Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

Abstract Main conclusion Long non-coding RNAs modulate gene activity in plant development and stress responses by various molecular mechanisms. Abstract Long non-coding RNAs (lncRNAs) are transcripts larger than 200 nucleotides without protein coding potential. Computational approaches have identified numerous lncRNAs in different plant species. Research in the past decade has unveiled that plant lncRNAs participate in a wide range of biological processes, including regulation of flowering time and morphogenesis of reproductive organs, as well as abiotic and biotic stress responses. LncRNAs execute their functions by interacting with DNA, RNA and protein molecules, and by modulating the expression level of their targets through epigenetic, transcriptional, post-transcriptional or translational regulation. In this review, we summarize characteristics of plant lncRNAs, discuss recent progress on understanding of lncRNA functions, and propose an experimental framework for functional characterization.

Download Full-text

Long Non-Coding RNAs as Emerging Regulators of Pathogen Response in Plants

Non-Coding RNA ◽

10.3390/ncrna8010004 ◽

2022 ◽

Vol 8 (1) ◽

pp. 4

Author(s):

Yashraaj Sharma ◽

Alok Sharma ◽

Madhu ◽

Shumayla ◽

Kashmir Singh ◽

...

Keyword(s):

Stress Responses ◽

Protein Modification ◽

Molecular Mechanisms ◽

Functional Characterization ◽

Reproductive Organ ◽

Biotic And Abiotic Stress ◽

Protein Coding ◽

Non Coding Rnas ◽

Pathogen Response ◽

Major Factors

Long non-coding RNAs (lncRNAs) are transcripts without protein-coding potential that contain more than 200 nucleotides that play important roles in plant survival in response to different stresses. They interact with molecules such as DNA, RNA, and protein, and play roles in the regulation of chromatin remodeling, RNA metabolism, and protein modification activities. These lncRNAs regulate the expression of their downstream targets through epigenetic changes, at the level of transcription and post-transcription. Emerging information from computational biology and functional characterization of some of them has revealed their diverse mechanisms of action and possible roles in biological processes such as flowering time, reproductive organ development, as well as biotic and abiotic stress responses. In this review, we have mainly focused on the role of lncRNAs in biotic stress response due to the limited availability of knowledge in this domain. We have discussed the available molecular mechanisms of certain known lncRNAs against specific pathogens. Further, considering that fungal, viral, and bacterial diseases are major factors in the global food crisis, we have highlighted the importance of lncRNAs against pathogen responses and the progress in plant research to develop a better understanding of their functions and molecular mechanisms.

Download Full-text

PVT1: A Rising Star among Oncogenic Long Noncoding RNAs

BioMed Research International ◽

10.1155/2015/304208 ◽

2015 ◽

Vol 2015 ◽

pp. 1-10 ◽

Cited By ~ 102

Author(s):

Teresa Colombo ◽

Lorenzo Farina ◽

Giuseppe Macino ◽

Paola Paci

Keyword(s):

Noncoding Rna ◽

Molecular Mechanisms ◽

Functional Characterization ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Competing Endogenous Rna ◽

Protein Coding ◽

Myc Oncogene ◽

Non Coding Rnas

It is becoming increasingly clear that short and long noncoding RNAs critically participate in the regulation of cell growth, differentiation, and (mis)function. However, while the functional characterization of short non-coding RNAs has been reaching maturity, there is still a paucity of well characterized long noncoding RNAs, even though large studies in recent years are rapidly increasing the number of annotated ones. The long noncoding RNA PVT1 is encoded by a gene that has been long known since it resides in the well-known cancer risk region 8q24. However, a couple of accidental concurrent conditions have slowed down the study of this gene, that is, a preconception on the primacy of the protein-coding over noncoding RNAs and the prevalent interest in its neighbor MYC oncogene. Recent studies have brought PVT1 under the spotlight suggesting interesting models of functioning, such as competing endogenous RNA activity and regulation of protein stability of important oncogenes, primarily of the MYC oncogene. Despite some advancements in modelling the PVT1 role in cancer, there are many questions that remain unanswered concerning the precise molecular mechanisms underlying its functioning.

Download Full-text

Deciphering the Mounting Complexity of the p53 Regulatory Network in Correlation to Long Non-Coding RNAs (lncRNAs) in Ovarian Cancer

Cells ◽

10.3390/cells9030527 ◽

2020 ◽

Vol 9 (3) ◽

pp. 527 ◽

Cited By ~ 10

Author(s):

Sonali Pal ◽

Manoj Garg ◽

Amit Kumar Pandey

Keyword(s):

Ovarian Cancer ◽

Molecular Mechanisms ◽

Human Cancer ◽

Critical Role ◽

Functional Characterization ◽

Great Promise ◽

Altered Expression ◽

Disease Biology ◽

Non Coding Rnas ◽

Post Transcriptional Regulation

Amongst the various gynecological malignancies affecting female health globally, ovarian cancer is one of the predominant and lethal among all. The identification and functional characterization of long non-coding RNAs (lncRNAs) are made possible with the advent of RNA-seq and the advancement of computational logarithm in understanding human disease biology. LncRNAs can interact with deoxyribonucleic acid (DNA), ribonucleic acid (RNA), proteins and their combinations. Moreover, lncRNAs regulate orchestra of diverse functions including chromatin organization and transcriptional and post-transcriptional regulation. LncRNAs have conferred their critical role in key biological processes in human cancer including tumor initiation, proliferation, cell cycle, apoptosis, necroptosis, autophagy, and metastasis. The interwoven function of tumor-suppressor protein p53-linked lncRNAs in the ovarian cancer paradigm is of paramount importance. Several lncRNAs operate as p53 regulators or effectors and modulates a diverse array of functions either by participating in various signaling cascades or via interaction with different proteins. This review highlights the recent progress made in the identification of p53 associated lncRNAs while elucidating their molecular mechanisms behind the altered expression in ovarian cancer tumorigenesis. Moreover, the development of novel clinical and therapeutic strategies for targeting lncRNAs in human cancers harbors great promise.

Download Full-text

LncExpDB: an expression database of human long non-coding RNAs

Nucleic Acids Research ◽

10.1093/nar/gkaa850 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D962-D968 ◽

Cited By ~ 2

Author(s):

Zhao Li ◽

Lin Liu ◽

Shuai Jiang ◽

Qianpeng Li ◽

Changrui Feng ◽

...

Keyword(s):

Expression Profiles ◽

Biological Functions ◽

Protein Coding ◽

Web Interfaces ◽

Functional Studies ◽

Protein Coding Genes ◽

Genes Expression ◽

Wide Range ◽

Non Coding Rnas ◽

User Friendly

Abstract Expression profiles of long non-coding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability. However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range of biological conditions. Here, we present LncExpDB (https://bigd.big.ac.cn/lncexpdb), an expression database of human lncRNAs that is devoted to providing comprehensive expression profiles of lncRNA genes, exploring their expression features and capacities, identifying featured genes with potentially important functions, and building interactions with protein-coding genes across various biological contexts/conditions. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101 293 high-quality human lncRNA genes derived from 1977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes’ expression reliability and capacities, identifies 25 191 featured genes, and further obtains 28 443 865 lncRNA-mRNA interactions. Moreover, user-friendly web interfaces enable interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.

Download Full-text

Functions and Roles of Long-Non-Coding RNAs in Human Nasopharyngeal Carcinoma

Cellular Physiology and Biochemistry ◽

10.1159/000487451 ◽

2018 ◽

Vol 45 (3) ◽

pp. 1191-1204 ◽

Cited By ~ 17

Author(s):

JingJing Wu ◽

Swei Sunny Hann

Keyword(s):

Nasopharyngeal Carcinoma ◽

Functional Characterization ◽

Clinical Information ◽

Stem Cell Differentiation ◽

Cancer Prognosis ◽

Protein Coding ◽

Rna Molecules ◽

Gene Therapies ◽

Non Coding Rnas

Nasopharyngeal carcinoma (NPC) is one of the most common cancers originating in the nasopharynx and occurring at high frequency in South-eastern Asia and North Africa. Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules and key regulators of developmental, physiological, and pathological processes in humans. Emerging studies have shown that lncRNAs play critical roles in tumorgenicity and cancer prognosis. With the development of deep sequencing analyses, an extensive amount of functional lncRNAs have been discovered in nasopharyngeal carcinoma tissues and cell lines. However, the roles and mechanisms of aberrantly expressed lncRNAs in the pathogenesis of NPC are not fully understood. In this review, we briefly illustrate the concept, identification, functional characterization, and summarize recent advancements of biological functions of lncRNAs with heterogeneous mechanistic characterization and their involvement in NPC. Then, we describe individual lncRNAs that have been associated with tumorgenesis, growth, invasion, cancer stem cell differentiation, metastasis, drug resistance and discuss the strategies of their therapeutic manipulation in NPC. We also review the emerging insights into the role of lncRNAs and their potential as biomarkers and therapeutic targets for novel treatment paradigms. Finally, we highlight the up-to-date of clinical information involving lncRNAs and future directions in the linking lncRNAs to potential gene therapies, and how modifications of lncRNAs can be exploited for prevention and treatment of NPC.

Download Full-text

Regulation of ST6GAL1 sialyltransferase expression in cancer cells

Glycobiology ◽

10.1093/glycob/cwaa110 ◽

2020 ◽

Author(s):

Kaitlyn A Dorsett ◽

Michael P Marciel ◽

Jihye Hwang ◽

Katherine E Ankenbauer ◽

Nikita Bhalerao ◽

...

Keyword(s):

Cancer Cells ◽

Translational Regulation ◽

Molecular Mechanisms ◽

Current Knowledge ◽

Sialic Acids ◽

Invasion Resistance ◽

Cell Behaviors ◽

Molecular Events ◽

Wide Range

Abstract The ST6GAL1 sialyltransferase, which adds α2–6 linked sialic acids to N-glycosylated proteins, is overexpressed in a wide range of human malignancies. Recent studies have established the importance of ST6GAL1 in promoting tumor cell behaviors such as invasion, resistance to cell stress, and chemoresistance. Furthermore, ST6GAL1 activity has been implicated in imparting cancer stem cell characteristics. However, despite the burgeoning interest in the role of ST6GAL1 in the phenotypic features of tumor cells, insufficient attention has been paid to the molecular mechanisms responsible for ST6GAL1 upregulation during neoplastic transformation. Evidence suggests that these mechanisms are multifactorial, encompassing genetic, epigenetic, transcriptional, and post-translational regulation. The purpose of this review is to summarize current knowledge regarding the molecular events that drive enriched ST6GAL1 expression in cancer cells.

Download Full-text

An expanded mouse testis transcriptome and mass spectrometry defines novel proteins

Reproduction ◽

10.1530/rep-19-0092 ◽

2020 ◽

Vol 159 (1) ◽

pp. 15-26 ◽

Cited By ~ 2

Author(s):

Jaya Gamble ◽

Joel Chick ◽

Kelly Seltzer ◽

Joel H Graber ◽

Steven Gygi ◽

...

Keyword(s):

Mass Spectrometry ◽

Cell Types ◽

Round Spermatid ◽

Novel Genes ◽

Protein Coding ◽

Novel Proteins ◽

Wide Range ◽

Novel Transcripts ◽

Coding Potential ◽

Novel Isoforms

The testis transcriptome is exceptionally complex. Despite its complexity, previous testis transcriptome analyses relied on a reductive method for transcript identification, thus underestimating transcriptome complexity. We describe here a more complete testis transcriptome generated by combining Tuxedo, a reductive method, and spliced-RUM, a combinatorial transcript-building approach. Forty-two percent of the expanded testis transcriptome is composed of unannotated RNAs with novel isoforms of known genes and novel genes constituting 78 and 9.8% of the newly discovered transcripts, respectively. Across tissues, novel transcripts were predominantly expressed in the testis with the exception of novel isoforms which were also highly expressed in the adult ovary. Within the testis, novel isoform expression was distributed equally across all cell types while novel genes were predominantly expressed in meiotic and post-meiotic germ cells. The majority of novel isoforms retained their protein-coding potential while most novel genes had low protein-coding potential. However, a subset of novel genes had protein-coding potentials equivalent to known protein-coding genes. Shotgun mass spectrometry of round spermatid total protein identified unique peptides from four novel genes along with seven annotated non-coding RNAs. These analyses demonstrate the testis expresses a wide range of novel transcripts that give rise to novel proteins.

Download Full-text

Signal Integration in Plant Abiotic Stress Responses via Multistep Phosphorelay Signaling

Frontiers in Plant Science ◽

10.3389/fpls.2021.644823 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jan Skalak ◽

Katrina Leslie Nicolas ◽

Radomira Vankova ◽

Jan Hejatko

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Environmental Conditions ◽

Molecular Mechanisms ◽

Geographical Location ◽

Survival Strategies ◽

Balance Growth ◽

Adaptive Responses ◽

Wide Range ◽

Sensor Kinases

Plants growing in any particular geographical location are exposed to variable and diverse environmental conditions throughout their lifespan. The multifactorial environmental pressure resulted into evolution of plant adaptation and survival strategies requiring ability to integrate multiple signals that combine to yield specific responses. These adaptive responses enable plants to maintain their growth and development while acquiring tolerance to a variety of environmental conditions. An essential signaling cascade that incorporates a wide range of exogenous as well as endogenous stimuli is multistep phosphorelay (MSP). MSP mediates the signaling of essential plant hormones that balance growth, development, and environmental adaptation. Nevertheless, the mechanisms by which specific signals are recognized by a commonly-occurring pathway are not yet clearly understood. Here we summarize our knowledge on the latest model of multistep phosphorelay signaling in plants and the molecular mechanisms underlying the integration of multiple inputs including both hormonal (cytokinins, ethylene and abscisic acid) and environmental (light and temperature) signals into a common pathway. We provide an overview of abiotic stress responses mediated via MSP signaling that are both hormone-dependent and independent. We highlight the mutual interactions of key players such as sensor kinases of various substrate specificities including their downstream targets. These constitute a tightly interconnected signaling network, enabling timely adaptation by the plant to an ever-changing environment. Finally, we propose possible future directions in stress-oriented research on MSP signaling and highlight its potential importance for targeted crop breeding.

Download Full-text

Characterization and identification of long non-coding RNAs based on feature relationship

10.1101/327882 ◽

2018 ◽

Cited By ~ 2

Author(s):

Guangyu Wang ◽

Hongyan Yin ◽

Boyang Li ◽

Chunlei Yu ◽

Fan Wang ◽

...

Keyword(s):

Prior Knowledge ◽

Large Scale ◽

Gc Content ◽

Training Data ◽

Significant Advance ◽

Protein Coding ◽

Reading Frame ◽

Wide Range ◽

Non Coding Rnas ◽

Computational Identification

ABSTRACTThe significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations. Here we first characterize lncRNAs by contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between ORF (open reading frame) length and GC content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (>90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species.

Download Full-text

Emerging Role of Long Non-Coding RNAs in Diabetic Vascular Complications

Frontiers in Endocrinology ◽

10.3389/fendo.2021.665811 ◽

2021 ◽

Vol 12 ◽

Author(s):

Vinay Singh Tanwar ◽

Marpadga A. Reddy ◽

Rama Natarajan

Keyword(s):

Drug Targets ◽

Molecular Mechanisms ◽

Microvascular Complications ◽

Vascular Complications ◽

Protein Coding ◽

Altered Expression ◽

Diabetic Vascular Complications ◽

Obesity And Diabetes ◽

Non Coding Rnas ◽

Species Specific

Chronic metabolic disorders such as obesity and diabetes are associated with accelerated rates of macrovascular and microvascular complications, which are leading causes of morbidity and mortality worldwide. Further understanding of the underlying molecular mechanisms can aid in the development of novel drug targets and therapies to manage these disorders more effectively. Long non-coding RNAs (lncRNAs) that do not have protein-coding potential are expressed in a tissue- and species-specific manner and regulate diverse biological processes. LncRNAs regulate gene expression in cis or in trans through various mechanisms, including interaction with chromatin-modifying proteins and other regulatory proteins and via posttranscriptional mechanisms, including acting as microRNA sponges or as host genes of microRNAs. Emerging evidence suggests that major pathological factors associated with diabetes such as high glucose, free fatty acids, proinflammatory cytokines, and growth factors can dysregulate lncRNAs in inflammatory, cardiac, vascular, and renal cells leading to altered expression of key inflammatory genes and fibrotic genes associated with diabetic vascular complications. Here we review recent reports on lncRNA characterization, functions, and mechanisms of action in diabetic vascular complications and translational approaches to target them. These advances can provide new insights into the lncRNA-dependent actions and mechanisms underlying diabetic vascular complications and uncover novel lncRNA-based biomarkers and therapies to reduce disease burden and mortality.

Download Full-text