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Functional Roles of Bromodomain Proteins in Cancer
cancers Review Functional Roles of Bromodomain Proteins in Cancer Samuel P. Boyson 1,2, Cong Gao 3, Kathleen Quinn 2,3, Joseph Boyd 3, Hana Paculova 3 , Seth Frietze 3,4,* and Karen C. Glass 1,2,4,* 1 Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; [email protected] 2 Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA; [email protected] 3 Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; [email protected] (C.G.); [email protected] (J.B.); [email protected] (H.P.) 4 University of Vermont Cancer Center, Burlington, VT 05405, USA * Correspondence: [email protected] (S.F.); [email protected] (K.C.G.) Simple Summary: This review provides an in depth analysis of the role of bromodomain-containing proteins in cancer development. As readers of acetylated lysine on nucleosomal histones, bromod- omain proteins are poised to activate gene expression, and often promote cancer progression. We examined changes in gene expression patterns that are observed in bromodomain-containing proteins and associated with specific cancer types. We also mapped the protein–protein interaction network for the human bromodomain-containing proteins, discuss the cellular roles of these epigenetic regu- lators as part of nine different functional groups, and identify bromodomain-specific mechanisms in cancer development. Lastly, we summarize emerging strategies to target bromodomain proteins in cancer therapy, including those that may be essential for overcoming resistance. Overall, this review provides a timely discussion of the different mechanisms of bromodomain-containing pro- Citation: Boyson, S.P.; Gao, C.; teins in cancer, and an updated assessment of their utility as a therapeutic target for a variety of Quinn, K.; Boyd, J.; Paculova, H.; cancer subtypes. -
Chip Validated H4k5ac (Clone RM140) Antibody with Positive and Negative Primer Sets
www.chromatrap.com Clywedog Rd South Wrexham Industrial Estate Wrexham LL13 9XS, United Kingdom Tel: +44 (0) 1978 666239/40 Email: [email protected] ChIP Validated H4K5ac (Clone RM140) Antibody with Positive and Negative Primer Sets Catalogue no: 900029 Chromatrap®’s ChIP Validated H4K5ac Antibody with Positive Primer Set provides a complete set of tools to assist with a successful ChIP assay. Including: H4K5ac antibody, control rabbit IgG, and positive primer set. The ChIP Validated H4K5ac Antibody with Positive Primer Set is not suitable for use with non-human species. Background: Histone 4 (H4) is one of the five core histone proteins, comprising the protein component of chromatin. H4 is ubiquitous within chromosomes and can be found bound to most gene sequences throughout the genome. Acetylation of lysine 5 on histone 4 (H4K5ac) is associated with open chromatin and active gene transcription. H4K5ac has been shown to have roles in epigenetic bookmarking, a process where genetic information is passed onto daughter cells during cell division. A rabbit IgG is included in this Antibody Primer Set as a negative control for the ChIP experiment. The H4K5ac positive primer set recognises the promoter of the GAPDH gene, associated with active transcription and is a suitable target for this antibody. Suggested Usage: Component Suggested Dilution Figure H4K5ac 2:1 (antibody: chromatin) 1 Rabbit IgG 2:1 (antibody: chromatin) 1 Positive Primer Set Dilute from 4M (provided) to 1M working concentration Please note: Optimal dilutions should be determined by the user. These volumes are stated as guidelines only. Advancements in Epigenetics *This product is for research use only. -
Quantitative Proteomics Methods for the Analysis of Histone Post-Translational Modifications
Université de Montréal Quantitative Proteomics Methods for the Analysis of Histone Post-translational Modifications par Nebiyu Ali Abshiru Département de Chimie Faculté des arts et des sciences Thèse présentée à la Faculté des études supérieures et postdoctorales en vue de l’obtention du grade de philosophiae doctor (Ph.D.) en chimie Septembre 2015 ©Nebiyu Ali Abshiru, 2015 i Résumé Les histones sont des protéines nucléaires hautement conservées chez les cellules des eucaryotes. Elles permettent d’organiser et de compacter l’ADN sous la forme de nucléosomes, ceux-ci representant les sous unités de base de la chromatine. Les histones peuvent être modifiées par de nombreuses modifications post-traductionnelles (PTMs) telles que l’acétylation, la méthylation et la phosphorylation. Ces modifications jouent un rôle essentiel dans la réplication de l’ADN, la transcription et l’assemblage de la chromatine. L’abondance de ces modifications peut varier de facon significative lors du developpement des maladies incluant plusieurs types de cancer. Par exemple, la perte totale de la triméthylation sur H4K20 ainsi que l’acétylation sur H4K16 sont des marqueurs tumoraux spécifiques a certains types de cancer chez l’humain. Par conséquent, l’étude de ces modifications et des événements determinant la dynamique des leurs changements d’abondance sont des atouts importants pour mieux comprendre les fonctions cellulaires et moléculaires lors du développement de la maladie. De manière générale, les modifications des histones sont étudiées par des approches biochimiques telles que les immuno-buvardage de type Western ou les méthodes d’immunoprécipitation de la chromatine (ChIP). Cependant, ces approches présentent plusieurs inconvénients telles que le manque de spécificité ou la disponibilité des anticorps, leur coût ou encore la difficulté de les produire et de les valider. -
16-0352 Technical Data Sheet
Nucleosome, Recombinant Human, H4K5ac dNuc, Biotinylated Catalog No. 16-0352 Lot No. 21147003-61 Pack Size 50 µg Product Description: Mononucleosomes assembled from recombinant human histones expressed in E. coli (two each of histones H2A, H2B, H3 and H4; accession numbers: H2A-P04908; H2B-O60814; H3.1-P68431; H4-P62805) wrapped by 147 base pairs of 601 positioning sequence DNA. Histone H4 (created by a proprietary synthetic method) is N-terminally acetylated and contains acetyl-lysine at position 5. The nucleosome is the basic subunit of chromatin. The 147 bp 601 sequence, identified by Lowary and Widom, has high affinity for histone octamers and is useful for nucleosome assembly. The DNA contains a 5’ biotin-TEG group. Western Blot Data: Western Analysis of Nucleosome, Recombinant Human, H4K5ac. Top Panel: Unmodified H4 Formulation: (Lane 1) and H4K5ac containing nucleosomes (Lane 2) were probed with an anti-H4K5ac antibody and analyzed via ECL Nucleosome, Recombinant Human, H4K5ac (27.3 µg protein readout. Only the H4K5ac sample produced a detectable weight, 50 µg total weight) in 50 µL of 10 mM Tris HCl pH 7.5, signal. Bottom Panel: Detail from Coomassie stained gel 25 mM NaCl, 1 mM EDTA, 2 mM DTT, 20% glycerol. Molarity = showing unmodified H4 nucleosome (Lane 1) and H4K5ac 5 μM. MW = 200,027.9 Da. nucleosome (Lane 2). Storage and Stability: Stable for six months at -80°C from date of receipt. For best results, aliquot and avoid multiple freeze/thaws. Application Notes: H4K5ac dNuc is highly purified and suitable for a variety of applications, including use as a substrate in enzymatic assays or for effector protein binding experiments. -
The Determinants of Nucleosome Patterns and the Impact of Phosphate Starvation on Nucleosome Patterns and Gene Expression in Rice
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 3-14-2018 The etD erminants of Nucleosome Patterns and the Impact of Phosphate Starvation on Nucleosome Patterns and Gene Expression in Rice Qi Zhang Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Agronomy and Crop Sciences Commons, Bioinformatics Commons, Genetics Commons, Genomics Commons, and the Plant Breeding and Genetics Commons Recommended Citation Zhang, Qi, "The eD terminants of Nucleosome Patterns and the Impact of Phosphate Starvation on Nucleosome Patterns and Gene Expression in Rice" (2018). LSU Doctoral Dissertations. 4502. https://digitalcommons.lsu.edu/gradschool_dissertations/4502 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. THE DETERMINANTS OF NUCLEOSOME PATTERNS AND THE IMPACT OF PHOSPHATE STARVATION ON NUCLEOSOME PATTERNS AND GENE EXPRESSION IN RICE A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Qi Zhang B.S., Sichuan Agricultural University, 2012 May 2018 ACKNOWLEDGEMENTS The journey towards the completion of the degree hasn’t been easy, and I would like to express my heartfelt gratitude to everyone who has been around me, listening to me, and supporting me. -
Machine Learning & Learning Machines
A Brief History • Bootstrapping • Bagging • Boosting (Schapire 1989) • Adaboost (Schapire 1995) What’s So Good About Adaboost • Improves classification accuracy • Can be used with many different classifiers • Commonly used in many areas • Simple to implement • Not prone to over-fitting Ex. “How May I Help You?” easy to find “rules of thumb” that are “often” correct • e.g.: “IF ‘card’ occurs in utterance THEN predict ‘Calling Card’ ” • hard to find single highly accurate prediction rule Bootstrap Estimation • Repeatedly draw n samples from D • For each set of samples, estimate a statistic • The bootstrap estimate is the mean of the individual estimates • Used to estimate a statistic (parameter) and its variance Bagging - Aggregate Bootstrapping • For i = 1 .. M – Draw n*<n samples from D with replacement – Learn classifier Ci • Final classifier is a vote of C1 .. CM • Increases classifier stability/reduces variance Boosting (Schapire 1989) • Randomly select n1 < n samples from D without replacement to obtain D1 – Train weak learner C1 • Select n2 < n samples from D with half of the samples misclassified by C1 to obtain D2 – Train weak learner C2 • Select all samples from D that C1 and C2 disagree on – Train weak learner C3 • Final classifier is vote of weak learners Adaboost - Adaptive Boosting • Instead of sampling, re-weight – Previous weak learner has only 50% accuracy over new distribution • Can be used to learn weak classifiers • Final classification based on weighted vote of weak classifiers Adaboost Terms • Learner = Hypothesis = Classifier • Weak Learner: < 50% error over any distribution • Strong Classifier: thresholded linear combination of weak learner outputs Basic idea of boosting technique In general Boosting Bagging Single Tree. -
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 -
Mouse Model of Endemic Burkitt Translocations Reveals the Long-Range Boundaries of Ig-Mediated Oncogene Deregulation
Mouse model of endemic Burkitt translocations reveals the long-range boundaries of Ig-mediated oncogene deregulation Alexander L. Kovalchuka,1, Camilo Ansarah-Sobrinhob,1,Ofir Hakimc,1, Wolfgang Reschb, Helena Tolarováb, Wendy Duboisd, Arito Yamaneb, Makiko Takizawab, Isaac Kleinf, Gordon L. Hagerc, Herbert C. Morse IIIa, Michael Potterd,1, Michel C. Nussenzweige,f,2, and Rafael Casellasb,g,2 aLaboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852; bGenomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892; cLaboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; dLaboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; eLaboratory of Molecular Immunology, and fHoward Hughes Medical Institute, The Rockefeller University, New York, NY 10065; and gCenter of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 Edited by Klaus Rajewsky, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany, and approved May 22, 2012 (received for review January 5, 2012) Human Burkitt lymphomas are divided into two main clinical human Burkitt lymphomas (BLs), mouse plasmacytomas (PCTs), variants: the endemic form, affecting African children infected with and rat immunocytomas (15, 16). malaria and the Epstein-Barr virus, and the sporadic form, distrib- Human BLs are divided into two main clinical variants: the uted across the rest of the world. However, whereas sporadic endemic form, affecting African children infected with malaria translocations decapitate Myc from 5′ proximal regulatory ele- and the Epstein-Barr virus, and the sporadic form, distributed ments, most endemic events occur hundreds of kilobases away across the rest of the world (17). -
Learning Chroma\N States from Chip-‐Seq Data
Learning Chroman States from ChIP-seq data Luca Pinello GC Yuan Lab Outline • Chroman structure, histone modificaons and combinatorial paerns • How to segment the genome in chroman states • How to use ChromHMM step by step • Further references 2 Epigene-cs and chroman structure • All (almost) the cells of our body share the same genome but have very different gene expression programs…. 3 h?p://jpkc.scu.edu.cn/ywwy/zbsw(E)/edetail12.htm The code over the code • The chroman structure and the accessibility are mainly controlled by: 1. Nucleosome posioning, 2. DNA methylaon, 3. Histone modificaons. 4 Histone Modificaons Specific histone modificaons or combinaons of modificaons confer unique biological func-ons to the region of the genome associated with them: • H3K4me3: promoters, gene acva.on • H3K27me3: promoters, poised enhancers, gene silencing • H2AZ: promoters • H3K4me1: enhancers • H3K36me3: transcribed regions • H3K9me3: gene silencing • H3k27ac: acve enhancers 5 Examples of *-Seq Measuring the genome genome fragmentation assembler DNA DNA reads “genome” ChIP-seq to measure histone data fragments Measuring the regulome (e.g., protein-binding of the genome) Chromatin Immunopreciptation genomic (ChIP) + intervals fragmentation Protein - peak caller bound by DNA bound DNA reads proteins REVIEWS fragments a also informative, as this ratio corresponds to the fraction ChIP–chip of nucleosomes with the particular modification at that location, averaged over all the cells assayed. One of the difficulties in conducting a ChIP–seq con- trol experiment is the large amount of sequencing that ChIP–seq may be necessary. For input DNA and bulk nucleosomes, many of the sequenced tags are spread evenly across the genome. -
Chip Validated H4k12ac (Clone RM202) Antibody with Positive and Negative Primer Sets
www.chromatrap.com Clywedog Rd South Wrexham Industrial Estate Wrexham LL13 9XS, United Kingdom Tel: +44 (0) 1978 666239/40 Email: [email protected] ChIP Validated H4K12ac (Clone RM202) Antibody with Positive and Negative Primer Sets Catalogue no: 900025 Chromatrap®’s ChIP Validated H4K12ac Antibody with Positive and Negative Primer Set provides a complete set of tools to assist with a successful ChIP assay. Including: H4K12ac antibody, control rabbit IgG, positive and negative primer sets. The ChIP Validated H4K12ac Antibody with Positive and Negative Primer Sets is not suitable for use with non-human species. Background: Histone 4 (H4) is one of the core histone proteins, comprising the protein component of chromatin. H4 is ubiquitous within chromosomes and can be found bound to most gene sequences throughout the genome. Lysine 12 on histone 4 (H4K12) can only be acetylated and is not associated with methylation. The histone modification H4K12ac is associated with active promoter regions and has roles in activating the transcription of genes, in particular genes with roles in memory and learning. H4K12ac can have an influence on paternal inheritance in the zygote, indicating the importance of this mark for embryo development. A rabbit IgG is included in this Antibody Primer Set as a negative control for the ChIP experiment. The H4K12ac positive primer set recognises the GREB1 gene. The negative primer set recognises the SAT2 gene. Suggested Usage: Component Suggested Dilution Figure H4K12ac 2:1 (antibody: chromatin) 1 Rabbit IgG 2:1 (antibody: chromatin) 1 Positive Primer Set Dilute from 4M (provided) to 1M working concentration Negative Primer Set Dilute from 4M (provided) to 1M working concentration Please note: Optimal dilutions should be determined by the user. -
H4k12ac Is Regulated by Estrogen Receptor-Alpha and Is Associated with BRD4 Function and Inducible Transcription
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 6, No. 9 H4K12ac is regulated by estrogen receptor-alpha and is associated with BRD4 function and inducible transcription Sankari Nagarajan1, Eva Benito2, Andre Fischer2,3 and Steven A. Johnsen1 1 Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany 2 Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany 3 Research Group for Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany Correspondence to: Steven A. Johnsen, email: [email protected] Keywords: Histone acetylation, bromodomain, estrogen, epigenetics, chromatin Received: December 04, 2014 Accepted: January 28, 2015 Published: January 31, 2015 This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Hormone-dependent gene expression requires dynamic and coordinated epigenetic changes. Estrogen receptor-positive (ER+) breast cancer is particularly dependent upon extensive chromatin remodeling and changes in histone modifications for the induction of hormone-responsive gene expression. Our previous studies established an important role of bromodomain-containing protein-4 (BRD4) in promoting estrogen-regulated transcription and proliferation of ER+ breast cancer cells. Here, we investigated the association between genome-wide occupancy of histone H4 acetylation at lysine 12 (H4K12ac) and BRD4 in the context of estrogen- induced transcription. Similar to BRD4, we observed that H4K12ac occupancy increases near the transcription start sites (TSS) of estrogen-induced genes as well as at distal ERα binding sites in an estrogen-dependent manner. -
Snipa Snpcard
SNiPAcard Block annotations Block info genomic range chr6:169,562,593-169,598,082 block size 35,490 bp variant count 24 variants Basic features Conservation/deleteriousness Linked genes phyloP μ = -0.515 [-2.942 – gene(s) hit or close-by RP11-417E7.1 , RP11-417E7.2 0.962] phastCons μ = 0.035 [0 – 0.384] eQTL gene(s) RP11-417E7.2 μ = -0.601 [-3.58 – 1.47] potentially regulated RP1-137D17.1 , RP11-417E7.1 , RP3-495K2.3 , THBS2 , WDR27 , XXyac- GERP++ gene(s) YX65C7_A.2 CADD μ = 2.299 [0.198 – 6.035] THBS2 disease gene(s) score Trait annotations Disease gene annotation gene trait source DB source entry/link THBS2 INTERVERTEBRAL DISC DISEASE OMIM MIM:603932 Direct effect on regulation cis-eQTL gene transcript probe tissue min(statistic) (type) source variant(s) RP11-417E7.2 ? ENSG00000261039 aorta 9.21×10-6 (p-value) GTEx Portal V6 2 Putative effect on regulation ENCODE promoter-associated distal DHS (Enhancer) SNiPA enhancer id variant(s) associated SNiPA promoter id associated gene(s) ENCE00000470093 1 ENCP00000050698 RP1-137D17.1 ENCP00000050686 RP3-495K2.3 ENCP00000050695 THBS2 ENCE00000470094 1 ENCP00000050689 RP11-417E7.1 ENCP00000050698 RP1-137D17.1 ENCP00000050686 RP3-495K2.3 ENCP00000050695 THBS2 ENCE00000470180 1 ENCP00000050690 XXyac-YX65C7_A.2 ENCE00000470279 1 ENCP00000050700 WDR27 Regulatory feature cluster element id variant(s) tissue/cell factors ENSR00001233874 1 NHLF H3K36me3, H3K27ac, DNase1 (promoter flanking region) embryonic stem cell (H1ESC) DNase1 HSMMtube H2AZ, H3K4me2, DNase1 Osteobl H3K27ac, H3K36me3 blood (K562)