keyword
MENU ▼
Read by QxMD icon Read
search

epigenomic

keyword
https://www.readbyqxmd.com/read/29053721/xx-disorder-of-sex-development-is-associated-with-an-insertion-on-chromosome-9-and-downregulation-of-rspo1-in-dogs-canis-lupus-familiaris
#1
Vicki N Meyers-Wallen, Adam R Boyko, Charles G Danko, Jennifer K Grenier, Jason G Mezey, Jessica J Hayward, Laura M Shannon, Chuan Gao, Afrah Shafquat, Edward J Rice, Shashikant Pujar, Stefanie Eggers, Thomas Ohnesorg, Andrew H Sinclair
Remarkable progress has been achieved in understanding the mechanisms controlling sex determination, yet the cause for many Disorders of Sex Development (DSD) remains unknown. Of particular interest is a rare XX DSD subtype in which individuals are negative for SRY, the testis determining factor on the Y chromosome, yet develop testes or ovotestes, and both of these phenotypes occur in the same family. This is a naturally occurring disorder in humans (Homo sapiens) and dogs (C. familiaris). Phenotypes in the canine XX DSD model are strikingly similar to those of the human XX DSD subtype...
2017: PloS One
https://www.readbyqxmd.com/read/29053670/pattern-based-search-of-epigenomic-data-using-genemo
#2
Alvin Zheng, Xiaoyi Cao, Sheng Zhong
Compared with the robust text-based search tools for genomic or RNA sequencing data, current methodologies for pattern-based searches of epigenomic and other functional genomic data are very limited. GeNemo is the first online search tool that accomplishes this goal. Users input their functional genomic data in the Browser Extensible Data (BED), Peaks, and bigWig formats, and may search for data in any of the three formats. Users may specify which types of datasets to search against, choosing from a variety of online datasets, with the Encyclopedia of DNA Elements (ENCODE) representing different epigenomic marks, transcriptional factor binding sites, and chromatin hypersensitivities or accessibilities in specific cell types, and developmental stages or species (mouse or human)...
October 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29052586/corrigendum-epigenomic-reprogramming-of-adult-cardiomyocyte-derived-cardiac-progenitor-cells
#3
Yiqiang Zhang, Jiang F Zhong, Hongyu Qiu, W Robb MacLellan, Eduardo Marbán, Charles Wang
This corrects the article DOI: 10.1038/srep17686.
October 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29052205/localization-of-chromatin-marks-in-arabidopsis-early-embryos
#4
Marcelina García-Aguilar, Daphné Autran
During early embryo development, profound changes in chromatin structure and regulation take place. It is difficult to study these changes in plant embryos however, largely because of their relative inaccessibility, which impedes the application of current epigenomic and biochemistry protocols. To circumvent this issue and to analyze the epigenetic status of the embryo at both the cellular and subcellular level, we describe here a simple method to immunolocalize chromatin marks in whole mount early Arabidopsis embryos, either within maternal tissues or isolated from seeds...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052188/a-method-to-identify-nucleolus-associated-chromatin-domains-nads
#5
Marie-Christine Carpentier, Ariadna Picart-Picolo, Frédéric Pontvianne
The nuclear context needs to be taken into consideration to better understand the mechanisms shaping the epigenome and its organization, and therefore its impact on gene expression. For example, in Arabidopsis, heterochromatin is preferentially localized at the nuclear and the nucleolar periphery. Although chromatin domains associating with the nuclear periphery remain to be identified in plant cells, Nucleolus Associated chromatin Domains (NADs) can be identified thanks to a protocol allowing the isolation of pure nucleoli...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052185/identification-of-differentially-methylated-regions-in-the-genome-of-arabidopsis-thaliana
#6
Kamal Kishore, Mattia Pelizzola
DNA methylation profiling in the epigenome of Arabidopsis thaliana (Arabidopsis) has provided great insights in the role of this epigenetic mark for the regulation of transcription in plants, and is often based on high-throughput sequencing. The analysis of these data involves a series of steps including quality checks, filtering, alignment, identification of methyl-cytosines, and the identification of differentially methylated regions. This chapter outlines the computational methodology required to profile genome-wide differential methylation patterns based on publicly available Arabidopsis base-resolution bisulfite sequencing data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29050361/bet-inhibitors-as-novel-therapeutic-agents-in-breast-cancer
#7
REVIEW
Alberto Ocaña, Cristina Nieto-Jiménez, Atanasio Pandiella
Tumoral cells not only depend on oncogenic abnormalities to maintain its malignant phenotype but on non-oncogenic vulnerabilities. Targeting epigenomics can modify specific cellular functions required for malignant transformation. The Bromodomain (BRD) family mediates their effect by recruiting proteins of the transcription machinery, recognizing acetylated-lysine residues in nucleosomal histones. Bromodomain and extra-terminal (BET) inhibitors have shown to produce growth inhibition in several tumors through the inhibition of the expression of several transcription factors...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29047347/the-dynamics-of-smoking-related-disturbed-methylation-a-two-time-point-study-of-methylation-change-in-smokers-non-smokers-and-former-smokers
#8
Rory Wilson, Simone Wahl, Liliane Pfeiffer, Cavin K Ward-Caviness, Sonja Kunze, Anja Kretschmer, Eva Reischl, Annette Peters, Christian Gieger, Melanie Waldenberger
BACKGROUND: The evidence for epigenome-wide associations between smoking and DNA methylation continues to grow through cross-sectional studies. However, few large-scale investigations have explored the associations using observations for individuals at multiple time-points. Here, through the use of the Illumina 450K BeadChip and data collected at two time-points separated by approximately 7 years, we investigate changes in methylation over time associated with quitting smoking or remaining a former smoker, and those associated with continued smoking...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29046734/epigenome-wide-association-study-of-asthma-and-wheeze-in-childhood-and-adolescence
#9
Ryan Arathimos, Matthew Suderman, Gemma C Sharp, Kimberley Burrows, Raquel Granell, Kate Tilling, Tom R Gaunt, John Henderson, Susan Ring, Rebecca C Richmond, Caroline L Relton
BACKGROUND: Asthma heritability has only been partially explained by genetic variants and is known to be sensitive to environmental factors, implicating epigenetic modifications such as DNA methylation in its pathogenesis. METHODS: Using data collected in the Avon Longitudinal Study of Parents and Children (ALSPAC), we assessed associations of asthma and wheeze with DNA methylation at 7.5 and 16.5 years, at over 450,000 CpG sites in DNA from the peripheral blood of approx...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29044423/cultured-bovine-embryo-biopsy-conserves-methylation-marks-from-original-embryo
#10
Noelia Fonseca Balvís, Soledad Garcia-Martinez, Serafín Pérez-Cerezales, Elena Ivanova, Isabel Gomez-Redondo, Meriem Hamdi, Dimitrios Rizos, Pilar Coy, Gavin Kelsey, Alfonso Gutierrez-Adan
A major limitation of embryo epigenotyping by chromatin immunoprecipitation analysis is the reduced amount of sample available from an embryo biopsy. We developed an in vitro system to expand trophectoderm cells from an embryo biopsy to overcome this limitation. This work analyzes whether expanded trophectoderm (EX) is representative of the trophectoderm (TE) methylation or adaptation to culture has altered its epigenome. We took a small biopsy from the trophectoderm (30-40 cells) of in vitro produced bovine-hatched blastocysts and cultured it on fibronectin-treated plates until we obtained ∼4 × 104 cells...
August 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29040761/pcsd-a-plant-chromatin-state-database
#11
Yue Liu, Tian Tian, Kang Zhang, Qi You, Hengyu Yan, Nannan Zhao, Xin Yi, Wenying Xu, Zhen Su
Genome-wide maps of chromatin states have become a powerful representation of genome annotation and regulatory activity. We collected public and in-house plant epigenomic data sets and applied a Hidden Markov Model to define chromatin states, which included 290 553 (36 chromatin states), 831 235 (38 chromatin states) and 3 936 844 (26 chromatin states) segments across the whole genome of Arabidopsis thaliana, Oryza sativa and Zea mays, respectively. We constructed a Plant Chromatin State Database (PCSD, http://systemsbiology...
October 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040751/epidenovo-a-platform-for-linking-regulatory-de-novo-mutations-to-developmental-epigenetics-and-diseases
#12
Fengbiao Mao, Qi Liu, Xiaolu Zhao, Haonan Yang, Sen Guo, Luoyuan Xiao, Xianfeng Li, Huajing Teng, Zhongsheng Sun, Yali Dou
De novo mutations (DNMs) have been shown to be a major cause of severe early-onset genetic disorders such as autism spectrum disorder and intellectual disability. Over one million DNMs have been identified in developmental disorders by next generation sequencing, but linking these DNMs to the genes that they impact remains a challenge, as the majority of them are embedded in non-coding regions. As most developmental diseases occur in the early stages of development or during childhood, it is crucial to clarify the details of epigenetic regulation in early development in order to interpret the mechanisms underlying developmental disorders...
October 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29039625/genetic-determinants-of-the-epigenome-in-development-and-cancer
#13
Adrian Bird
Although we have detailed maps of epigenetic marks on DNA and chromatin for many cell types and disease states, the origin and significance of these patterns is incompletely understood. Deregulation of the epigenome is a frequent accompaniment to cancer, and it is therefore important that we learn how it contributes to tumour formation. Here it is proposed that the roles of DNA sequence signals as determinants of the epigenome have been underappreciated. Taking as a paradigm the part played by the dinucleotide CpG in regulating gene expression via its effects on the epigenome, it is suggested that factors recognising other short, frequent sequence motifs also recruit chromatin modifying enzymes in response to DNA sequence...
October 17, 2017: Swiss Medical Weekly
https://www.readbyqxmd.com/read/29038614/dna-methylation-events-as-markers-for-diagnosis-and-management-of-acute-myeloid-leukemia-and-myelodysplastic-syndrome
#14
REVIEW
Geórgia Muccillo Dexheimer, Jayse Alves, Laura Reckziegel, Gabrielle Lazzaretti, Ana Lucia Abujamra
During the onset and progression of hematological malignancies, many changes occur in cellular epigenome, such as hypo- or hypermethylation of CpG islands in promoter regions. DNA methylation is an epigenetic modification that regulates gene expression and is a key event for tumorigenesis. The continuous search for biomarkers that signal early disease, indicate prognosis, and act as therapeutic targets has led to studies investigating the role of DNA in cancer onset and progression. This review focuses on DNA methylation changes as potential biomarkers for diagnosis, prognosis, response to treatment, and early toxicity in acute myeloid leukemia and myelodysplastic syndrome...
2017: Disease Markers
https://www.readbyqxmd.com/read/29036709/deep-learning-of-the-splicing-epi-genetic-code-reveals-a-novel-candidate-mechanism-linking-histone-modifications-to-esc-fate-decision
#15
Yungang Xu, Yongcui Wang, Jiesi Luo, Weiling Zhao, Xiaobo Zhou
Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036683/cr2cancer-a-database-for-chromatin-regulators-in-human-cancer
#16
Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036500/glioma-cpg-island-methylator-phenotype-g-cimp-biological-and-clinical-implications
#17
Tathiane M Malta, Camila F de Souza, Thais S Sabedot, Tiago C Silva, Maritza Q S Mosella, Steven N Kalkanis, James Snyder, Ana Valeria B Castro, Houtan Noushmehr
Gliomas are a heterogeneous group of brain tumors with distinct biological and clinical properties. Despite advances in surgical techniques and clinical regimens, treatment of high-grade glioma remains challenging and carries dismal rates of therapeutic success and overall survival. Challenges include the molecular complexity of gliomas, as well as inconsistencies in histopathological grading, resulting in an inaccurate prediction of disease progression and failure in the use of standard therapy. The updated 2016 World Health Organization (WHO) classification of tumors of the central nervous system reflects a refinement of tumor diagnostics by integrating the genotypic and phenotypic features, thereby narrowing the defined subgroups...
September 26, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29036466/insights-into-epigenome-evolution-from-animal-and-plant-methylomes
#18
Soojin V Yi
Evolutionary studies of DNA methylation begin to provide insights into the underlying forces governing the variation of genomic DNA methylation across different species. Comparisons of gross levels of DNA methylation between distantly related species indicate that the size of the genome and the level of genomic DNA methylation are positively correlated. In plant genomes, this can be reliably explained by the contents of repetitive sequences, while the underlying driver of this correlation is less clear in animal genomes...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29035320/personomics-the-missing-link-in-the-evolution-from-precision-medicine-to-personalized-medicine
#19
Roy C Ziegelstein
Clinical practice guidelines have been developed for many common conditions based on data from randomized controlled trials. When medicine is informed solely by clinical practice guidelines, however, the patient is not treated as an individual, but rather a member of a group. Precision medicine, as defined herein, characterizes unique biological characteristics of the individual or of specimens obtained from an individual to tailor diagnostics and therapeutics to a specific patient. These unique biological characteristics are defined by the tools of precision medicine: genomics, proteomics, metabolomics, epigenomics, pharmacogenomics, and other "-omics...
October 16, 2017: Journal of Personalized Medicine
https://www.readbyqxmd.com/read/29034560/estimation-of-a-significance-threshold-for-epigenome-wide-association-studies
#20
Ayden Saffari, Matt J Silver, Patrizia Zavattari, Loredana Moi, Amedeo Columbano, Emma L Meaburn, Frank Dudbridge
Epigenome-wide association studies (EWAS) are designed to characterise population-level epigenetic differences across the genome and link them to disease. Most commonly, they assess DNA-methylation status at cytosine-guanine dinucleotide (CpG) sites, using platforms such as the Illumina 450k array that profile a subset of CpGs genome wide. An important challenge in the context of EWAS is determining a significance threshold for declaring a CpG site as differentially methylated, taking multiple testing into account...
October 15, 2017: Genetic Epidemiology
keyword
keyword
85409
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"