Genes for Embryo Development Are Packaged in Blocks of Multivalent Chromatin in Zebrafish Sperm
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Genome-Wide Analysis of 5-Hmc in the Peripheral Blood of Systemic Lupus Erythematosus Patients Using an Hmedip-Chip
INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 35: 1467-1479, 2015 Genome-wide analysis of 5-hmC in the peripheral blood of systemic lupus erythematosus patients using an hMeDIP-chip WEIGUO SUI1*, QIUPEI TAN1*, MING YANG1, QIANG YAN1, HUA LIN1, MINGLIN OU1, WEN XUE1, JIEJING CHEN1, TONGXIANG ZOU1, HUANYUN JING1, LI GUO1, CUIHUI CAO1, YUFENG SUN1, ZHENZHEN CUI1 and YONG DAI2 1Guangxi Key Laboratory of Metabolic Diseases Research, Central Laboratory of Guilin 181st Hospital, Guilin, Guangxi 541002; 2Clinical Medical Research Center, the Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, P.R. China Received July 9, 2014; Accepted February 27, 2015 DOI: 10.3892/ijmm.2015.2149 Abstract. Systemic lupus erythematosus (SLE) is a chronic, Introduction potentially fatal systemic autoimmune disease characterized by the production of autoantibodies against a wide range Systemic lupus erythematosus (SLE) is a typical systemic auto- of self-antigens. To investigate the role of the 5-hmC DNA immune disease, involving diffuse connective tissues (1) and modification with regard to the onset of SLE, we compared is characterized by immune inflammation. SLE has a complex the levels 5-hmC between SLE patients and normal controls. pathogenesis (2), involving genetic, immunologic and envi- Whole blood was obtained from patients, and genomic DNA ronmental factors. Thus, it may result in damage to multiple was extracted. Using the hMeDIP-chip analysis and valida- tissues and organs, especially the kidneys (3). SLE arises from tion by quantitative RT-PCR (RT-qPCR), we identified the a combination of heritable and environmental influences. differentially hydroxymethylated regions that are associated Epigenetics, the study of changes in gene expression with SLE. -
Histone Variants: Deviants?
Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Histone variants: deviants? Rohinton T. Kamakaka2,3 and Sue Biggins1 1Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 2UCT/National Institutes of Health, Bethesda, Maryland 20892, USA Histones are a major component of chromatin, the pro- sealing the two turns of DNA. The nucleosome filament tein–DNA complex fundamental to genome packaging, is then folded into a 30-nm fiber mediated in part by function, and regulation. A fraction of histones are non- nucleosome–nucleosome interactions, and this fiber is allelic variants that have specific expression, localiza- probably the template for most nuclear processes. Addi- tion, and species-distribution patterns. Here we discuss tional levels of compaction enable these fibers to be recent progress in understanding how histone variants packaged into the small volume of the nucleus. lead to changes in chromatin structure and dynamics to The packaging of DNA into nucleosomes and chroma- carry out specific functions. In addition, we review his- tin positively or negatively affects all nuclear processes tone variant assembly into chromatin, the structure of in the cell. While nucleosomes have long been viewed as the variant chromatin, and post-translational modifica- stable entities, there is a large body of evidence indicat- tions that occur on the variants. ing that they are highly dynamic (for review, see Ka- makaka 2003), capable of being altered in their compo- Supplemental material is available at http://www.genesdev.org. sition, structure, and location along the DNA. Enzyme Approximately two meters of human diploid DNA are complexes that either post-translationally modify the packaged into the cell’s nucleus with a volume of ∼1000 histones or alter the position and structure of the nucleo- µm3. -
Subcloning, Expression, and Enzymatic Study of PRMT5
Georgia State University ScholarWorks @ Georgia State University Biology Theses Department of Biology Summer 7-12-2010 Subcloning, Expression, and Enzymatic Study of PRMT5 Ran Guo Georgia State University Follow this and additional works at: https://scholarworks.gsu.edu/biology_theses Part of the Biology Commons Recommended Citation Guo, Ran, "Subcloning, Expression, and Enzymatic Study of PRMT5." Thesis, Georgia State University, 2010. https://scholarworks.gsu.edu/biology_theses/26 This Thesis is brought to you for free and open access by the Department of Biology at ScholarWorks @ Georgia State University. It has been accepted for inclusion in Biology Theses by an authorized administrator of ScholarWorks @ Georgia State University. For more information, please contact [email protected]. SUBCLONING, EXPRESSION, AND ENZYMATIC STUDY OF PRMT5 by RAN GUO Under the Direction of Yujun George Zheng ABSTRACT Protein arginine methyltransferases (PRMTs) mediate the transfer of methyl groups to arginine residues in histone and non-histone proteins. PRMT5 is an important member of PRMTs which symmetrically dimethylates arginine 8 in histone H3 (H3R8) and arginine 3 in histone H4 (H4R3). PRMT5 was reported to inhibit some tumor suppressors in leukemia and lymphoma cells and regulate p53 gene, through affecting the promoter of p53. Through methylation of H4R3, PRMT5 can recruit DNA-methyltransferase 3A (DNMT3A) which regulates gene transcription. All the above suggest that PRMT5 has an important function of suppressing cell apoptosis and is a potential anticancer target. Currently, the enzymatic activities of PRMT5 are not clearly understood. In our study, we improved the protein expression methodology and greatly enhanced the yield and quality of the recombinant PRMT5. -
Inferring Causal Relationships Among Different Histone Modifications and Gene Expression
Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Inferring Causal Relationships among Different Histone Modifications and Gene Expression Hong Yu*, Shanshan Zhu*, Bing Zhou*, Huiling Xue and Jing-Dong J. Han Chinese Academy of Sciences Key Laboratory of Molecular Developmental Biology, Center for Molecular Systems Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Beijing, 100101, China * These authors contributed equally to this work. Correspondence should be addressed to J.-D.J.H ([email protected]). Running title: histone modification and gene expression network Keywords: histone modification, gene expression, Bayesian network, causal relationship, epigenetics 1 Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Histone modifications are major epigenetic factors regulating gene expression. They play important roles in maintaining stem cell pluripotency and in cancer pathogenesis. Different modifications may combine to form complex ‘histone codes’. Recent high throughput technologies, such as ‘ChIP-chip’ and ‘ChIP-seq’, have generated high resolution maps for many histone modifications on the human genome. Here we use these maps to build a Bayesian network to infer causal and combinatorial relationships among histone modifications and gene expression. A pilot network derived by the same method among polycomb group (PcG) genes and H3K27 trimethylation is accurately supported by current literature. Our unbiased network model among histone modifications is also well supported by cross validation results. It not only confirmed already known relationships, such as those of H3K27me3 to gene silencing, H3K4me3 to gene activation, and the effect of bivalent modification of both H3K4me3 and H3K27me3, but also identified many other relationships that may predict new epigenetic interactions important in epigenetic gene regulation. -
Histone H3K4 Demethylation Is Negatively Regulated by Histone H3 Acetylation in Saccharomyces Cerevisiae
Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae Vicki E. Maltbya, Benjamin J. E. Martina, Julie Brind’Amourb,1, Adam T. Chruscickia,1, Kristina L. McBurneya, Julia M. Schulzec, Ian J. Johnsona, Mark Hillsd, Thomas Hentrichc, Michael S. Koborc, Matthew C. Lorinczb, and LeAnn J. Howea,2 Departments of aBiochemistry and Molecular Biology and bMedical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; cCenter for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada V5Z 4H4; and dTerry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 1L3 Edited by Kevin Struhl, Harvard Medical School, Boston, MA, and approved September 12, 2012 (received for review February 6, 2012) Histone H3 lysine 4 trimethylation (H3K4me3) is a hallmark of of lysine-specific HDMs have been identified: amine oxidases, transcription initiation, but how H3K4me3 is demethylated during such as LSD1, and the JmjC (Jumonji C) domain–containing gene repression is poorly understood. Jhd2, a JmjC domain protein, demethylases. This latter class of demethylases can be split fur- was recently identified as the major H3K4me3 histone demethylase ther into several subfamilies, including the evolutionarily con- (HDM) in Saccharomyces cerevisiae. Although JHD2 is required for served JARID1 family of demethylases, which is characterized JHD2 removal of methylation upon gene repression, deletion of does not only by a JmjC domain but also by JmjN, AT-rich interactive, not result in increased levels of H3K4me3 in bulk histones, indicating C5HC2 zinc finger, and PHD finger domains (6). In the yeast S. that this HDM is unable to demethylate histones during steady-state cerevisiae, the lone member of the JARID1 family of demethy- conditions. -
Recognition of Histone Acetylation by the GAS41 YEATS Domain Promotes H2A.Z Deposition in Non-Small Cell Lung Cancer
Downloaded from genesdev.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer Chih-Chao Hsu,1,2,8 Jiejun Shi,3,8 Chao Yuan,1,2,7,8 Dan Zhao,4,5,8 Shiming Jiang,1,2 Jie Lyu,3 Xiaolu Wang,1,2 Haitao Li,4,5 Hong Wen,1,2 Wei Li,3 and Xiaobing Shi1,2,6 1Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; 2Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; 3Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; 4MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; 5Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; 6Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, USA Histone acetylation is associated with active transcription in eukaryotic cells. It helps to open up the chromatin by neutralizing the positive charge of histone lysine residues and providing binding platforms for “reader” proteins. The bromodomain (BRD) has long been thought to be the sole protein module that recognizes acetylated histones. Re- cently, we identified the YEATS domain of AF9 (ALL1 fused gene from chromosome 9) as a novel acetyl-lysine- binding module and showed that the ENL (eleven-nineteen leukemia) YEATS domain is an essential acetyl-histone reader in acute myeloid leukemias. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Deciphering the Histone Code to Build the Genome Structure
bioRxiv preprint doi: https://doi.org/10.1101/217190; this version posted November 20, 2017. 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. Deciphering the histone code to build the genome structure Kirti Prakasha,b,c,* and David Fournierd,* aPhysico-Chimie Curie, Institut Curie, CNRS UMR 168, 75005 Paris, France; bOxford Nanoimaging Ltd, OX1 1JD, Oxford, UK; cMicron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK; dFaculty of Biology and Center for Computational Sciences, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; *Correspondence: [email protected], [email protected] Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding. We consider four features that relate histone modifications to chromatin folding: charge neutrali- sation, molecular specificity, robustness and evolvability. Next, we present evidence for the association among different histone modi- fications at various levels of chromatin organisation and show how these relationships relate to function such as transcription, replica- tion and cell division. Finally, we propose a model where the histone code can set critical checkpoints for chromatin to fold reversibly be- tween different orders of the organisation in response to a biological stimulus. DNA | nucleosomes | histone modifications | chromatin domains | chro- mosomes | histone code | chromatin folding | genome structure Introduction The genetic information within chromosomes of eukaryotes is packaged into chromatin, a long and folded polymer of double-stranded DNA, histones and other structural and non- structural proteins. -
Identification of Molecular Targets in Head and Neck Squamous Cell Carcinomas Based on Genome-Wide Gene Expression Profiling
1489-1497 7/11/07 18:41 Page 1489 ONCOLOGY REPORTS 18: 1489-1497, 2007 Identification of molecular targets in head and neck squamous cell carcinomas based on genome-wide gene expression profiling SATOYA SHIMIZU1,2, NAOHIKO SEKI2, TAKASHI SUGIMOTO2, SHIGETOSHI HORIGUCHI1, HIDEKI TANZAWA3, TOYOYUKI HANAZAWA1 and YOSHITAKA OKAMOTO1 Departments of 1Otorhinolaryngology, 2Functional Genomics and 3Clinical Molecular Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan Received May 21, 2007; Accepted June 28, 2007 Abstract. DNA amplifications activate oncogenes and are patients and metastases develop in 15-25% of patients (1). hallmarks of nearly all advanced cancers including head and Many factors, such as TNM stage, pathological grade and neck squamous cell carcinoma (HNSCC). Some oncogenes tumor site, influence the prognosis of HNSCC but are not show both DNA copy number gain and mRNA overexpression. sufficient to predict outcome. In addition, treatment often Chromosomal comparative genomic hybridization and oligo- results in impairment of functions such as speech and nucleotide microarrays were used to examine 8 HNSCC cell swallowing, cosmetic disfiguration and mental pain. These lines and a plot of gene expression levels relative to their inflictions significantly erode quality of life. To overcome this position on the chromosome was produced. Three highly situation, there is a need to find novel biomarkers that classify up-regulated genes, NT5C3, ANLN and INHBA, were patients into prognostic groups, to aid identification of high- identified on chromosome 7p14. These genes were subjected risk patients who may benefit from different treatments. to quantitative real-time RT-PCR on cDNA and genomic Comparative genomic hybridization (CGH) has facilitated DNA derived from 8 HNSCC cell lines. -
BMC Genomics Biomed Central
BMC Genomics BioMed Central Research article Open Access Determination of enriched histone modifications in non-genic portions of the human genome Jeffrey A Rosenfeld1,2,3, Zhibin Wang4, Dustin E Schones4, Keji Zhao4, Rob DeSalle3 and Michael Q Zhang*1 Address: 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA, 2Department of Biology, New York University, New York, NY USA, 3American Museum of Natural History, New York, NY USA and 4Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD USA Email: Jeffrey A Rosenfeld - [email protected]; Zhibin Wang - [email protected]; Dustin E Schones - [email protected]; Keji Zhao - [email protected]; Rob DeSalle - [email protected]; Michael Q Zhang* - [email protected] * Corresponding author Published: 31 March 2009 Received: 8 September 2008 Accepted: 31 March 2009 BMC Genomics 2009, 10:143 doi:10.1186/1471-2164-10-143 This article is available from: http://www.biomedcentral.com/1471-2164/10/143 © 2009 Rosenfeld et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP- seq) has recently been used to identify the modification patterns for the methylation and acetylation of many different histone tails in genes and enhancers. Results: We have extended the analysis of histone modifications to gene deserts, pericentromeres and subtelomeres. Using data from human CD4+ T cells, we have found that each of these non- genic regions has a particular profile of histone modifications that distinguish it from the other non- coding regions. -
A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase. -
Transcription Shapes Genome-Wide Histone Acetylation Patterns
ARTICLE https://doi.org/10.1038/s41467-020-20543-z OPEN Transcription shapes genome-wide histone acetylation patterns Benjamin J. E. Martin 1, Julie Brind’Amour 2, Anastasia Kuzmin1, Kristoffer N. Jensen2, Zhen Cheng Liu1, ✉ Matthew Lorincz 2 & LeAnn J. Howe 1 Histone acetylation is a ubiquitous hallmark of transcription, but whether the link between histone acetylation and transcription is causal or consequential has not been addressed. 1234567890():,; Using immunoblot and chromatin immunoprecipitation-sequencing in S. cerevisiae, here we show that the majority of histone acetylation is dependent on transcription. This dependency is partially explained by the requirement of RNA polymerase II (RNAPII) for the interaction of H4 histone acetyltransferases (HATs) with gene bodies. Our data also confirms the targeting of HATs by transcription activators, but interestingly, promoter-bound HATs are unable to acetylate histones in the absence of transcription. Indeed, HAT occupancy alone poorly predicts histone acetylation genome-wide, suggesting that HAT activity is regulated post- recruitment. Consistent with this, we show that histone acetylation increases at nucleosomes predicted to stall RNAPII, supporting the hypothesis that this modification is dependent on nucleosome disruption during transcription. Collectively, these data show that histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases. 1 Department of Biochemistry and Molecular Biology, Life Sciences Institute, Molecular