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https://www.readbyqxmd.com/read/29614954/bs-seeker3-ultrafast-pipeline-for-bisulfite-sequencing
#1
Kevin Yu Yuan Huang, Yan-Jiun Huang, Pao-Yang Chen
BACKGROUND: DNA methylation is an important epigenetic modification critical in regulation and transgenerational inheritance. The methylation level can be estimated at single-nucleotide resolution by whole-genome bisulfite sequencing (BS-seq; WGBS). Current bisulfite aligners provide pipelines for processing the reads by WGBS; however, few are able to analyze the BS-seqs in a reasonable timeframe that meets the needs of the rapid expansion of epigenome sequencing in biomedical research...
April 3, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29593303/epigenetic-transgenerational-inheritance-of-altered-sperm-histone-retention-sites
#2
Millissia Ben Maamar, Ingrid Sadler-Riggleman, Daniel Beck, Michael K Skinner
A variety of environmental toxicants and factors have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. Epigenetic alterations in the germline (sperm or egg) are required to transmit transgenerational phenotypes. The current study was designed to investigate the potential role of histones in sperm to help mediate the epigenetic transgenerational inheritance. The agricultural fungicide vinclozolin and the pesticide DDT (dichlorodiphenyltrichloroethane) were independently used to promote the epigenetic transgenerational inheritance of disease...
March 28, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29573427/transgenerational-phenotype-aggravation-in-caf-1-mutants-reveals-parent-of-origin-specific-epigenetic-inheritance
#3
Iva Mozgova, Thomas Wildhaber, Minerva S Trejo-Arellano, Jiri Fajkus, Pawel Roszak, Claudia Köhler, Lars Hennig
Chromatin is assembled by histone chaperones such as chromatin assembly factor CAF-1. We had noticed that vigor of Arabidopsis thaliana CAF-1 mutants decreased over several generations. Because changes in mutant phenotype severity over generations are unusual, we asked how repeated selfing of Arabidopsis CAF-1 mutants affects phenotype severity. CAF-1 mutant plants of various generations were grown, and developmental phenotypes, transcriptomes and DNA cytosine-methylation profiles were compared quantitatively...
March 24, 2018: New Phytologist
https://www.readbyqxmd.com/read/29549716/human-and-animal-evidence-of-potential-transgenerational-inheritance-of-health-effects-an-evidence-map-and-state-of-the-science-evaluation
#4
REVIEW
Vickie R Walker, Abee L Boyles, Katherine E Pelch, Stephanie D Holmgren, Andrew J Shapiro, Chad R Blystone, Michael J Devito, Retha R Newbold, Robyn Blain, Pamela Hartman, Kristina A Thayer, Andrew A Rooney
BACKGROUND: An increasing number of reports suggest early life exposures result in adverse effects in offspring who were never directly exposed; this phenomenon is termed "transgenerational inheritance." Given concern for public health implications for potential effects of exposures transmitted to subsequent generations, it is critical to determine how widespread and robust this phenomenon is and to identify the range of exposures and possible outcomes. OBJECTIVES: This scoping report examines the evidence for transgenerational inheritance associated with exposure to a wide range of stressors in humans and animals to identify areas of consistency, uncertainty, data gaps, and to evaluate general risk of bias issues for the transgenerational study design...
March 14, 2018: Environment International
https://www.readbyqxmd.com/read/29531716/increased-transgenerational-epigenetic-variation-but-not-predictable-epigenetic-variants-after-environmental-exposure-in-two-apomictic-dandelion-lineages
#5
Veronica Preite, Carla Oplaat, Arjen Biere, Jan Kirschner, Wim H van der Putten, Koen J F Verhoeven
DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group ( Taraxacum alatum and T...
March 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29520039/transgenerational-epigenetic-influences-of-paternal-environmental-exposures-on-brain-function-and-predisposition-to-psychiatric-disorders
#6
REVIEW
Shlomo Yeshurun, Anthony J Hannan
In recent years, striking new evidence has demonstrated non-genetic inheritance of acquired traits associated with parental environmental exposures. In particular, this transgenerational modulation of phenotypic traits is of direct relevance to psychiatric disorders, including depression, post-traumatic stress disorder, and other anxiety disorders. Here we review the recent progress in this field, with an emphasis on acquired traits of psychiatric illnesses transmitted epigenetically via the male lineage. We discuss the transgenerational effects of paternal exposure to stress vs...
March 8, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29507096/not-just-heads-and-tails-the-complexity-of-the-sperm-epigenome
#7
Hannah B Gold, Yoon Hee Jung, Victor G Corces
Transgenerational inheritance requires mechanisms by which epigenetic information is transferred via gametes. Canonical thought holds that mammalian sperm chromatin would be incapable of carrying epigenetic information as post-translational modifications of histones because of their replacement with protamine proteins. Further, compaction of the sperm genome would hinder DNA accessibility of proteins involved in transcriptional regulation and genome architecture. In this review, we delineate the paternal chromatin remodeling events during spermatogenesis and fertilization...
March 5, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29506130/a-single-cell-epigenetic-model-for-parental-psychological-stress-induced-transgenerational-reprogramming-in-offspring
#8
Jinzhi Lei, Qing Nie, Dong-Bao Chen
Experimental evidence shows that parental psychological stress affects the long-term health of offspring in an inheritable fashion. Although epigenetic mechanisms, including DNA methylation, miRNA, and histone modifications, are involved in transgenerational programming, the underlining mechanisms of transgenerational inheritance remain unsolved. Here, we present a single-cell based computational model for transgenerational inheritance for investigating the long-term dynamics of phenotype changes in response to parental stress...
February 28, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29494917/histone-methylation-associated-transgenerational-inheritance-of-reproductive-defects-in-caenorhabditis-elegans-exposed-to-crude-oil-under-various-exposure-scenarios
#9
Jisu Yang, Nivedita Chatterjee, Youngho Kim, Ji-Yeon Roh, Jung-Hwan Kwon, Myung-Sook Park, Jinhee Choi
As part of a study to explore the long-term effects of the Hebei Spirit oil spill accident, transgenerational toxicity and associated epigenetic changes were investigated in the nematode Caenorhabditis elegans. Under experimental conditions, worms were exposed to Iranian heavy crude oil (IHC) under three different scenarios: partial early-life exposure (PE), partial late-life exposure (PL), and whole-life exposure (WE). Growth, reproduction, and histone methylation were monitored in the exposed parental worms (P0) and in three consecutive unexposed offspring generations (F1-3 )...
February 21, 2018: Chemosphere
https://www.readbyqxmd.com/read/29492313/transgenerational-epigenetics-and-environmental-justice
#10
REVIEW
Mark A Rothstein, Heather L Harrell, Gary E Marchant
Human transmission to offspring and future generations of acquired epigenetic modifications has not been definitively established, although there are several environmental exposures with suggestive evidence. This article uses three examples of hazardous substances with greater exposures in vulnerable populations: pesticides, lead, and diesel exhaust. It then considers whether, if there were scientific evidence of transgenerational epigenetic inheritance, there would be greater attention given to concerns about environmental justice in environmental laws, regulations, and policies at all levels of government...
July 2017: Environmental Epigenetics
https://www.readbyqxmd.com/read/29486114/transgenerational-dna-methylation-changes-in-daphnia-magna-exposed-to-chronic-gamma-irradiation
#11
Marie Trijau, Jana Asselman, Olivier Armant, Christelle Adam-Guillermin, Karel Ac De Schamphelaere, Frédéric Alonzo
Our aim was to investigate epigenetic changes in Daphnia magna after a 25-day chronic external gamma irradiation (generation F0 exposed to 6.5 µGy h-1 or 41.3 mGy h-1) and their potential inheritance by subsequent recovering generations, namely F2 (exposed as germline cells in F1 embryos) and F3 (the first truly unexposed generation). Effects on survival, growth and reproduction were observed and DNA was extracted for whole genome bisulfite sequencing in all generations. Results showed effects on reproduction in F0 but no effect in the subsequent generations F1, F2 and F3...
February 27, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29485126/investigating-the-genetic-and-epigenetic-basis-of-big-biological-questions-with-the-parthenogenetic-marbled-crayfish-a-review-and-perspectives
#12
Gunter Vogt
In the last 15 years, considerable attempts have been undertaken to develop the obligately parthenogenetic marbled crayfish Procambarus virginalis as a new model in biology. Its main advantage is the production of large numbers of offspring that are genetically identical to the mother, making this crustacean particularly suitable for research in epigenetics. Now, a draft genome, transcriptome and genome-wide methylome are available opening new windows for research. In this article, I summarize the biological advantages and genomic and epigenetic features of marbled crayfish and, based on first promising data, discuss what this new model could contribute to answering of ''big'' biological questions...
March 2018: Journal of Biosciences
https://www.readbyqxmd.com/read/29482626/alterations-in-sperm-dna-methylation-non-coding-rna-and-histone-retention-associate-with-ddt-induced-epigenetic-transgenerational-inheritance-of-disease
#13
Michael K Skinner, Millissia Ben Maamar, Ingrid Sadler-Riggleman, Daniel Beck, Eric Nilsson, Margaux McBirney, Rachel Klukovich, Yeming Xie, Chong Tang, Wei Yan
BACKGROUND: Environmental toxicants such as DDT have been shown to induce the epigenetic transgenerational inheritance of disease (e.g., obesity) through the germline. The current study was designed to investigate the DDT-induced concurrent alterations of a number of different epigenetic processes including DNA methylation, non-coding RNA (ncRNA) and histone retention in sperm. METHODS: Gestating females were exposed transiently to DDT during fetal gonadal development, and then, the directly exposed F1 generation, the directly exposed germline F2 generation and the transgenerational F3 generation sperm were investigated...
February 27, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29468522/mechanism-of-evolution-by-genetic-assimilation-equivalence-and-independence-of-genetic-mutation-and-epigenetic-modulation-in-phenotypic-expression
#14
REVIEW
Ken Nishikawa, Akira R Kinjo
Conrad H. Waddington discovered the phenomenon of genetic assimilation through a series of experiments on fruit flies. In those experiments, artificially exerted environmental stress induced plastic phenotypic changes in the fruit flies, but after some generations, the same phenotypic variant started to appear without the environmental stress. Both the initial state (where the phenotypic changes were environmentally induced and plastic) and the final state (where the phenotypic changes were genetically fixed and constitutive) are experimental facts...
February 21, 2018: Biophysical Reviews
https://www.readbyqxmd.com/read/29456083/placeholder-nucleosomes-underlie-germline-to-embryo-dna-methylation-reprogramming
#15
Patrick J Murphy, Shan Fu Wu, Cody R James, Candice L Wike, Bradley R Cairns
The fate and function of epigenetic marks during the germline-to-embryo transition is a key issue in developmental biology, with relevance to stem cell programming and transgenerational inheritance. In zebrafish, DNA methylation patterns are programmed in transcriptionally quiescent cleavage embryos; paternally inherited patterns are maintained, whereas maternal patterns are reprogrammed to match the paternal. Here, we provide the mechanism by demonstrating that "Placeholder" nucleosomes, containing histone H2A variant H2A...
February 9, 2018: Cell
https://www.readbyqxmd.com/read/29378808/protecting-and-diversifying-the-germline
#16
Ryan J Gleason, Amit Anand, Toshie Kai, Xin Chen
Gametogenesis represents the most dramatic cellular differentiation pathways in both female and male flies. At the genome level, meiosis ensures that diploid germ cells become haploid gametes. At the epigenome level, extensive changes are required to turn on and shut off gene expression in a precise spatiotemporally controlled manner. Research applying conventional molecular genetics and cell biology, in combination with rapidly advancing genomic tools have helped us to investigate (1) how germ cells maintain lineage specificity throughout their adult reproductive lifetime; (2) what molecular mechanisms ensure proper oogenesis and spermatogenesis, as well as protect genome integrity of the germline; (3) how signaling pathways contribute to germline-soma communication; and (4) if such communication is important...
February 2018: Genetics
https://www.readbyqxmd.com/read/29370380/prenatal-dexamethasone-exposure-induced-ovarian-developmental-toxicity-and-transgenerational-effect-in-rat-offspring
#17
Feng Lv, Yang Wan, Yunxi Chen, Linguo Pei, Daji Luo, Guanlan Fan, Mengcheng Luo, Dan Xu, Hui Wang
Prenatal dexamethasone exposure (PDE) induces multiorgan developmental toxicities in offspring. Here we verified the transgenerational inheritance effect of ovarian developmental toxicity by PDE and explored its intrauterine programming mechanism. Pregnant rats subcutaneously received 0.2 mg/kg/d dexamethasone from gestational day (GD) 9 to GD20. A subgroup was euthanized for fetuses on GD20, and the other group went on to spontaneous labor to produce F1 offspring. The adult F1 females were mated with normal males to produce the F2 and F3 generations...
March 1, 2018: Endocrinology
https://www.readbyqxmd.com/read/29349272/why-is-parental-lifespan-linked-to-children-s-chances-of-reaching-a-high-age-a-transgenerational-hypothesis
#18
Denny Vågerö, Vanda Aronsson, Bitte Modin
Purpose: Transgenerational determinants of longevity are poorly understood. We used data from four linked generations (G0, G1, G2 and G3) of the Uppsala Birth Cohort Multigeneration Study to address this issue. Methods: Mortality in G1 (N = 9565) was followed from 1961-2015 and analysed in relation to tertiles of their parents' (G0) age-at-death using Cox regression. Parental social class and marital status were adjusted for in the analyses, as was G1's birth order and adult social class...
April 2018: SSM—Population Health
https://www.readbyqxmd.com/read/29348834/activity-strengths-of-cortical-glutamatergic-and-gabaergic-neurons-are-correlated-with-transgenerational-inheritance-of-learning-ability
#19
Yulong Liu, Rongjing Ge, Xin Zhao, Rui Guo, Li Huang, Shidi Zhao, Sudong Guan, Wei Lu, Shan Cui, Shirlene Wang, Jin-Hui Wang
The capabilities of learning and memory in parents are presumably transmitted to their offsprings, in which genetic codes and epigenetic regulations are thought as molecular bases. As neural plasticity occurs during memory formation as cellular mechanism, we aim to examine the correlation of activity strengths at cortical glutamatergic and GABAergic neurons to the transgenerational inheritance of learning ability. In a mouse model of associative learning, paired whisker and odor stimulations led to odorant-induced whisker motion, whose onset appeared fast (high learning efficiency, HLE) or slow (low learning efficiency, LLE)...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29332303/mitochondrial-dna-nuclear-context-and-the-risk-for-carcinogenesis
#20
REVIEW
Brett A Kaufman, Martin Picard, Neal Sondheimer
The inheritance of mitochondrial DNA (mtDNA) from mother to child is complicated by differences in the stability of the mitochondrial genome. Although the germ line mtDNA is protected through the minimization of replication between generations, sequence variation can occur either through mutation or due to changes in the ratio between distinct genomes that are present in the mother (known as heteroplasmy). Thus, the unpredictability in transgenerational inheritance of mtDNA may cause the emergence of pathogenic mitochondrial and cellular phenotypes in offspring...
January 14, 2018: Environmental and Molecular Mutagenesis
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