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https://www.readbyqxmd.com/read/28633563/mammalian-synthetic-biology-engineering-biological-systems
#1
Joshua B Black, Pablo Perez-Pinera, Charles A Gersbach
The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution...
June 21, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28630587/the-most-common-technologies-and-tools-for-functional-genome-analysis
#2
Evelina Gasperskaja, Vaidutis Kučinskas
Since the sequence of the human genome is complete, the main issue is how to understand the information written in the DNA sequence. Despite numerous genome-wide studies that have already been performed, the challenge to determine the function of genes, gene products, and also their interaction is still open. As changes in the human genome are highly likely to cause pathological conditions, functional analysis is vitally important for human health. For many years there have been a variety of technologies and tools used in functional genome analysis...
2017: Acta medica Lituanica
https://www.readbyqxmd.com/read/28629478/genetic-epigenetic-interactions-in-cis-a-major-focus-in-the-post-gwas-era
#3
REVIEW
Catherine Do, Alyssa Shearer, Masako Suzuki, Mary Beth Terry, Joel Gelernter, John M Greally, Benjamin Tycko
Studies on genetic-epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in the post-genome-wide-association-study (GWAS) era. Such maps can nominate regulatory sequence variants that underlie GWAS signals for common diseases, ranging from neuropsychiatric disorders to cancers. Conversely, mQTLs need to be filtered out when searching for non-genetic effects in epigenome-wide association studies (EWAS)...
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629399/epigenomics-dissecting-hybridization-and-polyploidization
#4
Scott A Jackson
Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication affect gene expression.
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629288/p53-mutation-and-epigenetic-imprinted-igf2-h19-gene-analysis-in-mesenchymal-stem-cells-derived-from-amniotic-fluid-amnion-endometrium-and-wharton-s-jelly
#5
Tatsanee Phermthai, Puttachart Pokathikorn, Suparat Wichitwiengrat, Sasiprapa Thongbopit, Kittima Tungprasertpol, Suphakde Julavijitphong
Mesenchymal stem cells (MSC) are promising cells for medical therapy. In in vitro expansion, MSC can give rise to progeny with genomic and epigenomic alterations, resulting in senescence, loss terminal differentiation and transformation to cancer. However, MSC genome protects its genetic instability via a guardian function of the P53 tumor suppressor gene and epigenetic balance system during MSC culture. Mutations of P53 and epigenetic alterations have been reported to disrupt the quality and quantity of MSC and initiate tumorigenesis...
June 19, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/28626222/the-role-of-epigenetics-in-renal-ageing
#6
REVIEW
Paul G Shiels, Dagmara McGuinness, Maria Eriksson, Jeroen P Kooman, Peter Stenvinkel
An ability to separate natural ageing processes from processes specific to morbidities is required to understand the heterogeneity of age-related organ dysfunction. Mechanistic insight into how epigenetic factors regulate ageing throughout the life course, linked to a decline in renal function with ageing, is already proving to be of value in the analyses of clinical and epidemiological cohorts. Noncoding RNAs provide epigenetic regulatory circuits within the kidney, which reciprocally interact with DNA methylation processes, histone modification and chromatin...
June 19, 2017: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/28625497/pitfalls-and-opportunities-for-epigenomic-analyses-focused-on-disease-diagnosis-prognosis-and-therapy
#7
REVIEW
Volker M Lauschke, Maxim Ivanov, Magnus Ingelman-Sundberg
No abstract text is available yet for this article.
June 15, 2017: Trends in Pharmacological Sciences
https://www.readbyqxmd.com/read/28624982/towards-ageing-well-use-it-or-lose-it-exercise-epigenetics-and-cognition
#8
Irene Maeve Rea
More and more people are living into the 90s or becoming centenarians. But, the gift of increased 'age span' seldom equates with an improved 'health-span'. Governments across the world are expressing concern about the epidemic of chronic disease, and have responded by initiating policies that make prevention, reduction and treatment of chronic disease, a public health priority. But understanding, how to age long and well, with the avoidance of chronic disease and later life complex disease morbidity is challenging...
June 17, 2017: Biogerontology
https://www.readbyqxmd.com/read/28624605/transplacental-exposure-to-environmental-carcinogens-association-with-childhood-cancer-risks-and-the-role-of-modulating-factors
#9
REVIEW
A Fucic, V Guszak, A Mantovani
Biological responses to carcinogens from environmental exposure during adulthood are modulated over years or decades. Conversely, during transplacental exposure, the effects on the human foetus change within weeks, intertwining with developmental mechanisms: even short periods of transplacental exposure may be imprinted in the organism for a lifetime. The pathways leading to childhood and juvenile cancers, such as leukaemias, neuroblastoma/brain tumours, hepatoblastoma, and Willm's tumor involve prenatally-induced genomic, epigenomic and/or non-genomic effects caused by xenobiotics...
June 14, 2017: Reproductive Toxicology
https://www.readbyqxmd.com/read/28624579/epigenome-wide-association-study-identifies-methylation-sites-associated-with-liver-enzymes-and-hepatic-steatosis
#10
Jana Nano, Mohsen Ghanbari, Wenshi Wang, Paul S de Vries, Klodian Dhana, Taulant Muka, André G Uitterlinden, Joyce B J van Meurs, Albert Hofman, Oscar H Franco, Qiuwei Pan, Sarwa Darwish Murad, Abbas Dehghan
BACKGROUND & AIMS: Epigenetic mechanisms might be involved in the regulation of liver enzyme level. We aimed to identify CpG sites at which DNA methylation levels are associated with blood levels of liver enzymes and hepatic steatosis. METHODS: We conducted an epigenome-wide association study in whole blood for liver enzymes levels including gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), and aspartate aminotransferase (AST), among a discovery set of 731 participants of the Rotterdam Study and sought replication in a non-overlapping sample of 719 individuals...
June 14, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28623160/basic-concepts-in-molecular-biology-related-to-genetics-and-epigenetics
#11
Dolores Corella, Jose M Ordovas
The observation that "one size does not fit all" for the prevention and treatment of cardiovascular disease, among other diseases, has driven the concept of precision medicine. The goal of precision medicine is to provide the best-targeted interventions tailored to an individual's genome. The human genome is composed of billions of sequence arrangements containing a code that controls how genes are expressed. This code depends on other nonstatic regulators that surround the DNA and constitute the epigenome...
June 13, 2017: Revista Española de Cardiología
https://www.readbyqxmd.com/read/28622364/ipirid-integrative-approach-for-pirna-prediction-using-genomic-and-epigenomic-data
#12
Anouar Boucheham, Vivien Sommard, Farida Zehraoui, Adnane Boualem, Mohamed Batouche, Abdelhafid Bendahmane, David Israeli, Fariza Tahi
Many computational tools have been proposed during the two last decades for predicting piRNAs, which are molecules with important role in post-transcriptional gene regulation. However, these tools are mostly based on only one feature that is generally related to the sequence. Discoveries in the domain of piRNAs are still in their beginning stages, and recent publications have shown many new properties. Here, we propose an integrative approach for piRNA prediction in which several types of genomic and epigenomic properties that can be used to characterize these molecules are examined...
2017: PloS One
https://www.readbyqxmd.com/read/28621329/single-cell-multi-omics-sequencing-of-mouse-early-embryos-and-embryonic-stem-cells
#13
Fan Guo, Lin Li, Jingyun Li, Xinglong Wu, Boqiang Hu, Ping Zhu, Lu Wen, Fuchou Tang
Single-cell epigenome sequencing techniques have recently been developed. However, the combination of different layers of epigenome sequencing in an individual cell has not yet been achieved. Here, we developed a single-cell multi-omics sequencing technology (single-cell COOL-seq) that can analyze the chromatin state/nucleosome positioning, DNA methylation, copy number variation and ploidy simultaneously from the same individual mammalian cell. We used this method to analyze the reprogramming of the chromatin state and DNA methylation in mouse preimplantation embryos...
June 16, 2017: Cell Research
https://www.readbyqxmd.com/read/28621160/epigenome-wide-association-study-of-chronic-obstructive-pulmonary-disease-and-lung-function-in-koreans
#14
Mi Kyeong Lee, Yoonki Hong, Sun-Young Kim, Woo Jin Kim, Stephanie J London
AIM: To identify differentially methylated probes (DMPs) and regions (DMRs) in relation to chronic obstructive pulmonary disease (COPD) and lung function traits. METHODS: We performed an epigenome-wide association study of COPD and spirometric parameters, including forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC, in blood DNA using the Infinium HumanMethylation450 (n = 100, a Korean COPD cohort). RESULTS: We found one significant DMP (cg03559389, DIP2C) and 104 significant DMRs after multiple-testing correction...
June 16, 2017: Epigenomics
https://www.readbyqxmd.com/read/28620075/experience-dependent-epigenomic-reorganization-in-the-hippocampus
#15
Corey G Duke, Andrew J Kennedy, Cristin F Gavin, Jeremy J Day, J David Sweatt
Using a hippocampus-dependent contextual threat learning and memory task, we report widespread, coordinated DNA methylation changes in CA1 hippocampus of Sprague-Dawley rats specific to threat learning at genes involved in synaptic transmission. Experience-dependent alternations in gene expression and DNA methylation were observed as early as 1 h following memory acquisition and became more pronounced after 24 h. Gene ontology analysis revealed significant enrichment of functional categories related to synaptic transmission in genes that were hypomethylated at 24 h following threat learning...
July 2017: Learning & Memory
https://www.readbyqxmd.com/read/28619824/the-histone-3-lysine-4-methyltransferase-setd1b-is-a-maternal-effect-gene-required-for-the-oogenic-gene-expression-program
#16
David Brici, Qinyu Zhang, Susanne Reinhardt, Andreas Dahl, Hella Hartmann, Kerstin Schmidt, Neha Goveas, Jiahao Huang, Lenka Gahurova, Gavin Kelsey, Konstantinos Anastassiadis, A Francis Stewart, Andrea Kranz
Germ cell development involves major reprogramming of the epigenome to prime the zygote for totipotency. Histone 3 lysine 4 (H3K4) methylations are universal epigenetic marks mediated in mammals by six H3K4 methyltransferases related to fly Trithorax, including two yeast Set1 orthologs: Setd1a and Setd1b. Whereas Setd1a plays no role in oogenesis, we report that Setd1b deficiency causes female sterility. Oocyte specific Gdf9iCre conditional knockout (Setd1b(Gdf9) cKO) ovaries develop through all stages however follicular loss accumulated with age and unfertilized metaphase II (MII) oocytes exhibited irregularities of the zona pellucida and meiotic spindle...
June 15, 2017: Development
https://www.readbyqxmd.com/read/28619369/mechanisms-of-atherosclerosis-and-cardiovascular-disease-in-antiphospholipid-syndrome-and-systemic-lupus-erythematosus-new-therapeutic-approaches
#17
REVIEW
Chary Lopez-Pedrera, M Ángeles Aguirre-Zamorano, Carlos Pérez-Sánchez
Systemic lupus erythematosus (SLE) and antiphospholipid syndrome (APS) are 2 highly related autoimmune-rheumatic diseases associated with an increased risk of developing cardiovascular (CV) diseases. Despite the great progresses made in understanding the pathological mechanisms leading to CV diseases in those pathologies, there is still the unmet need to improve long term prognosis. CV diseases in SLE and APS is thought to happen as the result of a complex interaction between traditional CV risk factors, immune deregulation and disease activity, including the synergic effect of cytokines, chemokines, adipokines, proteases, autoantibodies, adhesion receptors, oxidative stress and a plethora of intracellular signalling molecules...
June 12, 2017: Medicina Clínica
https://www.readbyqxmd.com/read/28619030/integrative-analysis-of-dna-methylation-mrnas-and-small-rnas-during-maize-embryo-dedifferentiation
#18
Hongjun Liu, Langlang Ma, Xuerong Yang, Lin Zhang, Xing Zeng, Shupeng Xie, Huanwei Peng, Shibin Gao, Haijian Lin, Guangtang Pan, Yongrui Wu, Yaou Shen
BACKGROUND: Maize (Zea mays) is an important model crop for transgenic studies. However, genetic transformation of maize requires embryonic calli derived from immature embryo, and the impact of utilizing tissue culture methods on the maize epigenome is poorly understood. Here, we generated whole-genome MeDIP-seq data examining DNA methylation in dedifferentiated and normal immature maize embryos. RESULTS: We observed that most of the dedifferentiated embryos exhibited a methylation increase compared to normal embryos...
June 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28614722/quantitative-analysis-of-the-dna-methylation-sensitivity-of-transcription-factor-complexes
#19
Judith F Kribelbauer, Oleg Laptenko, Siying Chen, Gabriella D Martini, William A Freed-Pastor, Carol Prives, Richard S Mann, Harmen J Bussemaker
Although DNA modifications play an important role in gene regulation, the underlying mechanisms remain elusive. We developed EpiSELEX-seq to probe the sensitivity of transcription factor binding to DNA modification in vitro using massively parallel sequencing. Feature-based modeling quantifies the effect of cytosine methylation ((5)mC) on binding free energy in a position-specific manner. Application to the human bZIP proteins ATF4 and C/EBPβ and three different Pbx-Hox complexes shows that (5)mCpG can both increase and decrease affinity, depending on where the modification occurs within the protein-DNA interface...
June 13, 2017: Cell Reports
https://www.readbyqxmd.com/read/28611825/epigenetic-combinatorial-patterns-predict-disease-variants
#20
Yu Zhang
Most genetic variants identified in genome-wide association studies are noncoding and are likely tagging nearby causal variants. It is a challenging task to pinpoint the precise locations of disease-causal variants and understand their functions in disease. A promising approach to improve fine mapping is to integrate the functional data currently available on hundreds of human tissues and cell types. Although there are several methods that use functional data to prioritize disease variants, they mainly use linear models, or equivalent naive likelihood-based models for prediction...
2017: Frontiers in Genetics
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