Abiotic Stress Tolerance in Soybean : Regulated by ncRNA

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
YASIN JESHIMA KHAN ◽  
HUSNARA Tyagi ◽  
Anil kumar Singh ◽  
Santosh kumar. Magadum
Keyword(s):  
Abiotic Stresses ◽  
Target Genes ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Vital Role ◽  
Grain Legume ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Cellular Environment ◽  
Non Coding Rnas

Plants respond through a cascade of reactions resulting in varied cellular environment leading to alterations in the patterns of protein expression resulting in phonotypic changes. Single cell genomics and global proteomics came out to be powerful tools and efficient techniques in studying stress tolerant plants. Non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. Small ncRNAs play a vital role in post transcriptional gene regulation by either translational repression or by inducing mRNA cleavage. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs too have a similar structure, function, and biogenesis like miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences.In this review, we focus on the involvement of ncRNAs in comabting abiotic stresses of soybean. This review emphasis on previously known miRNAs as they play important role in several abiotic stresses like drought, salinity, chilling and heat stress by their diverse roles in mediating biological processes like gene expression, chromatin formation, defense of genome against invading viruses. This review attempts to elucidate the various kinds of non-coding RNAs explored, their discovery, biogenesis, functions, and response for different type of abiotic stresses and future aspects for crop improvement in the context of soybean, a representative grain legume.

LncRNAs a New Target for Post-Stroke Recovery

2020 ◽  
Vol 26 (26) ◽  
pp. 3115-3121
Author(s):  
Jun Yang ◽  
Jingjing Zhao ◽  
Xu Liu ◽  
Ruixia Zhu
Keyword(s):  
Ischemic Stroke ◽  
Microglial Activation ◽  
Vital Role ◽  
Stroke Recovery ◽  
Biological Processes ◽  
Current Development ◽  
Post Stroke ◽  
Cascade Processes ◽  
Non Coding Rnas ◽  
Neuron Injury

LncRNAs (long non-coding RNAs) are endogenous molecules, involved in complicated biological processes. Increasing evidence has shown that lncRNAs play a vital role in the post-stroke pathophysiology. Furthermore, several lncRNAs were reported to mediate ischemia cascade processes include apoptosis, bloodbrain barier breakdown, angiogenesis, microglial activation induced neuroinflammation which can cause neuron injury and influence neuron recovery after ischemic stroke. In our study, we first summarize current development about lncRNAs and post-stroke, focus on the regulatory roles of lncRNAs on pathophysiology after stroke. We also reviewed genetic variation in lncRNA associated with functional outcome after ischemic stroke. Additionally, lncRNA-based therapeutics offer promising strategies to decrease brain damage and promote neurological recovery following ischemic stroke. We believe that lncRNAs will become promising for the frontier strategies for IS and can open up a new path for the treatment of IS in the future.

scholarly journals Emerging microRNA biomarkers for colorectal cancer diagnosis and prognosis

Open Biology ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 180212 ◽  
Author(s):  
Bing Chen ◽  
Zijing Xia ◽  
Ya-Nan Deng ◽  
Yanfang Yang ◽  
Peng Zhang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Target Genes ◽  
Research Use ◽  
Biological Processes ◽  
Functional Roles ◽  
Analytical Technique ◽  
Diagnosis And Prognosis ◽  
Recurrence Prediction ◽  
Extracellular Mirnas ◽  
Non Coding Rnas

MicroRNAs (miRNAs) are one abundant class of small, endogenous non-coding RNAs, which regulate various biological processes by inhibiting expression of target genes. miRNAs have important functional roles in carcinogenesis and development of colorectal cancer (CRC), and emerging evidence has indicated the feasibility of miRNAs as robust cancer biomarkers. This review summarizes the progress in miRNA-related research, including study of its oncogene or tumour-suppressor roles and the advantages of miRNA biomarkers for CRC diagnosis, treatment and recurrence prediction. Along with analytical technique improvements in miRNA research, use of the emerging extracellular miRNAs is feasible for CRC diagnosis and prognosis.

scholarly journals Systematic Prediction of the Impacts of Mutations in MicroRNA Seed Sequences

2017 ◽  
Vol 14 (1) ◽  
Author(s):  
Anindya Bhattacharya ◽  
Yan Cui
Keyword(s):  
Target Genes ◽  
Computational Method ◽  
Seed Region ◽  
Biological Processes ◽  
Crucial Importance ◽  
Single Nucleotide ◽  
Knowledge Based ◽  
Original Target ◽  
Non Coding Rnas ◽  
Comprehensive Reference

AbstractMicroRNAs are a class of small non-coding RNAs that are involved in many important biological processes and the dysfunction of microRNA has been associated with many diseases. The seed region of a microRNA is of crucial importance to its target recognition. Mutations in microRNA seed regions may disrupt the binding of microRNAs to their original target genes and make them bind to new target genes. Here we use a knowledge-based computational method to systematically predict the functional effects of all the possible single nucleotide mutations in human microRNA seed regions. The result provides a comprehensive reference for the functional assessment of the impacts of possible natural and artificial single nucleotide mutations in microRNA seed regions.

Genomics Approaches for Abiotic Stress in Crop Resources

2014 ◽  
Vol 955-959 ◽  
pp. 3709-3712
Author(s):  
Mao Bo Zheng ◽  
Hai Bin Zhao ◽  
Yan Ming Zhang
Keyword(s):  
Abiotic Stress ◽  
Plant Species ◽  
Abiotic Stresses ◽  
Crop Improvement ◽  
Biological Processes ◽  
Rapid Progress ◽  
Entire Genome ◽  
Molecular Responses ◽  
Intergenic Regions

Rapid progress of crop genomics is making possible to undertake detailed structural and functional comparisons of genes involved in various biological processes among important crops and other plant species. These genomics-based approaches aim to decipher the entire genome, including genic and intergenic regions, to gain insights into plant molecular responses which will in turn provide specific strategies for crop improvement,especially in abiotic stresses. The objectives of this article are to review genomics approaches in crop resources and summarize to improve abiotic stresses by genomics. At last, we look forward and consider the significant of genomics approaches for abiotic stress in crop resources.

scholarly journals Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System

Life ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 148
Author(s):  
Xiaolan Chen ◽  
Bahareldin Ali Abdalla ◽  
Zhenhui Li ◽  
Qinghua Nie
Keyword(s):  
Immune System ◽  
Circular Rnas ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Transfer Rnas ◽  
Small Nuclear Rnas ◽  
Non Coding Rnas ◽  
Avian Diseases ◽  
Regulatory Rnas ◽  
Functional Mechanisms

The identified non-coding RNAs (ncRNAs) include circular RNAs, long non-coding RNAs, microRNAs, ribosomal RNAs, small interfering RNAs, small nuclear RNAs, piwi-interacting RNAs, and transfer RNAs, etc. Among them, long non-coding RNAs, circular RNAs, and microRNAs are regulatory RNAs that have different functional mechanisms and were extensively participated in various biological processes. Numerous research studies have found that circular RNAs, long non-coding RNAs, and microRNAs played their important roles in avian immune system during the infection of parasites, virus, or bacterium. Here, we specifically review and expand this knowledge with current advances of circular RNAs, long non-coding RNAs, and microRNAs in the regulation of different avian diseases and discuss their functional mechanisms in response to avian diseases.

scholarly journals Regulatory non-coding RNAs: a new frontier in regulation of plant biology

2021 ◽  
Author(s):  
Sailaja Bhogireddy ◽  
Satendra K. Mangrauthia ◽  
Rakesh Kumar ◽  
Arun K. Pandey ◽  
Sadhana Singh ◽  
...  
Keyword(s):  
Stress Responses ◽  
Crop Improvement ◽  
Plant Biology ◽  
Circular Rnas ◽  
Homologous Sequence ◽  
Small Interfering Rnas ◽  
Rna Molecules ◽  
New Frontier ◽  
Non Coding Rnas

AbstractBeyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.

scholarly journals Conventional and Molecular Breeding Tools for Accelerating Genetic Gain in Faba Bean (Vicia Faba L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Kedar N. Adhikari ◽  
Hamid Khazaei ◽  
Lamiae Ghaouti ◽  
Fouad Maalouf ◽  
Albert Vandenberg ◽  
...  
Keyword(s):  
Grain Yield ◽  
Faba Bean ◽  
Genetic Gain ◽  
Dna Markers ◽  
Abiotic Stresses ◽  
Selection Process ◽  
Abiotic Stress Tolerance ◽  
Ascochyta Blight ◽  
Grain Legume ◽  
Breeding Programs

Faba bean is a cool-season grain legume crop, which is grown worldwide for food and feed. Despite a decrease in area under faba bean in the past, the interest in growing faba bean is increasing globally due to its high seed protein content and its excellent ecological service. The crop is, however, exposed to diverse biotic and abiotic stresses causing unstable, low grain yield. Although, sources of resistance to main diseases, such as ascochyta blight (Ascochyta fabae Speg.), rust (Uromyces viciae-fabae (Pers.) Schroet.), chocolate spot (Botrytis fabae Sard.) and gall disease (Physioderma viciae), have been identified, their resistance is only partial and cannot prevent grain yield losses without agronomical practices. Tightly associated DNA markers for host plant resistance genes are needed to enhance the level of resistance. Less progress has been made for abiotic stresses. Different breeding methods are proposed, but until now line breeding, based on the pedigree method, is the dominant practice in breeding programs. Nonetheless, the low seed multiplication coefficient and the requirement for growing under insect-proof enclosures to avoid outcrossing hampers breeding, along with the lack of tools such as double haploid system and cytoplasmic male sterility. This reduces breeding population size and speed of breeding hence the chances of capturing rare combinations of favorable alleles. Availability and use of the DNA markers such as vicine-convicine (vc−) and herbicide tolerance in breeding programs have encouraged breeders and given confidence in marker assisted selection. Closely linked QTL for several biotic and abiotic stress tolerance are available and their verification and conversion in breeder friendly platform will enhance the selection process. Recently, genomic selection and speed breeding techniques together with genomics have come within reach to accelerate the genetic gains in faba bean. Advancements in genomic resources with other breeding tools, methods and platforms will enable to accelerate the breeding process for enhancing genetic gain in this species.

scholarly journals PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Wenyi Wu ◽  
Yan Wu ◽  
Dahui Hu ◽  
Yincong Zhou ◽  
Yanshi Hu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Abiotic Stresses ◽  
Plant Stress ◽  
Biological Information ◽  
Network Visualization ◽  
Circular Rnas ◽  
Biological Processes ◽  
Current Version ◽  
Plant Stress Responses ◽  
Non Coding Rnas

Abstract Non-coding RNAs (ncRNAs) are recognized as key regulatory molecules in many biological processes. Accumulating evidence indicates that ncRNA-related mechanisms play important roles in plant stress responses. Although abundant plant stress-responsive ncRNAs have been identified, these experimentally validated results have not been gathered into a single public domain archive. Therefore, we established PncStress by curating experimentally validated stress-responsive ncRNAs in plants, including microRNAs, long non-coding RNAs and circular RNAs. The current version of PncStress contains 4227 entries from 114 plants covering 48 biotic and 91 abiotic stresses. For each entry, PncStress has biological information and network visualization. Serving as a manually curated database, PncStress will become a valuable resource in support of plant stress response research.

scholarly journals OsDOF18, A DOF Transcription Factor from Rice Confers Abiotic Stress Tolerance in Escherichia coli

2017 ◽  
Vol 60 (2) ◽  
pp. 70-79
Author(s):  
Syed Muhammad Saqlan Naqvi ◽  
Farah Deeba ◽  
Tasawar Sultana ◽  
Ghazala Kaukab Raja
Keyword(s):  
Escherichia Coli ◽  
Dna Binding ◽  
Abiotic Stresses ◽  
Abiotic Stress Tolerance ◽  
Three Dimensional ◽  
Vital Role ◽  
Dimensional Structure ◽  
Multiple Sequence ◽  
E Coli ◽  
Tolerant Plants

DNA binding with one finger proteins (DOF) play vital role in many cellular including bioticand abiotic stresses. In present study, OsDOF18, a member of DOF gene family from Oryza sativa wascloned into GST expression vector (pGEX4T-1) and sequenced. The sequence was subjected to in silicocharacterisation including similarity search, multiple sequence alignment followed by phylogenetic study.The three dimensional structure was predicted by I-TASSER server followed by authentication usingPROCHECK and QMEAN tools. Analysis of OsDOF18 by RT-qPCR confirmed the association of OsDOF18with abiotic stresses including salinity and drought. DNA binding domain containing region was clonedand over-expressed in Escherichia coli for stress analysis. OsDOF18 protein improved the E. coli survivabilityagainst salinity and drought stresses. The results suggested OsDOF18 as a stress-related gene in rice thatmay be used in generating stress tolerant plants.

scholarly journals miRinGO: Prediction of biological processes indirectly targeted by human microRNAs

2020 ◽  
Author(s):  
Mohammed Sayed ◽  
Juw Won Park
Keyword(s):  
Target Genes ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Go Enrichment ◽  
R Shiny ◽  
Canonical Approach ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation ◽  
Go Enrichment Analysis ◽  
Shiny Application

AbstractMicroRNAs are small non-coding RNAs that are known for their role in post-transcriptional regulation of target genes. Typically, their functions are predicted by first identifying their target genes and then finding biological processes enriched in these targets. Current tools for miRNA functional analysis use only genes with physical binding sites as their targets and exclude other genes that are indirectly targeted transcriptionally through transcription factors. Here, we introduce a method to predict gene ontology (GO) annotations indirectly targeted by microRNAs. The proposed method resulted in better performance in predicting known miRNA-GO term associations compared to the canonical approach. To facilitate miRNA GO enrichment analysis, we developed an R Shiny application, miRinGO, that is freely available from GitHub at https://github.com/Fadeel/miRinGO

Sign in / Sign up

Export Citation Format

Share Document