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      Genome-Wide Analysis of Histone H3 Lysine 4 Trimethylation in Peripheral Blood Mononuclear Cells of Minimal Change Nephrotic Syndrome Patients

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          Abstract

          Background: Studies of the epigenome have attracted some interest in nephrology. However, to date, our knowledge about the alterations in histone modification in minimal change nephrotic syndrome (MCNS) is unknown. This study aimed to investigate the variations in histone H3 lysine 4 trimethylation (H3K4me3) in peripheral blood mononuclear cells of patients with MCNS. Methods: H3K4me3 variations were analyzed in peripheral blood mononuclear cells, from 15 MCNS patients and 15 healthy subjects, using the ChIP-chip approach. ChIP real-time PCR is used to validate the microarray results. In addition, mRNA expression and DNA methylation status can also be further analyzed by quantitative (q) RT-PCR and methyl-DNA immunoprecipitation-q PCR, respectively. Results: 848 increased and 231 decreased H3K4me3 probes displaying significant H3K4me3 differences were found in MCNS patients compared with healthy subjects. The results of ChIP real-time PCR coincided well with the microarray. Expression analysis by qRT-PCR revealed positive correlations between mRNA and H3K4me3 levels. DNA methylation alterations were found on selected positive genes (IL4R, HIVEP3, HPSE2, CDH13 and PRKD2). In addition, we also found that there is an inverse relationship between H3K4me3 and promoter DNA methylation in MCNS patients. Conclusion: Our studies indicate that there are significant alterations of H3K4me3 in MCNS patients. These significant H3K4me3 candidates may help to explain the immunological disturbance involved in MCNS patients.

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          Most cited references38

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          The diverse functions of histone lysine methylation.

          Covalent modifications of histone tails have fundamental roles in chromatin structure and function. One such modification, lysine methylation, has important functions in many biological processes that include heterochromatin formation, X-chromosome inactivation and transcriptional regulation. Here, we summarize recent advances in our understanding of how lysine methylation functions in these diverse biological processes, and raise questions that need to be addressed in the future.
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            Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer.

            CpG island hypermethylation and global genomic hypomethylation are common epigenetic features of cancer cells. Less attention has been focused on histone modifications in cancer cells. We characterized post-translational modifications to histone H4 in a comprehensive panel of normal tissues, cancer cell lines and primary tumors. Using immunodetection, high-performance capillary electrophoresis and mass spectrometry, we found that cancer cells had a loss of monoacetylated and trimethylated forms of histone H4. These changes appeared early and accumulated during the tumorigenic process, as we showed in a mouse model of multistage skin carcinogenesis. The losses occurred predominantly at the acetylated Lys16 and trimethylated Lys20 residues of histone H4 and were associated with the hypomethylation of DNA repetitive sequences, a well-known characteristic of cancer cells. Our data suggest that the global loss of monoacetylation and trimethylation of histone H4 is a common hallmark of human tumor cells.
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              Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark.

              Cells employ elaborate mechanisms to introduce structural and chemical variation into chromatin. Here, we focus on one such element of variation: methylation of lysine 4 in histone H3 (H3K4). We assess a growing body of literature, including treatment of how the mark is established, the patterns of methylation, and the functional consequences of this epigenetic signature. We discuss structural aspects of the H3K4 methyl recognition by the downstream effectors and propose a distinction between sequence-specific recruitment mechanisms and stabilization on chromatin through methyl-lysine recognition. Finally, we hypothesize how the unique properties of the polyvalent chromatin fiber and associated effectors may amplify small differences in methyl-lysine recognition, simultaneously allowing for a dynamic chromatin architecture.
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                Author and article information

                Journal
                AJN
                Am J Nephrol
                10.1159/issn.0250-8095
                American Journal of Nephrology
                S. Karger AG
                0250-8095
                1421-9670
                2009
                December 2009
                01 October 2009
                : 30
                : 6
                : 505-513
                Affiliations
                aSecond Clinical Medical College, Jinan University, Guangzhou, and bFirst Affiliated Hospital, Shantou University Medical College, Shantou, China
                Article
                243811 Am J Nephrol 2009;30:505–513
                10.1159/000243811
                19797895
                525ac37c-e108-4ca4-8bed-07b37ca80456
                © 2009 S. Karger AG, Basel

                Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher. Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug. Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.

                History
                : 17 June 2009
                : 20 August 2009
                Page count
                Figures: 1, Tables: 8, References: 50, Pages: 9
                Categories
                Original Report: Laboratory Investigation

                Cardiovascular Medicine,Nephrology
                Microarray,Chromatin immunoprecipitation,Histone H3 lysine 4,Minimal change nephrotic syndrome,Trimethylation

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