keyword(s):

Cell Division ◽

Cell Signaling ◽

Transcription Regulation ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Open Reading Frames ◽

Protein Coding ◽

Small Proteins ◽

Coding Potential ◽

Reading Frames

ABSTRACT Recent advancements in genetic and proteomic technologies have revealed that more of the genome encodes proteins than originally thought possible. Specifically, some putative long noncoding RNAs (lncRNAs) have been misannotated as noncoding. Numerous lncRNAs have been found to contain short open reading frames (sORFs) which have been overlooked because of their small size. Many of these sORFs encode small proteins or micropeptides with fundamental biological importance. These micropeptides can aid in diverse processes, including cell division, transcription regulation, and cell signaling. Here we discuss strategies for establishing the coding potential of putative lncRNAs and describe various functions of known micropeptides.

Download Full-text

Long noncoding RNAs in hematopoiesis

F1000Research ◽

10.12688/f1000research.8349.1 ◽

2016 ◽

Vol 5 ◽

pp. 1771 ◽

Cited By ~ 3

Author(s):

Xu Zhang ◽

Wenqian Hu

Keyword(s):

Gene Expression ◽

Developmental Stages ◽

Regulation Of Gene Expression ◽

Noncoding Rnas ◽

High Specificity ◽

Long Noncoding Rnas ◽

Mammalian Development ◽

Functional Protein ◽

Protein Coding ◽

Functional Roles

Mammalian development is under tight control to ensure precise gene expression. Recent studies reveal a new layer of regulation of gene expression mediated by long noncoding RNAs. These transcripts are longer than 200nt that do not have functional protein coding capacity. Interestingly, many of these long noncoding RNAs are expressed with high specificity in different types of cells, tissues, and developmental stages in mammals, suggesting that they may have functional roles in diverse biological processes. Here, we summarize recent findings of long noncoding RNAs in hematopoiesis, which is one of the best-characterized mammalian cell differentiation processes. Then we provide our own perspectives on future studies of long noncoding RNAs in this field.

Download Full-text

Application of Long Noncoding RNAs in Osteosarcoma: Biomarkers and Therapeutic Targets

Cellular Physiology and Biochemistry ◽

10.1159/000479205 ◽

2017 ◽

Vol 42 (4) ◽

pp. 1407-1419 ◽

Cited By ~ 72

Author(s):

Zhihong Li ◽

Pengcheng Dou ◽

Tang Liu ◽

Shasha He

Keyword(s):

Prognostic Biomarker ◽

Noncoding Rnas ◽

Therapeutic Targets ◽

Therapeutic Strategies ◽

Long Noncoding Rnas ◽

Protein Coding ◽

Rna Molecules ◽

Primary Bone ◽

Coding Potential ◽

Potential Biomarkers

Osteosarcoma is the most common primary bone malignancy in children and adolescents. Although improvements in therapeutic strategies were achieved, the outcome remains poor for most patients with metastatic or recurrent osteosarcoma. Therefore, it is imperative to identify novel and effective prognostic biomarker and therapeutic targets for the disease. Long noncoding RNAs (lncRNAs) are a novel class of RNA molecules defined as transcripts >200 nucleotides that lack protein coding potential. Many lncRNAs are deregulated in cancer and are important regulators for malignancies. Nine lncRNAs (91H, BCAR4, FGFR3-AS1, HIF2PUT, HOTTIP, HULC, MALAT-1, TUG1, UCA1) are upregulated and considered oncogenic for osteosarcoma. Loc285194 and MEG3 are two lncRNAs downregulated and as tumor suppressor for the disease. Moreover, the expressions of LINC00161 and ODRUL are associated with chemo-resistance of osteosarcoma. The mechanisms for these lncRNAs in regulating development of osteosarcoma are diverse, e.g. ceRNA, Wnt/β-catenin pathway, etc. The lncRNAs identified may serve as potential biomarkers or therapeutic targets for osteosarcoma.

Download Full-text

PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs

Nucleic Acids Research ◽

10.1093/nar/gkaa910 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D1489-D1495 ◽

Cited By ~ 1

Author(s):

Jingjing Jin ◽

Peng Lu ◽

Yalong Xu ◽

Zefeng Li ◽

Shizhou Yu ◽

...

Keyword(s):

Noncoding Rna ◽

Regulatory Networks ◽

Expression Patterns ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Data Driven ◽

Rna Seq ◽

Protein Coding ◽

User Friendly ◽

Coding Potential

Abstract 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 of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research. However, currently available plant lncRNA databases have some deficiencies, including the lack of lncRNA data from some model plants, uneven annotation standards, a lack of visualization for expression patterns, and the absence of epigenetic information. To overcome these problems, we upgraded our Plant Long noncoding RNA Database (PLncDB, http://plncdb.tobaccodb.org/), which was based on a uniform annotation pipeline. PLncDB V2.0 currently contains 1 246 372 lncRNAs for 80 plant species based on 13 834 RNA-Seq datasets, integrating lncRNA information from four other resources including EVLncRNAs, RNAcentral and etc. Expression patterns and epigenetic signals can be visualized using multiple tools (JBrowse, eFP Browser and EPexplorer). Targets and regulatory networks for lncRNAs are also provided for function exploration. In addition, PLncDB V2.0 is hierarchical and user-friendly and has five built-in search engines. We believe PLncDB V2.0 is useful for the plant lncRNA community and data mining studies and provides a comprehensive resource for data-driven lncRNA research in plants.

Download Full-text

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

Non-Coding RNA ◽

10.3390/ncrna7010012 ◽

2021 ◽

Vol 7 (1) ◽

pp. 12

Author(s):

Camille Fonouni-Farde ◽

Federico Ariel ◽

Martin Crespi

Keyword(s):

Gene Expression ◽

Cellular Localization ◽

Molecular Mechanisms ◽

Gene Expression Regulation ◽

Large Fraction ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Genomic Research ◽

Protein Coding ◽

Wide Range

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.

Download Full-text

Identification of 170 New Long Noncoding RNAs in Schistosoma mansoni

BioMed Research International ◽

10.1155/2018/1264697 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Victor F. Oliveira ◽

Lauro A. G. Moares ◽

Ester A. Mota ◽

Liana K. Jannotti-Passos ◽

Paulo M. Z. Coelho ◽

...

Keyword(s):

Schistosoma Mansoni ◽

Cancer Progression ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Rna Seq ◽

Protein Coding ◽

Functional Studies ◽

Significant Gene ◽

Coding Potential ◽

Human And Mouse

Long noncoding RNAs (lncRNAs) are transcripts generally longer than 200 nucleotides with no or poor protein coding potential, and most of their functions are also poorly characterized. Recently, an increasing number of studies have shown that lncRNAs can be involved in various critical biological processes such as organism development or cancer progression. Little, however, is known about their effects in helminths parasites, such as Schistosoma mansoni. Here, we present a computational pipeline to identify and characterize lncRNAs from RNA-seq data with high confidence from S. mansoni adult worms. Through the utilization of different criteria such as genome localization, exon number, gene length, and stability, we identified 170 new putative lncRNAs. All novel S. mansoni lncRNAs have no conserved synteny including human and mouse. These closest protein coding genes were enriched in 10 significant Gene Ontology terms related to metabolism, transport, and biosynthesis. Fifteen putative lncRNAs showed differential expression, and three displayed sex-specific differential expressions in praziquantel sensitive and resistant adult worm couples. Together, our method can predict a set of novel lncRNAs from the RNA-seq data. Some lncRNAs are shown to be differentially expressed suggesting that those novel lncRNAs can be given high priority in further functional studies focused on praziquantel resistance.

Download Full-text

The Role of lncRNA in the Development of Tumors, Including Breast Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms22168427 ◽

2021 ◽

Vol 22 (16) ◽

pp. 8427

Author(s):

Beata Smolarz ◽

Anna Zadrożna-Nowak ◽

Hanna Romanowicz

Keyword(s):

Breast Cancer ◽

Breast Carcinoma ◽

Present Article ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Regulation Of Transcription ◽

Ribonucleic Acids ◽

Detailed Review ◽

Cellular Processes

Long noncoding RNAs (lncRNAs) are the largest groups of ribonucleic acids, but, despite the increasing amount of literature data, the least understood. Given the involvement of lncRNA in basic cellular processes, especially in the regulation of transcription, the role of these noncoding molecules seems to be of great importance for the proper functioning of the organism. Studies have shown a relationship between disturbed lncRNA expression and the pathogenesis of many diseases, including cancer. The present article presents a detailed review of the latest reports and data regarding the importance of lncRNA in the development of cancers, including breast carcinoma.

Download Full-text