scholarly journals Can Forest Trees Cope with Climate Change?—Effects of DNA Methylation on Gene Expression and Adaptation to Environmental Change

2021 ◽  
Vol 22 (24) ◽  
pp. 13524
Author(s):  
Ewelina A. Klupczyńska ◽  
Ewelina Ratajczak
Keyword(s):  
Climate Change ◽  
Gene Expression ◽  
Dna Methylation ◽  
Global Climate ◽  
Regional Climate ◽  
Expression Patterns ◽  
Forest Tree ◽  
Epigenetic Modifications ◽  
Specific Expression ◽  
Epigenome Editing

Epigenetic modifications, including chromatin modifications and DNA methylation, play key roles in regulating gene expression in both plants and animals. Transmission of epigenetic markers is important for some genes to maintain specific expression patterns and preserve the status quo of the cell. This article provides a review of existing research and the current state of knowledge about DNA methylation in trees in the context of global climate change, along with references to the potential of epigenome editing tools and the possibility of their use for forest tree research. Epigenetic modifications, including DNA methylation, are involved in evolutionary processes, developmental processes, and environmental interactions. Thus, the implications of epigenetics are important for adaptation and phenotypic plasticity because they provide the potential for tree conservation in forest ecosystems exposed to adverse conditions resulting from global warming and regional climate fluctuations.

scholarly journals Dynamics of DNA Methylation and Its Functions in Plant Growth and Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Suresh Kumar ◽  
Trilochan Mohapatra
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Genome Stability ◽  
De Novo ◽  
Developmental Process ◽  
Global Climate ◽  
Regulation Of Gene Expression ◽  
Biotic Stresses ◽  
Epigenome Editing ◽  
Dna Base

Epigenetic modifications in DNA bases and histone proteins play important roles in the regulation of gene expression and genome stability. Chemical modification of DNA base (e.g., addition of a methyl group at the fifth carbon of cytosine residue) switches on/off the gene expression during developmental process and environmental stresses. The dynamics of DNA base methylation depends mainly on the activities of the writer/eraser guided by non-coding RNA (ncRNA) and regulated by the developmental/environmental cues. De novo DNA methylation and active demethylation activities control the methylation level and regulate the gene expression. Identification of ncRNA involved in de novo DNA methylation, increased DNA methylation proteins guiding DNA demethylase, and methylation monitoring sequence that helps maintaining a balance between DNA methylation and demethylation is the recent developments that may resolve some of the enigmas. Such discoveries provide a better understanding of the dynamics/functions of DNA base methylation and epigenetic regulation of growth, development, and stress tolerance in crop plants. Identification of epigenetic pathways in animals, their existence/orthologs in plants, and functional validation might improve future strategies for epigenome editing toward climate-resilient, sustainable agriculture in this era of global climate change. The present review discusses the dynamics of DNA methylation (cytosine/adenine) in plants, its functions in regulating gene expression under abiotic/biotic stresses, developmental processes, and genome stability.

scholarly journals Passive and active DNA methylation and the interplay with genetic variation in gene regulation

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Maria Gutierrez-Arcelus ◽  
Tuuli Lappalainen ◽  
Stephen B Montgomery ◽  
Alfonso Buil ◽  
Halit Ongen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Gene Regulation ◽  
Genetic Variation ◽  
Genomic Sequence ◽  
Expression Patterns ◽  
Active Role ◽  
Epigenetic Mark ◽  
Sequencing Data ◽  
Specific Expression

DNA methylation is an essential epigenetic mark whose role in gene regulation and its dependency on genomic sequence and environment are not fully understood. In this study we provide novel insights into the mechanistic relationships between genetic variation, DNA methylation and transcriptome sequencing data in three different cell-types of the GenCord human population cohort. We find that the association between DNA methylation and gene expression variation among individuals are likely due to different mechanisms from those establishing methylation-expression patterns during differentiation. Furthermore, cell-type differential DNA methylation may delineate a platform in which local inter-individual changes may respond to or act in gene regulation. We show that unlike genetic regulatory variation, DNA methylation alone does not significantly drive allele specific expression. Finally, inferred mechanistic relationships using genetic variation as well as correlations with TF abundance reveal both a passive and active role of DNA methylation to regulatory interactions influencing gene expression.

scholarly journals Response of altitudinal vegetation belts of the Tianshan Mountains in northwestern China to climate change during 1989–2015

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yong Zhang ◽  
Lu-yu Liu ◽  
Yi Liu ◽  
Man Zhang ◽  
Cheng-bang An
Keyword(s):  
Climate Change ◽  
Global Climate Change ◽  
Global Climate ◽  
Animal Husbandry ◽  
Forest Tree ◽  
Tianshan Mountains ◽  
Northwestern China ◽  
Temperature And Precipitation ◽  
Altitudinal Belts ◽  
The Impact

AbstractWithin the mountain altitudinal vegetation belts, the shift of forest tree lines and subalpine steppe belts to high altitudes constitutes an obvious response to global climate change. However, whether or not similar changes occur in steppe belts (low altitude) and nival belts in different areas within mountain systems remain undetermined. It is also unknown if these, responses to climate change are consistent. Here, using Landsat remote sensing images from 1989 to 2015, we obtained the spatial distribution of altitudinal vegetation belts in different periods of the Tianshan Mountains in Northwestern China. We suggest that the responses from different altitudinal vegetation belts to global climate change are different. The changes in the vegetation belts at low altitudes are spatially different. In high-altitude regions (higher than the forest belts), however, the trend of different altitudinal belts is consistent. Specifically, we focused on analyses of the impact of changes in temperature and precipitation on the nival belts, desert steppe belts, and montane steppe belts. The results demonstrated that the temperature in the study area exhibited an increasing trend, and is the main factor of altitudinal vegetation belts change in the Tianshan Mountains. In the context of a significant increase in temperature, the upper limit of the montane steppe in the eastern and central parts will shift to lower altitudes, which may limit the development of local animal husbandry. The montane steppe in the west, however, exhibits the opposite trend, which may augment the carrying capacity of pastures and promote the development of local animal husbandry. The lower limit of the nival belt will further increase in all studied areas, which may lead to an increase in surface runoff in the central and western regions.

Acute Exercise Increases the Expression of KIR2DS4 by Promoter Demethylation in NK Cells

2018 ◽  
Vol 40 (01) ◽  
pp. 62-70 ◽  
Author(s):  
Alexander Schenk ◽  
Walter Pulverer ◽  
Christine Koliamitra ◽  
Claus Bauer ◽  
Suzana Ilic ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Nk Cells ◽  
Promoter Methylation ◽  
Acute Exercise ◽  
Nk Cell ◽  
Epigenetic Modifications ◽  
Control Group ◽  
Chronic Exercise ◽  
Positive Effects

AbstractPositive effects of exercise on cancer prevention and progression have been proposed to be mediated by stimulating natural killer (NK) cells. Because NK cell receptors are regulated by epigenetic modifications, we investigated whether acute aerobic exercise and training change promoter DNA methylation and gene expression of the activating KIR2DS4 and the inhibiting KIR3DL1 gene. Sixteen healthy women (50–60 years) performed a graded exercise test (GXT) and were randomized into either a passive control group or an intervention group performing a four-week endurance exercise intervention. Blood samples (pre-, post-GXT and post-training) were used for isolation of DNA/RNA of NK cells to assess DNA promoter methylation by targeted deep-amplicon sequencing and gene expression by qRT-PCR. Potential changes in NK cell subsets were determined by flow cytometry. Acute and chronic exercise did not provoke significant alterations of NK cell proportions. Promoter methylation decreased and gene expression increased for KIR2DS4 after acute exercise. A high gene expression correlated with a low methylation of CpGs that were altered by acute exercise. Chronic exercise resulted in a minor decrease of DNA methylation and did not alter gene expression. Acute exercise provokes epigenetic modifications, affecting the balance between the activating KIR2DS4 and the inhibiting KIR3DL1, with potential benefits on NK cell function.

scholarly journals Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

2016 ◽  
Vol 311 (6) ◽  
pp. L1245-L1258 ◽  
Author(s):  
Isaac K. Sundar ◽  
Irfan Rahman
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Dna Methylation ◽  
Cigarette Smoke ◽  
Histone Modifications ◽  
Expression Patterns ◽  
Chromatin Modification ◽  
Gene Expression Patterns ◽  
Validation Data ◽  
Histone Marks

Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb. We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.

scholarly journals Hindu Kush Himalayan Ecosystem as a Common Concern of Humankind: Imperative for Better Regional Jurisprudence

2017 ◽  
pp. 42-52
Author(s):  
Debasis Poddar
Keyword(s):  
Climate Change ◽  
Global Climate Change ◽  
Global Climate ◽  
Regional Climate ◽  
Critical Role ◽  
Regional Climate Change ◽  
Mountain Glaciers ◽  
Common Concern ◽  
Hindu Kush ◽  
The World

Hindu Kush Himalayan region (hereafter the HKH) - with 3500 odd kilometres stretched in eight countries- is default resource generation hub for about one-fifth population of the world. The ecosystem-growing delicate these days- seems to play a critical role for the survival of flora and fauna along with the maintenance of all its life-sustaining mountain glaciers. Ten major rivers to carry forward hitherto sustainable development of these peoples fall into question now. Further, in the wake of global climate change today, the delicate HKH ecosystem becomes increasingly fragile to unfold manifold consequences and thereby take its toll on the population. And the same might turn apocalyptic in its magnanimity of irreversibledamage. Like time-bomb, thus, climate ticks to get blown off. As it is getting already too delayed for timely resort to safeguards, if still not taken care of in time, lawmakers ought to find the aftermath too late to lament for. Besides being conscious for climate discipline across the world, collective efforts on the part of all regional states together are imperative to minimize the damage. Therefore, each one has put hands together to be saved from the doomsday that appears to stand ahead to accelerate a catastrophicend, in the given speed of global climate change. As the largest Himalayan state and its central positioning at the top of the HKH, Nepal has had potential to play a criticalrole to engage regional climate change regime and thereby spearhead climate diplomacy worldwide to play regional capital of the HKH ecosystem. As regional superpower, India has had potential to usurp leadership avatar to this end. With reasoningof his own, the author pleads for better jurisprudence to attain regional environmental integrity inter se- rather than regional environmental integration alone- to defendthe vulnerable HKH ecosystem since the same constitutes common concern of humankind and much more so for themselves. Hence, to quote from Shakespeare, “To be or not to be, that is the question” is reasonable here. While states are engaged in the spree to cause mutually agreed destruction, global climate change- with deadly aftermath- poses the last and final unifier for them to turn United Nations in rhetoric sense o f the term.

scholarly journals Cell-type Specific Expression Quantitative Trait Loci Associated with Alzheimer Disease in Blood and Brain Tissue

2020 ◽  
Author(s):  
Devanshi Patel ◽  
Xiaoling Zhang ◽  
John J. Farrell ◽  
Jaeyoon Chung ◽  
Thor D. Stein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Eqtl Analysis ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

ABSTRACTBecause regulation of gene expression is heritable and context-dependent, we investigated AD-related gene expression patterns in cell-types in blood and brain. Cis-expression quantitative trait locus (eQTL) mapping was performed genome-wide in blood from 5,257 Framingham Heart Study (FHS) participants and in brain donated by 475 Religious Orders Study/Memory & Aging Project (ROSMAP) participants. The association of gene expression with genotypes for all cis SNPs within 1Mb of genes was evaluated using linear regression models for unrelated subjects and linear mixed models for related subjects. Cell type-specific eQTL (ct-eQTL) models included an interaction term for expression of “proxy” genes that discriminate particular cell type. Ct-eQTL analysis identified 11,649 and 2,533 additional significant gene-SNP eQTL pairs in brain and blood, respectively, that were not detected in generic eQTL analysis. Of note, 386 unique target eGenes of significant eQTLs shared between blood and brain were enriched in apoptosis and Wnt signaling pathways. Five of these shared genes are established AD loci. The potential importance and relevance to AD of significant results in myeloid cell-types is supported by the observation that a large portion of GWS ct-eQTLs map within 1Mb of established AD loci and 58% (23/40) of the most significant eGenes in these eQTLs have previously been implicated in AD. This study identified cell-type specific expression patterns for established and potentially novel AD genes, found additional evidence for the role of myeloid cells in AD risk, and discovered potential novel blood and brain AD biomarkers that highlight the importance of cell-type specific analysis.

scholarly journals Observed Changes of Rain-Season Precipitation in China from 1960 to 2018

2021 ◽  
Vol 18 (19) ◽  
pp. 10031
Author(s):  
Yanyu Zhang ◽  
Shuying Zang ◽  
Xiangjin Shen ◽  
Gaohua Fan
Keyword(s):  
Climate Change ◽  
Global Climate ◽  
Regional Climate ◽  
Precipitation Amount ◽  
Heavy Precipitation ◽  
Central China ◽  
The Tibetan Plateau ◽  
Natural Ecosystems ◽  
Daily Precipitation Data ◽  
Rain Season

Precipitation during the main rain season is important for natural ecosystems and human activities. In this study, according to daily precipitation data from 515 weather stations in China, we analyzed the spatiotemporal variation of rain-season (May–September) precipitation in China from 1960 to 2018. The results showed that rain-season precipitation decreased over China from 1960 to 2018. Rain-season heavy (25 ≤ p < 50 mm/day) and very heavy (p ≥ 50 mm/day) precipitation showed increasing trends, while rain-season moderate (10 ≤ p < 25 mm/day) and light (0.1 ≤ p < 10 mm/day) precipitation showed decreasing trends from 1960 to 2018. The temporal changes of precipitation indicated that rain-season light and moderate precipitation displayed downward trends in China from 1980 to 2010 and rain-season heavy and very heavy precipitation showed fluctuant variation from 1960 to 2018. Changes of rain-season precipitation showed clear regional differences. Northwest China and the Tibetan Plateau showed the largest positive trends of precipitation amount and days. In contrast, negative trends were found for almost all precipitation grades in North China Plain, Northeast China, and North Central China. Changes toward drier conditions in these regions probably had a severe impact on agricultural production. In East China, Southeast China and Southwest China, heavy and very heavy precipitation had increased while light and moderate precipitation had decreased. This result implied an increasing risk of flood and mudslides in these regions. The advance in understanding of precipitation change in China will contribute to exactly predict the regional climate change under the background of global climate change.

scholarly journals An integrative multi-omics approach in Sjögren’s Syndrome identifies novel genetic drivers with regulatory function and disease-specificity

2020 ◽  
Author(s):  
María Teruel ◽  
Guillermo Barturen ◽  
Manuel Martínez-Bueno ◽  
Miguel Barroso ◽  
Olivia Castelli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Sjögren’S Syndrome ◽  
Genetic Variants ◽  
Sjögren's Syndrome ◽  
Expression Patterns ◽  
Sjogren’S Syndrome ◽  
Sjogren's Syndrome ◽  
Regulatory Function ◽  
Sjögren‘S Syndrome

ABSTRACTPrimary Sjögren’s syndrome (SS) is a systemic autoimmune disease characterized by lymphocytic infiltration and damage of exocrine salivary and lacrimal glands. The etiology of SS is complex with environmental triggers and genetic factors involved. By conducting an integrated multi-omics study we identified vast coordinated hypomethylation and overexpression effects, that also exhibit increased variability, in many already known IFN-regulated genes. We report a novel epigenetic signature characterized by increased DNA methylation levels in a large number of novel genes enriched in pathways such as collagen metabolism and extracellular matrix organization. We identified new genetic variants associated with SS that mediate their risk by altering DNA methylation or gene expression patterns, as well as disease-interacting genetic variants that exhibit regulatory function only in the SS population. Our study sheds new light on the interaction between genetics, DNA methylation, gene expression and SS, and contributes to elucidate the genetic architecture of gene regulation in an autoimmune population.

scholarly journals Development of cDNA normalization system and preliminary transcription analysis of KCS genes in apple tissues

2011 ◽  
Vol 59 (3) ◽  
pp. 9-12 ◽  
Author(s):  
Zsolt Albert ◽  
Cs. Deák ◽  
A. Miskó ◽  
M. Tóth ◽  
I. Papp
Keyword(s):  
Gene Expression ◽  
Expression System ◽  
Expression Patterns ◽  
Housekeeping Genes ◽  
Apple Fruit ◽  
Rt Pcr ◽  
Specific Primers ◽  
Specific Expression ◽  
Transcription Analysis ◽  
Tissue Specific

Wax production is an important aspect of apple (Malus domestica Borkh.) fruit development from both theoretical and practical point of views. The complex molecular mechanism that controls wax biosynthesis is still widely unknown but many studies focused on this topic. We aimed to develop further the experimental framework of these efforts with a description of an improved reference genes expression system. Results in the literature show that similarities exist among the expression of some housekeeping genes of different plant species. Based on these considerations and on gene expression data from Arabidopsis thaliana, some genes in apple were assigned for analysis. EST sequences of apple were used to design specific primers for RT-PCR experiments. Isolation of intact RNA from different apple tissues and performing RT-PCR reaction were also key point in obtaining expression patterns. To monitor DNA contamination of the RNA samples, specific primers were used that amplify intron-containing sequences from the cDNA. We found that actin primers can be used for the detection of intron containing genomic DNA, and tubulin primers are good internal controls in RT-PCR experiments. We were able to make a difference between tissue-specific and tissue-independent gene-expression, furthermore we found tissue specific differences between the expression patterns of candidate genes, that are potentially involved in wax-biosynthesis. Our results show that KCS1 and KCS4 are overexpressed in the skin tissue, this could mean that these genes have skin-specific expression in apple fruit.

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