scholarly journals Epigenomics of Plant’s Responses to Environmental Stress

2017 ◽  
Author(s):  
Suresh Kumar
Keyword(s):  
Gene Expression ◽  
Nuclear Dna ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Epigenetic Changes ◽  
Post Translational Modifications ◽  
Genome Wide ◽  
A Cell ◽  
Non Coding Rnas ◽  
Function Activity

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

scholarly journals Epigenomics of Plant’s Responses to Environmental Stress

2017 ◽  
Author(s):  
Suresh Kumar
Keyword(s):  
Gene Expression ◽  
Nuclear Dna ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Epigenetic Changes ◽  
Post Translational Modifications ◽  
Genome Wide ◽  
A Cell ◽  
Non Coding Rnas ◽  
Function Activity

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

scholarly journals Epigenomics of Plant’s Responses to Environmental Stress

2017 ◽  
Author(s):  
Suresh Kumar
Keyword(s):  
Gene Expression ◽  
Nuclear Dna ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Epigenetic Changes ◽  
Post Translational Modifications ◽  
Genome Wide ◽  
A Cell ◽  
Non Coding Rnas ◽  
Function Activity

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of small non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

scholarly journals Genome-Wide Analysis of Alternative Splicing and Non-Coding RNAs Reveal Complicated Transcriptional Regulation in Cannabis sativa L.

2021 ◽  
Vol 22 (21) ◽  
pp. 11989
Author(s):  
Bin Wu ◽  
Yanni Li ◽  
Jishuang Li ◽  
Zhenzhen Xie ◽  
Mingbao Luan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Biosynthetic Pathway ◽  
Cannabis Sativa ◽  
Transcriptional Level ◽  
Gene Expression And Regulation ◽  
Structural Genes ◽  
Key Enzymes ◽  
Genome Wide ◽  
Non Coding Rnas

It is of significance to mine the structural genes related to the biosynthetic pathway of fatty acid (FA) and cellulose as well as explore the regulatory mechanism of alternative splicing (AS), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the biosynthesis of cannabinoids, FA and cellulose, which would enhance the knowledge of gene expression and regulation at post-transcriptional level in Cannabis sativa L. In this study, transcriptome, small RNA and degradome libraries of hemp ‘Yunma No.1’ were established, and comprehensive analysis was performed. As a result, a total of 154, 32 and 331 transcripts encoding key enzymes involved in the biosynthesis of cannabinoids, FA and cellulose were predicted, respectively, among which AS occurred in 368 transcripts. Moreover, 183 conserved miRNAs, 380 C. sativa-specific miRNAs and 7783 lncRNAs were predicted. Among them, 70 miRNAs and 17 lncRNAs potentially targeted 13 and 17 transcripts, respectively, encoding key enzymes or transporters involved in the biosynthesis of cannabinoids, cellulose or FA. Finally, the crosstalk between AS and miRNAs or lncRNAs involved in cannabinoids and cellulose was also predicted. In summary, all these results provided insights into the complicated network of gene expression and regulation in C. sativa.

scholarly journals Capture, amplification, and global profiling of microRNAs from low quantities of whole cell lysate

The Analyst ◽  
2017 ◽  
Vol 142 (17) ◽  
pp. 3203-3211 ◽  
Author(s):  
Nayi Wang ◽  
Jijun Cheng ◽  
Rong Fan ◽  
Jun Lu
Keyword(s):  
Gene Expression ◽  
Regulatory Network ◽  
Transcriptional Level ◽  
Control Gene ◽  
Whole Cell Lysate ◽  
Cell Lysate ◽  
Control Gene Expression ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Complex Regulatory Network

MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression at the post-transcriptional levelviaa complex regulatory network that requires genome-wide miRNA profiling to dissect.

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

Abstract P252: Loss of HMGB2 Induces Chromatin Remodeling and Hypertrophic Growth in Cardiomyocytes

2011 ◽  
Vol 109 (suppl_1) ◽  
Author(s):  
Sarah Franklin ◽  
Haodong Chen ◽  
Scherise Mitchell-Jordan ◽  
Shuxun Ren ◽  
Peipei Ping ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mass Spectrometry ◽  
Chromatin Remodeling ◽  
Nuclear Dna ◽  
Specific Pattern ◽  
Altered Expression ◽  
Hypertrophic Growth ◽  
Knock Down ◽  
Genome Wide ◽  
Chromatin Structural

Nuclear DNA is packaged around the octameric nucleosome core particle, constituting the basic building block of chromatin. Non-nucleosome chromatin structural molecules have been shown to induce higher order packaging of DNA into structurally compact and inactive heterochromatin, or loosely packed and active euchromatin. These chromatin remodeling events are thought to establish a cell type specific pattern of gene expression. During the development of cardiac hypertrophy and failure, genes normally only expressed during development are re-activated. While a number of transcription factors involved in these changes in fetal gene expression have been identified, the means for genome-wide structural remodeling of DNA are unknown. To identify factors controlling genomic plasticity in cardiomyocytes, we used mass spectrometry to quantify chromatin-associated proteins from cardiac nuclei during stages of hypertrophy and failure in the mouse. Adult mice were subjected to cardiac pressure overload by transverse aortic constriction. Chromatin was fractionated from cardiac nuclei and DNA-bound proteins were acid extracted and analyzed by mass spectrometry. We measured chromatin occupancy patterns for >300 proteins during distinct stages of heart failure. To explore the isoform specific roles of individual chromatin structural proteins, we used siRNA to knock-down expression of two high mobility group proteins (HMGB1 and 2) exhibiting altered expression in the hypertrophic heart. Loss of HMGB2 (but not HMGB1) induced robust hypertrophic growth in cardiomyocytes. qRT-PCR analyses demonstrated that HMGB2 is responsible for some but not all changes in the fetal gene program (ANF increased 150% and SERCA decreased 20%, whereas α- and β-MHC were unchanged). To further explore the endogenous regions of the genome under control of HMGB2 packing, we performed microarrays following HMGB2 knockdown. Hypertrophy or HMGB2 knock-down induced global chromatin remodeling conducive to gene expression, as measured by histone post-translational modifications and the ratio of core to linker histones. These studies reveal a novel role of HMGB2 to inhibit hypertrophic growth and provide insights into general principles for genome-wide chromatin remodeling.

Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat

2021 ◽  
Author(s):  
Juan Manuel Crescente ◽  
Diego Zavallo ◽  
Mariana del Vas ◽  
Sebastian Asurmendi ◽  
Marcelo Helguera ◽  
...  
Keyword(s):  
Gene Expression ◽  
Triticum Aestivum ◽  
Transposable Elements ◽  
Small Rna ◽  
Translational Repression ◽  
High Homology ◽  
Genome Wide ◽  
Target Sites ◽  
The Common ◽  
Non Coding Rnas

Abstract Plant microRNAs (miRNAs) are a class of small non-coding RNAs that are 20–24 nucleotides length and can repress gene expression at post-transcriptional levels by target degradation or translational repression. There is increasing evidence that some microRNAs can be derived from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs) in plants. We used public small RNA, degradome libraries and the common wheat (Triticum aestivum) genome to screen miRNAs production and target sites. We also created a comprehensive wheat MITE database using known and identifying novel elements. We found high homology between MITEs and 14% of all the miRNAs production sites in wheat. Furthermore, we show that MITE-derived miRNAs have preference for target degradation sites with MITE insertions in 3' UTR regions in wheat.

scholarly journals Distinct CoREST complexes act in a cell-type-specific manner

2019 ◽  
Author(s):  
Igor Mačinković ◽  
Ina Theofel ◽  
Tim Hundertmark ◽  
Kristina Kovač ◽  
Stephan Awe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Germ Line ◽  
Protein Complexes ◽  
Specific Gene ◽  
S2 Cells ◽  
Cell Type ◽  
Specific Gene Expression ◽  
Genome Wide ◽  
A Cell ◽  
Cell Type Specific

Abstract CoREST has been identified as a subunit of several protein complexes that generate transcriptionally repressive chromatin structures during development. However, a comprehensive analysis of the CoREST interactome has not been carried out. We use proteomic approaches to define the interactomes of two dCoREST isoforms, dCoREST-L and dCoREST-M, in Drosophila. We identify three distinct histone deacetylase complexes built around a common dCoREST/dRPD3 core: A dLSD1/dCoREST complex, the LINT complex and a dG9a/dCoREST complex. The latter two complexes can incorporate both dCoREST isoforms. By contrast, the dLSD1/dCoREST complex exclusively assembles with the dCoREST-L isoform. Genome-wide studies show that the three dCoREST complexes associate with chromatin predominantly at promoters. Transcriptome analyses in S2 cells and testes reveal that different cell lineages utilize distinct dCoREST complexes to maintain cell-type-specific gene expression programmes: In macrophage-like S2 cells, LINT represses germ line-related genes whereas other dCoREST complexes are largely dispensable. By contrast, in testes, the dLSD1/dCoREST complex prevents transcription of germ line-inappropriate genes and is essential for spermatogenesis and fertility, whereas depletion of other dCoREST complexes has no effect. Our study uncovers three distinct dCoREST complexes that function in a lineage-restricted fashion to repress specific sets of genes thereby maintaining cell-type-specific gene expression programmes.

microRNAs: a new frontier in kallikrein research

2008 ◽  
Vol 389 (6) ◽  
Author(s):  
George M. Yousef
Keyword(s):  
Gene Expression ◽  
Human Tissue ◽  
In Silico ◽  
Regulatory Mechanism ◽  
Transcriptional Level ◽  
Regulate Gene Expression ◽  
New Frontier ◽  
Experimental Approaches ◽  
Non Coding Rnas ◽  
Regulate Gene

Abstract microRNAs (miRNAs) are a recently discovered class of small non-coding RNAs that regulate gene expression. Rapidly accumulating evidence has revealed that miRNAs are associated with cancer. The human tissue kalli-krein gene family is the largest contiguous family of proteases in the human genome, containing 15 genes. Many kallikreins have been reported as potential tumor markers. In this review, recent bioinformatics and experimental evidence is presented indicating that kallikreins are potential miRNA targets. The available experimental approaches to investigate these interactions and the potential diagnostic and therapeutic applications are also discussed. miRNAs represent a possible regulatory mechanism for controlling kallikrein expression at the post-transcriptional level. Many miRNAs were predicted to target kallikreins and a single miRNA can target more than one kallikrein. Recent evidence suggests that miRNAs can also exert ‘quantitative’ control of kallikreins by utilizing multiple targeting sites in the kallikrein mRNA. More research is needed to experimentally verify the in silico predictions and to investigate the possible role in tumor initiation and/or progression.

scholarly journals Study strategies for long non-coding RNAs and their roles in regulating gene expression

2015 ◽  
Vol 20 (2) ◽  
Author(s):  
Dan Qin ◽  
Cunshuan Xu
Keyword(s):  
Gene Expression ◽  
Regulatory Network ◽  
Experimental Methods ◽  
Study Strategies ◽  
Mechanisms Of Action ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Non Coding Rnas

AbstractLong non-coding RNAs (lncRNAs) have attracted considerable attention recently due to their involvement in numerous key cellular processes and in the development of various disorders. New high-throughput methods enable their study on a genome-wide scale. Numerous lncRNAs have been identified and characterized as important members of the biological regulatory network, with significant roles in regulating gene expression at the epigenetic, transcriptional and post-transcriptional levels. This paper summarizes the diverse mechanisms of action of these lncRNAs and looks at the study strategies in this field. A major challenge in future study is to establish more effective bioinformatics and experimental methods to explore the functions, detailed mechanisms of action and structures deciding the functional diversity of lncRNAs, since the vast majority remain unresolved.

Sign in / Sign up

Export Citation Format

Share Document