Functions of DNA Methylation: Islands, Start Sites, Gene Bodies and Beyond
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Dna Methylation Post Transcriptional Modification
Dna Methylation Post Transcriptional Modification Blistery Benny backbiting her tug-of-war so protectively that Scot barrel very weekends. Solanaceous and unpossessing Eric pubes her creatorships abrogating while Raymundo bereave some limitations demonstrably. Clair compresses his catchings getter epexegetically or epidemically after Bernie vitriols and piffling unchangeably, hypognathous and nourishing. To explore quantitative and dynamic properties of transcriptional regulation by. MeSH Cochrane Library. In revere last check of man series but left house with various gene expression profile of the effect of. Moreover interpretation of transcriptional changes during COVID-19 has been. In transcriptional modification by post transcriptional repression and posted by selective breeding industry: patterns of dna methylation during gc cells and the study of dna. DNA methylation regulates transcriptional homeostasis of. Be local in two ways Post Translational Modifications of amino acid residues of histone. International journal of cyclic gmp in a chromatin dynamics: unexpected results in alternative splicing of reusing and diagnosis of dmrs has been identified using whole process. Dam in dna methylation to violent outbursts that have originated anywhere in england and post transcriptional gene is regulated at the content in dna methylation post transcriptional modification of. A seven sample which customers post being the dtc company for analysis. Fei zhao y, methylation dynamics and modifications on lysine is an essential that. Tag-based our Generation Sequencing. DNA methylation and histone modifications as epigenetic. Thc content of. Lysine methylation has been involved in both transcriptional activation H3K4. For instance aberrance of DNA methylation andor demethylation has been. Chromosome conformation capture from 3C to 5C and will ChIP-based modification. -
Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases
cells Review Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases Paulina Prorok 1 , Inga R. Grin 2,3, Bakhyt T. Matkarimov 4, Alexander A. Ishchenko 5 , Jacques Laval 5, Dmitry O. Zharkov 2,3,* and Murat Saparbaev 5,* 1 Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany; [email protected] 2 SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; [email protected] 3 Center for Advanced Biomedical Research, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia 4 National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; [email protected] 5 Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif, France; [email protected] (A.A.I.); [email protected] (J.L.) * Correspondence: [email protected] (D.O.Z.); [email protected] (M.S.); Tel.: +7-(383)-3635187 (D.O.Z.); +33-(1)-42115404 (M.S.) Abstract: It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the Citation: Prorok, P.; Grin, I.R.; major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field Matkarimov, B.T.; Ishchenko, A.A.; and alkylating metabolic radicals added to these threats. -
The International Human Epigenome Consortium (IHEC): a Blueprint for Scientific Collaboration and Discovery
The International Human Epigenome Consortium (IHEC): A Blueprint for Scientific Collaboration and Discovery Hendrik G. Stunnenberg1#, Martin Hirst2,3,# 1Department of Molecular Biology, Faculties of Science and Medicine, Radboud University, Nijmegen, The Netherlands 2Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4. 3Canada’s Michael Smith Genome Science Center, BC Cancer Agency, Vancouver, BC, Canada V5Z 4S6 #Corresponding authors [email protected] [email protected] Abstract The International Human Epigenome Consortium (IHEC) coordinates the generation of a catalogue of high-resolution reference epigenomes of major primary human cell types. The studies now presented (cell.com/XXXXXXX) highlight the coordinated achievements of IHEC teams to gather and interpret comprehensive epigenomic data sets to gain insights in the epigenetic control of cell states relevant for human health and disease. One of the great mysteries in developmental biology is how the same genome can be read by cellular machinery to generate the plethora of different cell types required for eukaryotic life. As appreciation grew for the central roles of transcriptional and epigenetic mechanisms in specification of cellular fates and functions, researchers around the world encouraged scientific funding agencies to develop an organized and standardized effort to exploit epigenomic assays to shed additional light on this process (Beck, Olek et al. 1999, Jones and Martienssen 2005, American Association for Cancer Research Human Epigenome Task and European Union 2008). In March 2009, leading scientists and international health research funding agency representatives were invited to a meeting in Bethesda (MD, USA) to gauge the level of interest in an international epigenomics project and to identify potential areas of focus. -
DNA Methylation, Imprinting and Cancer
European Journal of Human Genetics (2002) 10, 6±16 ã 2002 Nature Publishing Group All rights reserved 1018-4813/02 $25.00 www.nature.com/ejhg REVIEW DNA methylation, imprinting and cancer Christoph Plass*,1 and Paul D Soloway*,2 1Division of Human Cancer Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, OH 43210, USA; 2Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, NY 14263, USA It is well known that a variety of genetic changes influence the development and progression of cancer. These changes may result from inherited or spontaneous mutations that are not corrected by repair mechanisms prior to DNA replication. It is increasingly clear that so called epigenetic effects that do not affect the primary sequence of the genome also play an important role in tumorigenesis. This was supported initially by observations that cancer genomes undergo changes in their methylation state and that control of parental allele-specific methylation and expression of imprinted loci is lost in several cancers. Many loci acquiring aberrant methylation in cancers have since been identified and shown to be silenced by DNA methylation. In many cases, this mechanism of silencing inactivates tumour suppressors as effectively as frank mutation and is one of the cancer-predisposing hits described in Knudson's two hit hypothesis. In contrast to mutations which are essentially irreversible, methylation changes are reversible, raising the possibility of developing therapeutics based on restoring the normal methylation state to cancer-associated genes. Development of such therapeutics will require identifying loci undergoing methylation changes in cancer, understanding how their methylation influences tumorigenesis and identifying the mechanisms regulating the methylation state of the genome. -
Lecture: 28 TRANSAMINATION, DEAMINATION and DECARBOXYLATION
Lecture: 28 TRANSAMINATION, DEAMINATION AND DECARBOXYLATION Protein metabolism is a key physiological process in all forms of life. Proteins are converted to amino acids and then catabolised. The complete hydrolysis of a polypeptide requires mixture of peptidases because individual peptidases do not cleave all peptide bonds. Both exopeptidases and endopeptidases are required for complete conversion of protein to amino acids. Amino acid metabolism The amino acids not only function as energy metabolites but also used as precursors of many physiologically important compounds such as heme, bioactive amines, small peptides, nucleotides and nucleotide coenzymes. In normal human beings about 90% of the energy requirement is met by oxidation of carbohydrates and fats. The remaining 10% comes from oxidation of the carbon skeleton of amino acids. Since the 20 common protein amino acids are distinctive in terms of their carbon skeletons, amino acids require unique degradative pathway. The degradation of the carbon skeletons of 20 amino acids converges to just seven metabolic intermediates namely. i. Pyruvate ii. Acetyl CoA iii. Acetoacetyl CoA iv. -Ketoglutarate v. Succinyl CoA vi. Fumarate vii. Oxaloacetate Pyruvate, -ketoglutarate, succinyl CoA, fumarate and oxaloacetate can serve as precursors for glucose synthesis through gluconeogenesis.Amino acids giving rise to these intermediates are termed as glucogenic. Those amino acids degraded to yield acetyl CoA or acetoacetate are termed ketogenic since these compounds are used to synthesize ketone bodies. Some amino acids are both glucogenic and ketogenic (For example, phenylalanine, tyrosine, tryptophan and threonine. Catabolism of amino acids The important reaction commonly employed in the breakdown of an amino acid is always the removal of its -amino group. -
DNA DEAMINATION REPAIR ENZYMES in BACTERIAL and HUMAN SYSTEMS Rongjuan Mi Clemson University, [email protected]
Clemson University TigerPrints All Dissertations Dissertations 12-2008 DNA DEAMINATION REPAIR ENZYMES IN BACTERIAL AND HUMAN SYSTEMS Rongjuan Mi Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Part of the Biochemistry Commons Recommended Citation Mi, Rongjuan, "DNA DEAMINATION REPAIR ENZYMES IN BACTERIAL AND HUMAN SYSTEMS" (2008). All Dissertations. 315. https://tigerprints.clemson.edu/all_dissertations/315 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. DNA DEAMINATION REPAIR ENZYMES IN BACTERIAL AND HUMAN SYSTEMS A Dissertation Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Biochemistry by Rongjuan Mi December 2008 Accepted by: Dr. Weiguo Cao, Committee Chair Dr. Chin-Fu Chen Dr. James C. Morris Dr. Gary Powell ABSTRACT DNA repair enzymes and pathways are diverse and critical for living cells to maintain correct genetic information. Single-strand-selective monofunctional uracil DNA glycosylase (SMUG1) belongs to Family 3 of the uracil DNA glycosylase superfamily. We report that a bacterial SMUG1 ortholog in Geobacter metallireducens (Gme) and the human SMUG1 enzyme are not only uracil DNA glycosylases (UDG), but also xanthine DNA glycosylases (XDG). Mutations at M57 (M57L) and H210 (H210G, H210M, H210N) can cause substantial reductions in XDG and UDG activities. Increased selectivity is achieved in the A214R mutant of Gme SMUG1 and G60Y completely abolishes XDG and UDG activity. Most interestingly, a proline substitution at the G63 position switches the Gme SMUG1 enzyme to an exclusive uracil DNA glycosylase. -
A Machine Learning Framework for Precise 3D Domain Boundary Prediction at Base-Level Resolution
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.03.282186; this version posted September 29, 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 4.0 International license. preciseTAD: A machine learning framework for precise 3D domain boundary prediction at base-level resolution Spiro C. Stilianoudakis1 ([email protected]), Mikhail G. Dozmorov1* (mikhail.dozmorov@ vcuhealth.org) 1 Dept. of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA * To whom correspondence should be addressed Abstract The low resolution of high-throughput chromatin conformation capture data limits the precise mapping of boundaries of topologically associating domains and chromatin loops. We developed preciseTAD, an optimized random forest model trained on high-resolution genome annotation data (e.g., CTCF ChIP- seq) to predict the location of domain boundaries at base-level resolution. Distance between boundaries and annotations, random under-sampling, and transcription factor binding sites resulted in best model performance. preciseTAD boundaries were more enriched for CTCF, RAD21, SMC3, and ZNF143, and conserved across cell lines. Using genome annotations, pre-trained models can detect boundaries in cells without Hi-C data. preciseTAD is available at https://bioconductor.org/packages/preciseTAD Keywords Hi-C, TAD, machine learning, random forest, DBSCAN Background The advent of chromosome conformation capture (3C) sequencing technologies, and its successor Hi-C, have revealed a hierarchy of the 3-dimensional (3D) structure of the human genome such as chromatin loops [1], Topologically Associating Domains (TADs) [2,3], and A/B compartments [4]. -
Functional Implications of DNA Methylation in Adipose Biology
Diabetes Volume 68, May 2019 871 Functional Implications of DNA Methylation in Adipose Biology Xiang Ma and Sona Kang Diabetes 2019;68:871–878 | https://doi.org/10.2337/dbi18-0057 The twin epidemics of obesity and type 2 diabetes (T2D) variants have not been tested for causality, and even if are a serious health, social, and economic issue. The proven causal, they cannot fully explain many clinical dysregulation of adipose tissue biology is central to the features such as high heritability, high discordance in adult development of these two metabolic disorders, as adi- monozygotic twins, and the close relationship with envi- pose tissue plays a pivotal role in regulating whole-body ronmental factors (2–5). Therefore, it has long been metabolism and energy homeostasis (1). Accumulating speculated that nongenetic variation, such as epigenetic evidence indicates that multiple aspects of adipose bi- alterations, plays a role in pathogenesis. This notion has PERSPECTIVES IN DIABETES ology are regulated, in part, by epigenetic mechanisms. been borne out by a recent epigenome-wide association The precise and comprehensive understanding of the study that linked alterations in DNA methylation to whole- epigenetic control of adipose tissue biology is crucial to body insulin sensitivity (6). identifying novel therapeutic interventions that target DNA methylation is a reversible epigenetic mark in- epigenetic issues. Here, we review the recent findings volving the covalent transfer of a methyl group to the C-5 on DNA methylation events and machinery in regulating the developmental processes and metabolic function of position of a cytosine residue by DNA methyltransferases adipocytes. We highlight the following points: 1) DNA (DNMTs), usually in the context of a cytosine-guanine methylation is a key epigenetic regulator of adipose dinucleotide (CpG) doublet. -
Cpg Islands and the Regulation of Transcription
Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW CpG islands and the regulation of transcription Aime´e M. Deaton and Adrian Bird1 The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom Vertebrate CpG islands (CGIs) are short interspersed DNA In spite of their link with transcription, the functional sequences that deviate significantly from the average significance of CGIs is only just beginning to emerge. CGI genomic pattern by being GC-rich, CpG-rich, and pre- promoters turn out to have distinctive patterns of tran- dominantly nonmethylated. Most, perhaps all, CGIs are scription initiation and chromatin configuration. Their sites of transcription initiation, including thousands that regulation involves proteins (some of which specifically are remote from currently annotated promoters. Shared bind nonmethylated CpG) that influence the modifica- DNA sequence features adapt CGIs for promoter function tion status of CGI chromatin. In addition, the CpG moieties by destabilizing nucleosomes and attracting proteins that themselves are sometimes subject to cytosine methylation, create a transcriptionally permissive chromatin state. which correlates with stable shutdown of the associated Silencing of CGI promoters is achieved through dense promoter. Here we examine the properties shared by ver- CpG methylation or polycomb recruitment, again using tebrate CGIs and how transcription is regulated at these their distinctive DNA sequence composition. CGIs are sites. Recent related reviews include Illingworth and Bird therefore generically equipped to influence local chroma- (2009), Mohn and Schubeler (2009), and Blackledge and tin structure and simplify regulation of gene activity. Klose (2011). Vertebrate genomes are methylated predominantly at the Evolutionary conservation of CGIs dinucleotide CpG, and consequently are CpG-deficient owing to the mutagenic properties of methylcytosine CGIs are distinct in vertebrates due to their lack of DNA (Coulondre et al. -
Dynamics and Function of DNA Methylation in Plants
REVIEWS Dynamics and function of DNA methylation in plants Huiming Zhang1,2*, Zhaobo Lang1,2 and Jian- Kang Zhu 1,2,3* Abstract | DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant developmental abnormalities. A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review, we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so- called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions. DNA methylation at the 5ʹ position of cytosine contrib- and regulatory factors are generally not lethal. However, utes to the epigenetic regulation of nuclear gene expres- DNA methylation appears to be more crucial for devel- sion and to genome stability1,2. Epigenetic changes, opment and environmental- stress responses in plants including DNA methylation, histone modifications and that have more complex genomes. Recent findings histone variants and some non- coding RNA (ncRNA) have uncovered important -
Amino Acid Catabolism: Urea Cycle the Urea Bi-Cycle Two Issues
BI/CH 422/622 OUTLINE: OUTLINE: Protein Degradation (Catabolism) Digestion Amino-Acid Degradation Inside of cells Urea Cycle – dealing with the nitrogen Protein turnover Ubiquitin Feeding the Urea Cycle Activation-E1 Glucose-Alanine Cycle Conjugation-E2 Free Ammonia Ligation-E3 Proteosome Glutamine Amino-Acid Degradation Glutamate dehydrogenase Ammonia Overall energetics free Dealing with the carbon transamination-mechanism to know Seven Families Urea Cycle – dealing with the nitrogen 1. ADENQ 5 Steps 2. RPH Carbamoyl-phosphate synthetase oxidase Ornithine transcarbamylase one-carbon metabolism Arginino-succinate synthetase THF Arginino-succinase SAM Arginase 3. GSC Energetics PLP uses Urea Bi-cycle 4. MT – one carbon metabolism 5. FY – oxidases Amino Acid Catabolism: Urea Cycle The Urea Bi-Cycle Two issues: 1) What to do with the fumarate? 2) What are the sources of the free ammonia? a-ketoglutarate a-amino acid Aspartate transaminase transaminase a-keto acid Glutamate 1 Amino Acid Catabolism: Urea Cycle The Glucose-Alanine Cycle • Vigorously working muscles operate nearly anaerobically and rely on glycolysis for energy. a-Keto acids • Glycolysis yields pyruvate. – If not eliminated (converted to acetyl- CoA), lactic acid will build up. • If amino acids have become a fuel source, this lactate is converted back to pyruvate, then converted to alanine for transport into the liver. Excess Glutamate is Metabolized in the Mitochondria of Hepatocytes Amino Acid Catabolism: Urea Cycle Excess glutamine is processed in the intestines, kidneys, and liver. (deaminating) (N,Q,H,S,T,G,M,W) OAA à Asp Glutamine Synthetase This costs another ATP, bringing it closer to 5 (N,Q,H,S,T,G,M,W) 29 N 2 Amino Acid Catabolism: Urea Cycle Excess glutamine is processed in the intestines, kidneys, and liver. -
Generative Modeling of Multi-Mapping Reads with Mhi-C Advances Analysis of Hi-C Studies Ye Zheng1, Ferhat Ay2,3, Sunduz Keles1,4*
TOOLS AND RESOURCES Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies Ye Zheng1, Ferhat Ay2,3, Sunduz Keles1,4* 1Department of Statistics, University of Wisconsin-Madison, Madison, United States; 2La Jolla Institute for Allergy and Immunology, La Jolla, United States; 3School of Medicine, University of California, San Diego, La Jolla, United States; 4Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, United States Abstract Current Hi-C analysis approaches are unable to account for reads that align to multiple locations, and hence underestimate biological signal from repetitive regions of genomes. We developed and validated mHi-C, a multi-read mapping strategy to probabilistically allocate Hi-C multi-reads. mHi-C exhibited superior performance over utilizing only uni-reads and heuristic approaches aimed at rescuing multi-reads on benchmarks. Specifically, mHi-C increased the sequencing depth by an average of 20% resulting in higher reproducibility of contact matrices and detected interactions across biological replicates. The impact of the multi-reads on the detection of significant interactions is influenced marginally by the relative contribution of multi-reads to the sequencing depth compared to uni-reads, cis-to-trans ratio of contacts, and the broad data quality as reflected by the proportion of mappable reads of datasets. Computational experiments highlighted that in Hi-C studies with short read lengths, mHi-C rescued multi-reads can emulate the effect of longer reads. mHi-C also revealed biologically supported bona fide promoter-enhancer interactions and topologically associating domains involving repetitive genomic regions, thereby *For correspondence: unlocking a previously masked portion of the genome for conformation capture studies.