Epigenomics Core

EPIGENOMICS CORE The Epigenomics Core provides sample quality control, library preparation and sequencing for the study of cytosine and histone modifications. Products & Services We offer a wide variety of services in epigenomics and bioinformatics resources, including: • Genome-wide DNA Methylation Profiling ❍ Whole-genome bisulfite sequencing: whole-genome base-pair resolution quantification of DNA methylation ❍ ERRBS (Enhanced Reduced Representation Bisulfite Sequencing): Quantitative base-pair measurement of cytosine methylation at ~3M CpGs genome-wide located at promoters, CpG islands and shores, and intergenic regulatory regions ❍ meDIP-seq: Antibody-based method for identification of mC-enriched areas across the genome. ❍ Support with data analysis • Targeted (locus-specific) DNA Methylation ❍ Primer design consultation and training ❍ Bisulfite conversion of DNA and PCR amplification of target sequences ❍ MassARRAY EpiTYPER sequencing ❍ Pyrosequencing ❍ Support with data analysis • Chromatin Modification: ChIP-Seq ❍ Library preparation of user-provided immunoprecipitated DNA ChIP-seq data analysis ❍ Histone Modification by ChIP-Seq (limited initial availability) • Hydroxymethylation ❍ Genome-wide and Target Specific Epigenomics Core Email the Core to set up a consultation, including a FREE initial consultation to scope Biomedical Research Core Facilities your project and ascertain how best to your meet your specific project needs. MSRB II 2568 1150 W. Medical Center Drive Ann Arbor, MI 48109-0674 OVER Coming soon to the Core • Chromatin Accessibility Cost Estimates & Fees About the BRCF For project-specific costs and fees, please contact the Core. The BRCF, part of the University of Michigan Medical School Office of Research, is a collection of centralized labs and services offering state-of-the- art instruments, resources and expertise to biomedical researchers, investigators and educators. For more information on the BRCF, visit research.med.umich.edu/brcf From top-notch library preparation and sample quality controls to expert analysis, the Epigenomics Core strives to offer the best in epigenomics and bioinformatics resources. – Claudia Lalancette, Ph.D., Managing Director, Epigenomics Core CONTACT US Dana Dolinoy Hours & Location Ph.D., Faculty Director Open Monday-Friday BIOMEDICAL RESEARCH CORE FACILITIES 8:30 a.m.- 4:30 p.m. Claudia Lalancette University of Michigan Medical School MSRB II 2568 Ph.D., Managing Director 1150 W. Medical Center Drive 2570 MSRB II • 1150 W. Medical Center Drive 734-764-2223 Ann Arbor, MI 48109-0674 Ann Arbor, MI 48109-5674 [email protected] 734-647-4776 Maureen Sartor [email protected] Ph.D., Faculty Bioinformatics Director research.med.umich.edu/ epigenomicscore Karthik R Padmanabhan Ph.D., Senior Bioinformatics Analyst Sonoko Natsume Senior Research Lab Technician.

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Integrative Analysis for Elucidating Transcriptomics Landscapes of Glucocorticoid-Induced Osteoporosis
fcell-08-00252 April 13, 2020 Time: 17:59 # 1 ORIGINAL RESEARCH published: 16 April 2020 doi: 10.3389/fcell.2020.00252 Integrative Analysis for Elucidating Transcriptomics Landscapes of Glucocorticoid-Induced Osteoporosis Xiaoxia Ying1†, Xiyun Jin2†, Pingping Wang2†, Yuzhu He1, Haomiao Zhang1, Xiang Ren1, Songling Chai1, Wenqi Fu1, Pengcheng Zhao1, Chen Chen1, Guowu Ma1* and Huiying Liu1* 1 2 Edited by: School of Stomatology, Dalian Medical University, Dalian, China, School of Life Sciences and Technology, Harbin Institute Yongchun Zuo, of Technology, Harbin, China Inner Mongolia University, China Reviewed by: Osteoporosis is the most common bone metabolic disease, characterized by bone Liang Yu, mass loss and bone microstructure changes due to unbalanced bone conversion, Xidian University, China Yanshuo Chu, which increases bone fragility and fracture risk. Glucocorticoids are clinically used to The University of Texas MD Anderson treat a variety of diseases, including inflammation, cancer and autoimmune diseases. Cancer Center, United States However, excess glucocorticoids can cause osteoporosis. Herein we performed an *Correspondence: Guowu Ma integrated analysis of two glucocorticoid-related microarray datasets. The WGCNA [email protected] analysis identified 3 and 4 glucocorticoid-related gene modules, respectively. Differential Huiying Liu expression analysis revealed 1047 and 844 differentially expressed genes in the two [email protected] datasets. After integrating differentially expressed glucocorticoid-related genes, we †These authors have contributed equally to this work found that most of the robust differentially expressed genes were up-regulated. Through protein-protein interaction analysis, we obtained 158 glucocorticoid-related candidate Specialty section: This article was submitted to genes. Enrichment analysis showed that these genes are significantly enriched in the Epigenomics and Epigenetics, osteoporosis related pathways.
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EPIGENOMICS: BEYOND Cpg ISLANDS
REVIEWS EPIGENOMICS: BEYOND CpG ISLANDS Melissa J. Fazzari* and John M. Greally† Epigenomic studies aim to define the location and nature of the genomic sequences that are epigenetically modified. Much progress has been made towards whole-genome epigenetic profiling using molecular techniques, but the analysis of such large and complex data sets is far from trivial given the correlated nature of sequence and functional characteristics within the genome. We describe the statistical solutions that help to overcome the problems with data-set complexity, in anticipation of the imminent wealth of data that will be generated by new genome- wide epigenetic profiling and DNA sequence analysis techniques. So far, epigenomic studies have succeeded in identifying CpG islands, but recent evidence points towards a role for transposable elements in epigenetic regulation, causing the fields of study of epigenetics and transposable element biology to converge. Epigenetic inheritance involves the transmission of issues of correlation and causality — for example, the information not encoded in DNA sequences from cell DNA sequence feature might be the effect of the epige- to daughter cell or from generation to generation. netic process rather than mechanistically involved in Covalent modifications of the DNA or its packaging directing it. As new techniques to characterize epigenetic histones are responsible for transmitting epigenetic processes throughout the genome are being applied, we information. Epigenomics can be defined as a genome- have the potential to generate large amounts of data to wide approach to studying epigenetics. This term facilitate epigenomic studies. It is a good time now to encompasses whole-genome studies of epigenetic consider these issues so that we can design our analytical processes and the identification of the DNA sequences approaches appropriately.
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Epigenetics and Systems Biology 1St Edition Ebook
EPIGENETICS AND SYSTEMS BIOLOGY 1ST EDITION PDF, EPUB, EBOOK Leonie Ringrose | 9780128030769 | | | | | Epigenetics and Systems Biology 1st edition PDF Book Regulation of lipogenic gene expression by lysine-specific histone demethylase-1 LSD1. BEDTools: a flexible suite of utilities for comparing genomic features. New technologies are also needed to study higher order chromatin organization and function. For example, acetylation of the K14 and K9 lysines of the tail of histone H3 by histone acetyltransferase enzymes HATs is generally related to transcriptional competence. The idea that multiple dynamic modifications regulate gene transcription in a systematic and reproducible way is called the histone code , although the idea that histone state can be read linearly as a digital information carrier has been largely debunked. Namespaces Article Talk. It seems existing structures act as templates for new structures. As part of its efforts, the society launched a journal, Epigenetics , in January with the goal of covering a full spectrum of epigenetic considerations—medical, nutritional, psychological, behavioral—in any organism. Sooner or later, with the advancements in biomedical tools, the detection of such biomarkers as prognostic and diagnostic tools in patients could possibly emerge out as alternative approaches. Genotype—phenotype distinction Reaction norm Gene—environment interaction Gene—environment correlation Operon Heritability Quantitative genetics Heterochrony Neoteny Heterotopy. The lysine demethylase, KDM4B, is a key molecule in androgen receptor signalling and turnover. Khan, A. Hidden categories: Webarchive template wayback links All articles lacking reliable references Articles lacking reliable references from September Wikipedia articles needing clarification from January All articles with unsourced statements Articles with unsourced statements from June This mechanism enables differentiated cells in a multicellular organism to express only the genes that are necessary for their own activity.
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Long Non-Coding Rnas, the Dark Matter: an Emerging Regulatory Component in Plants
International Journal of Molecular Sciences Review Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants Muhammad Waseem 1,2,3 , Yuanlong Liu 1,2,3 and Rui Xia 1,2,3,* 1 State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510640, China; [email protected] (M.W.); [email protected] (Y.L.) 2 Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510640, China 3 Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510640, China * Correspondence: [email protected] Abstract: Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Ad- vances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants.
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Systems Biology and Its Relevance to Alcohol Research
Commentary: Systems Biology and Its Relevance to Alcohol Research Q. Max Guo, Ph.D., and Sam Zakhari, Ph.D. Systems biology, a new scientific discipline, aims to study the behavior of a biological organization or process in order to understand the function of a dynamic system. This commentary will put into perspective topics discussed in this issue of Alcohol Research & Health, provide insight into why alcohol-induced disorders exemplify the kinds of conditions for which a systems biological approach would be fruitful, and discuss the opportunities and challenges facing alcohol researchers. KEY WORDS: Alcohol-induced disorders; alcohol research; biomedical research; systems biology; biological systems; mathematical modeling; genomics; epigenomics; transcriptomics; metabolomics; proteomics ntil recently, most biologists’ emerging discipline that deals with, Alcohol Research & Health intend to efforts have been devoted to and takes advantage of, these enormous address. In this commentary, we will Ureducing complex biological amounts of data. Although scientists try to put the topics discussed in this systems to the properties of individual and engineers have applied the concept issue into perspective, provide views molecules. However, with the com of an integrated systemic approach for on the significance of systems biology pleted sequencing of the genomes of years, systems biology has only emerged as a new, distinct discipline to study 1 High-throughput genomics is the study of the structure humans, mice, rats, and many other and function of an organism’s complete genetic content, organisms, technological advances in complex biological systems in the past or genome, using technology that analyzes a large num the fields of high-throughput genomics1 several years.
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Enhanced Jbrowse Plugins for Epigenomics Data Visualization Brigitte T
Hofmeister and Schmitz BMC Bioinformatics (2018) 19:159 https://doi.org/10.1186/s12859-018-2160-z SOFTWARE Open Access Enhanced JBrowse plugins for epigenomics data visualization Brigitte T. Hofmeister1* and Robert J. Schmitz2* Abstract Background: New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. Results: We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifically, we have focused on visualizing DNA base modifications, small non-coding RNAs, stranded read coverage, and sequence motif density. Additionally, we present several plugins for improved user experience such as configurable, high-quality screenshots. Conclusions: In visualizing epigenomics with traditional genomics data, we see these plugins improving scientific communication and leading to discoveries within the field of epigenomics. Keywords: Epigenomics, Genomics, Genome browser, Visualization Background seq) [15], assay for transposase-accessible chromatin As next-generation sequencing techniques for detecting sequencing (ATAC-seq) [16], RNA-seq [17–19], and and quantifying DNA nucleotide variants, histone small RNA-seq [20] have been instrumental in advancing modifications and RNA transcripts become widely the field of epigenomics. Epigenomic data sets generated implemented, it is imperative that graphical tools such from these techniques typically include: DNA base modifi- as genome browsers are able to properly visualize these cations, mRNAs, small RNAs, histone modifications and specialized data sets. Current genome browsers such as variants, chromatin accessibility, and DNA sequence UCSC genome browser [1], AnnoJ [2], IGV [3], WashU motifs. These techniques have allowed researchers to map EpiGenome Browser [4], Epiviz [5], IGB [6], and JBrowse the epigenomic landscape at high resolution, greatly [7], have limited capability to visualize these data sets advancing our understanding of gene regulation.
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Epigenomics Challenge Exposed Group DNA Methylation Gene Expression (Sequencing) (Microarray) A
S P L C C E N B S P L C C E N B S P L C C E N B S P L C C E N B H U E O O X E E H U E O O X E E H U E O O X E E H U E O O X E E A B A N L P T N A B A N L P T N A B A N L P T N A B A N L P T N R L R T L L W C R L R T L L W C R L R T L L W C R L R T L L W C E I N R A O O H E I N R A O O H E I N R A O O H E I N R A O O H S I B R R M S I B R R M S I B R R M S I B R R M H B O E K A H C B O E K A H B O E K A H B O E K A B C B S C C U R R O U R R H U R C R O U R R E T A C K O C L T A C K E N T A K O C T A C K Why should you be part of N N P O L P O N E A P O L L P O E E T sbvU O IMPROVERL E T R E T U N O L E T C E L L N A E U N S C T E L N E U N S H T L B L B A B T H W E L B T B A A B T W B E E T B H E E T H M L A B N L R A M O L R B B N L R A O E A E I N R O A E I I N R O sbv IMPROVER? A B O I R E E I I R A R N O I E E I I R R N R X S C R X S B C R R O R B A X T S B E R K E R B X T S B E K K C N P H R H A P H U K T N P H U H A A P H U H U T W U W L A M T L O T W L T M T T L O T Verification of Systems Biology Research M EpigenomicsC A T E C C E A T B C O T E O R B E O C O E E O R E N A R O R E E O R O R E E in the age of Collaborative Competition E O E R K E N R O R K E R E N K N E X E N K N E N T X L T B N T K L T B sbv IMPROVER stands for Systems Biology Verification combined with P K L E C P L E C W R E T L R R E T C H L A L N E H I A L N O Industrial Methodology for Process Verification in Research.
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Epigenomics and Genotype-Phenotype Association
Liu et al. BMC Biology (2020) 18:80 https://doi.org/10.1186/s12915-020-00792-6 RESEARCH ARTICLE Open Access Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human Shuli Liu1,2, Ying Yu2, Shengli Zhang2, John B. Cole1, Albert Tenesa3,4, Ting Wang5, Tara G. McDaneld6,LiMa7*, George E. Liu1* and Lingzhao Fang1,3,7* Abstract Background: Lack of comprehensive functional annotations across a wide range of tissues and cell types severely hinders the biological interpretations of phenotypic variation, adaptive evolution, and domestication in livestock. Here we used a combination of comparative epigenomics, genome-wide association study (GWAS), and selection signature analysis, to shed light on potential adaptive evolution in cattle. Results: We cross-mapped 8 histone marks of 1300 samples from human to cattle, covering 178 unique tissues/cell types. By uniformly analyzing 723 RNA-seq and 40 whole genome bisulfite sequencing (WGBS) datasets in cattle, we validated that cross-mapped histone marks captured tissue-specific expression and methylation, reflecting tissue-relevant biology. Through integrating cross-mapped tissue-specific histone marks with large-scale GWAS and selection signature results, we for the first time detected relevant tissues and cell types for 45 economically important traits and artificial selection in cattle. For instance, immune tissues are significantly associated with health and reproduction traits, multiple tissues for milk production and body conformation traits (reflecting their highly polygenic architecture), and thyroid for the different selection between beef and dairy cattle. Similarly, we detected relevant tissues for 58 complex traits and diseases in humans and observed that immune and fertility traits in humans significantly correlated with those in cattle in terms of relevant tissues, which facilitated the identification of causal genes for such traits.
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Translational Genomics, Proteomics and Interactomics
Running Title: Oncogenomics and Cancer Interactomics Translational Oncogenomics and Human Cancer Interactome Networks: Techniques and Complex System Dynamic Approaches Review 05/06/2011 I.C. Baianu AFC-NMR & NIR Microspectroscopy Facility, College of ACES, FSHN & NPRE Departments, University of Illinois at Urbana, Urbana, IL. 61801, USA Abstract An overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications of such results are individualized human cancer therapies or, in general, `personalized medicine'. Several cancer detection techniques are currently under development both in the direction of improved detection sensitivity and increased time resolution of cellular events, with the limits of single molecule detection and picosecond time resolution already reached. The urgency for the complete mapping of a human cancer interactome with the help
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Epigenome Prediction of Gene Expression Using a Dynamical System Approach
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.03.234740; this version posted August 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Epigenome Prediction of Gene Expression using a Dynamical System Approach James Brunnery Center for Individualized Medicine Microbiome Program, Mayo Clinic Rochester, MN 55901, USA yE-mail: [email protected] www.mayo.edu Jacob Kim Department of Biological Sciences, Columbia University New York, NY 10027, USA www.columbia.edu Timothy Downing The Henry Samueli School of Engineering, University of California Irvine Irvine, CA 92697, USA www.uci.edu Eric Mjolsness Departments of Computer Science and Mathematics, University of California Irvine Irvine, CA 92697, USA www.uci.edu Kord M. Koberz Department of Physiological Nursing and Bakar Computational Health Sciences Institute, University of California San Francisco San Francisco, CA 94143, USA zE-mail: [email protected] www.ucsf.edu Gene regulation is an important fundamental biological process. The regulation of gene ex- pression is managed through a variety of methods including epigentic processes (e.g., DNA methylation). Understanding the role of epigenetic changes in gene expression is a funda- mental question of molecular biology. Predictions of gene expression values from epigenetic data have tremendous research and clinical potential. Dynamical systems can be used to generate a model to predict gene expression using epigenetic data and a gene regulatory network (GRN).
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Functions and Therapeutic Applications of Antisense Rnas in Cancer
Open Access Austin Journal of Cancer and Clinical Research Editorial Functions and Therapeutic Applications of Antisense RNAs in Cancer Deva Magendhra Rao AK, Arvinden VR, RNAs are chromatin remodeling, RNA masking, RNAi (RNA Rajkumar T and Samson M* interference) and TI (transcriptional interference) [7]. Chromatin Department of Molecular Oncology, Cancer Institute reprogramming by as RNATARID (TCF21 antisense RNA inducing (WIA) of Chennai, India demethylation) has been reported to aid in demethylation elucidating *Corresponding author: Samson M, Department a novel epigenetic modulation. TARID physically interacts with of Molecular Oncology, Cancer Institute (WIA) No: 38, TCF21 promoter and localizes GADD45A (growth arrest and DNA- Sardar Patel Road, Adyar, Chennai 600036, India damage inducible, alpha) which in turn recruits TDG (thymine- Received: June 21, 2017; Accepted: July 03, 2017; DNA glycosylase) for TET (Ten Eleven Translocation) mediated Published: July 14, 2017 conversion of 5-methylcytosine to 5-hydroxymethylation and this demethylation eventually increases the expression of the tumor Introduction suppressor TCF21 [8]. Antisense RNAs might form sense/antisense Non-coding RNAs transcribed from opposite strand of the (SAS) duplex masking the sense transcript from processes like splicing, protein coding sense strand are collectively termed as antisense RNAs localization and stabilization by deliberately preventing protein-RNA (asRNAs). Effective in binding to both DNA and RNA, asRNAs are interaction. EMT (Epithelial mesenchymal transition) induction reported to have a putative role in transcriptional interference and by Zeb2 over expression is an example of RNA masking exerted mRNA instability [1]. Also known as Natural Antisense Transcripts by as RNA of Zeb2 which prevents the splicing of 5’UTR of Zeb2 (NATs), these are classified under long non-coding RNAs (lncRNAs) retaining the intra-ribosomal entry site for an efficient expression.
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Conserved Expression of Natural Antisense Transcripts in Mammals Maurice HT Ling1, Yuguang Ban1, Hongxiu Wen2, San Ming Wang2 and Steven X Ge1*
Ling et al. BMC Genomics 2013, 14:243 http://www.biomedcentral.com/1471-2164/14/243 RESEARCH ARTICLE Open Access Conserved expression of natural antisense transcripts in mammals Maurice HT Ling1, Yuguang Ban1, Hongxiu Wen2, San Ming Wang2 and Steven X Ge1* Abstract Background: Recent studies had found thousands of natural antisense transcripts originating from the same genomic loci of protein coding genes but from the opposite strand. It is unclear whether the majority of antisense transcripts are functional or merely transcriptional noise. Results: Using the Affymetrix Exon array with a modified cDNA synthesis protocol that enables genome-wide detection of antisense transcription, we conducted large-scale expression analysis of antisense transcripts in nine corresponding tissues from human, mouse and rat. We detected thousands of antisense transcripts, some of which show tissue-specific expression that could be subjected to further study for their potential function in the corresponding tissues/organs. The expression patterns of many antisense transcripts are conserved across species, suggesting selective pressure on these transcripts. When compared to protein-coding genes, antisense transcripts show a lesser degree of expression conservation. We also found a positive correlation between the sense and antisense expression across tissues. Conclusion: Our results suggest that natural antisense transcripts are subjected to selective pressure but to a lesser degree compared to sense transcripts in mammals. Background Through our previous study, we developed an Antisense Recent studies suggest that a substantial portion of mam- Transcriptome analysis using Exon array (ATE) approach malian genomes are transcribed as non-coding RNA [1-4], for high-throughput expression analysis of NATs by using including cis-natural antisense transcripts (cis-NATs) commercial oligonucleotide DNA microarrays [22].
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