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Lv P, Yang X, Zhao X, Zhao Z, Du J. Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer ( Ostrinia furnacalis). Genome Res 2024; 34:725-739. [PMID: 38866549 PMCID: PMC11216315 DOI: 10.1101/gr.278661.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024]
Abstract
Diapause represents a crucial adaptive strategy used by insects to cope with changing environmental conditions. In North China, the Asian corn borer (Ostrinia furnacalis) enters a winter larval diapause stage. Although there is growing evidence implicating epigenetic mechanisms in diapause regulation, it remains unclear whether dynamic genome-wide profiles of epigenetic modifications exist during this process. By investigating multiple histone modifications, we have discovered the essential roles of H3K9me3 and H3K27me3 during diapause of the Asian corn borer. Building upon previous findings in vertebrates highlighting the connection between DNA methylation and repressive histone methylations, we have examined changes in the genome-wide profile of H3K9me3, H3K27me3, and DNA methylation at the nondiapause, prediapause, and diapause stages. Data analysis reveals significant alterations in these three modifications during diapause. Moreover, we observe a correlation between the H3K9me3 and H3K27me3 modification sites during diapause, whereas DNA modifications show little association with either H3K9me3 or H3K27me3. Integrative analysis of epigenome and expression data unveils the relationship between these epigenetic modifications and gene expression levels at corresponding diapause stages. Furthermore, by studying the function of histone modifications on genes known to be important in diapause, especially those involved in the juvenile pathway, we discover that the juvenile hormone pathway lies downstream from H3K9me3 and H3K27me3 histone modifications. Finally, the analysis of gene loci with modified modifications unreported in diapause uncovers novel pathways potentially crucial in diapause regulation. This study provides a valuable resource for future investigations aiming to elucidate the underlying mechanisms of diapause.
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Affiliation(s)
- Pengfei Lv
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xingzhuo Yang
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xianguo Zhao
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhangwu Zhao
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Juan Du
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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Zhimulev I, Vatolina T, Levitsky V, Tsukanov A. Developmental and Housekeeping Genes: Two Types of Genetic Organization in the Drosophila Genome. Int J Mol Sci 2024; 25:4068. [PMID: 38612878 PMCID: PMC11012173 DOI: 10.3390/ijms25074068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
We developed a procedure for locating genes on Drosophila melanogaster polytene chromosomes and described three types of chromosome structures (gray bands, black bands, and interbands), which differed markedly in morphological and genetic properties. This was reached through the use of our original methods of molecular and genetic analysis, electron microscopy, and bioinformatics data processing. Analysis of the genome-wide distribution of these properties led us to a bioinformatics model of the Drosophila genome organization, in which the genome was divided into two groups of genes. One was constituted by 65, in which the genome was divided into two groups, 62 genes that are expressed in most cell types during life cycle and perform basic cellular functions (the so-called "housekeeping genes"). The other one was made up of 3162 genes that are expressed only at particular stages of development ("developmental genes"). These two groups of genes are so different that we may state that the genome has two types of genetic organization. Different are the timings of their expression, chromatin packaging levels, the composition of activating and deactivating proteins, the sizes of these genes, the lengths of their introns, the organization of the promoter regions of the genes, the locations of origin recognition complexes (ORCs), and DNA replication timings.
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Affiliation(s)
- Igor Zhimulev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia;
| | - Tatyana Vatolina
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia;
| | - Victor Levitsky
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia; (V.L.); (A.T.)
| | - Anton Tsukanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia; (V.L.); (A.T.)
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Guo M, Li X, Li T, Liu R, Pang W, Luo J, Zeng W, Zheng Y. YTHDF2 promotes DNA damage repair by positively regulating the histone methyltransferase SETDB1 in spermatogonia†. Biol Reprod 2024; 110:48-62. [PMID: 37812443 DOI: 10.1093/biolre/ioad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/04/2023] [Accepted: 10/06/2023] [Indexed: 10/10/2023] Open
Abstract
Genomic integrity is critical for sexual reproduction, ensuring correct transmission of parental genetic information to the descendant. To preserve genomic integrity, germ cells have evolved multiple DNA repair mechanisms, together termed as DNA damage response. The RNA N6-methyladenosine is the most abundant mRNA modification in eukaryotic cells, which plays important roles in DNA damage response, and YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) is a well-acknowledged N6-methyladenosine reader protein regulating the mRNA decay and stress response. Despite this, the correlation between YTHDF2 and DNA damage response in germ cells, if any, remains enigmatic. Here, by employing a Ythdf2-conditional knockout mouse model as well as a Ythdf2-null GC-1 mouse spermatogonial cell line, we explored the role and the underlying mechanism for YTHDF2 in spermatogonial DNA damage response. We identified that, despite no evident testicular morphological abnormalities under the normal circumstance, conditional mutation of Ythdf2 in adult male mice sensitized germ cells, including spermatogonia, to etoposide-induced DNA damage. Consistently, Ythdf2-KO GC-1 cells displayed increased sensitivity and apoptosis in response to DNA damage, accompanied by the decreased SET domain bifurcated 1 (SETDB1, a histone methyltransferase) and H3K9me3 levels. The Setdb1 knockdown in GC-1 cells generated a similar phenotype, but its overexpression in Ythdf2-null GC-1 cells alleviated the sensitivity and apoptosis in response to DNA damage. Taken together, these results demonstrate that the N6-methyladenosine reader YTHDF2 promotes DNA damage repair by positively regulating the histone methyltransferase SETDB1 in spermatogonia, which provides novel insights into the mechanisms underlying spermatogonial genome integrity maintenance and therefore contributes to safe reproduction.
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Affiliation(s)
- Ming Guo
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xueliang Li
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianjiao Li
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruifang Liu
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weijun Pang
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jun Luo
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenxian Zeng
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Zheng
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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Luo S, Zhang H, Xie Y, Huang J, Luo D, Zhang Q. Decreased SUV39H1 at the promoter region leads to increased CREMα and accelerates autoimmune response in CD4 + T cells from patients with systemic lupus erythematosus. Clin Epigenetics 2022; 14:181. [PMID: 36536372 PMCID: PMC9764740 DOI: 10.1186/s13148-022-01411-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Overproduction of cAMP-responsive element modulator α (CREMα) in total T cells from patients with systemic lupus erythematosus (SLE) can inhibit IL-2 and increase IL-17A. These ultimately promote progression of SLE. This study aims to investigate the expression of CREMα in SLE CD4+ T cells and find out the mechanisms for the regulation of CREMα in SLE CD4+ T cells. RESULTS CREMα mRNA was overexpressed in CD4+ T cells from SLE patients. The levels of histone H3 lysine 9 trimethylation (H3K9me3) and suppressor of variation 3-9 homolog 1 (SUV39H1) at the CREMα promoter of SLE CD4+ T cells were markedly decreased. Down-regulating SUV39H1 in normal CD4+ T cells elevated the levels of CREMα, IL-17A, and histone H3 lysine 4 trimethylation (H3K4me3) in the CREMα promoter region, and lowered IL-2, H3K9me3, DNA methylation, and DNA methyltransferase 3a (DNMT3a) enrichments within the CREMα promoter, while no sharp change in SET domain containing 1 (Set1) at the CREMα promoter. Up-regulating SUV39H1 in SLE CD4+ T cells had the opposite effects. The DNA methylation and DNMT3a levels were obviously reduced, and H3K4me3 enrichment was greatly increased at the CREMα promoter of CD4+ T cells from SLE patients. The Set1 binding in the CREMα promoter region upgraded significantly, and knocking down Set1 in SLE CD4+ T cells alleviated the H3K4me3 enrichment within this region, suppressed CREMα and IL-17A productions, and promoted the levels of IL-2, CREMα promoter DNA methylation, and DNMT3a. But there were no obviously alterations in H3K9me3 and SUV39H1 amounts in the region after transfection. CONCLUSIONS Decreased SUV39H1 in the CREMα promoter region of CD4+ T cells from SLE patients contributes to under-expression of H3K9me3 at this region. In the meantime, the Set1 binding at the CREMα promoter of SLE CD4+ T cells is up-regulated. As a result, DNMT3a and DNA methylation levels alleviate, and H3K4me3 binding increases. All these lead to overproduction of CREMα. Thus, the secretion of IL-2 down-regulates and the concentration of IL-17A up-regulates, ultimately promoting SLE.
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Affiliation(s)
- Shuangyan Luo
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
| | - Huilin Zhang
- grid.216417.70000 0001 0379 7164Clinical Nursing Teaching and Research Section, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
| | - Yuming Xie
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
| | - Junke Huang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
| | - Danhong Luo
- Department of Dermatology, The Fifth People’s Hospital of Hainan Province, #49 Longkun South Rd, Haikou, 570206 Hainan People’s Republic of China
| | - Qing Zhang
- grid.216417.70000 0001 0379 7164Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, 410011 Hunan People’s Republic of China
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Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements. Cells 2022; 11:cells11050761. [PMID: 35269383 PMCID: PMC8909793 DOI: 10.3390/cells11050761] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/10/2022] [Accepted: 02/18/2022] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are abundant components of constitutive heterochromatin of the most diverse evolutionarily distant organisms. TEs enrichment in constitutive heterochromatin was originally described in the model organism Drosophila melanogaster, but it is now considered as a general feature of this peculiar portion of the genomes. The phenomenon of TE enrichment in constitutive heterochromatin has been proposed to be the consequence of a progressive accumulation of transposable elements caused by both reduced recombination and lack of functional genes in constitutive heterochromatin. However, this view does not take into account classical genetics studies and most recent evidence derived by genomic analyses of heterochromatin in Drosophila and other species. In particular, the lack of functional genes does not seem to be any more a general feature of heterochromatin. Sequencing and annotation of Drosophila melanogaster constitutive heterochromatin have shown that this peculiar genomic compartment contains hundreds of transcriptionally active genes, generally larger in size than that of euchromatic ones. Together, these genes occupy a significant fraction of the genomic territory of heterochromatin. Moreover, transposable elements have been suggested to drive the formation of heterochromatin by recruiting HP1 and repressive chromatin marks. In addition, there are several pieces of evidence that transposable elements accumulation in the heterochromatin might be important for centromere and telomere structure. Thus, there may be more complexity to the relationship between transposable elements and constitutive heterochromatin, in that different forces could drive the dynamic of this phenomenon. Among those forces, preferential transposition may be an important factor. In this article, we present an overview of experimental findings showing cases of transposon enrichment into the heterochromatin and their positive evolutionary interactions with an impact to host genomes.
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Ma X, Wang B, Li Z, Ding X, Wen Y, Shan W, Hu W, Wang X, Xia Y. Effects of glufosinate-ammonium on male reproductive health: Focus on epigenome and transcriptome in mouse sperm. CHEMOSPHERE 2022; 287:132395. [PMID: 34597628 DOI: 10.1016/j.chemosphere.2021.132395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/18/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
Glufosinate-ammonium (GLA) is a widely used herbicide with emerging concern over its neural and reproductive toxicity. To uncover potential effects of GLA on male reproductive health in mammals, adult male C57BL/6J mice were administered 0.2 mg/kg·d GLA for 5 weeks. After examination on fertility, testis histology and semen quality in the GLA group, we performed deep sequencing to identify repressive epigenetic marks including DNA methylation and histone modifications (H3K27me3 and H3K9me3), together with mRNA transcript levels in sperm. Then, we integrated multi-omics sequencing data to comprehensively explore GLA-induced epigenetic and transcriptomic alterations. We found no significant difference either on fertility, testis histology or semen quality-related indicators. As for epigenome, the protein level of H3K27me3 was significantly increased in GLA sperm. Next generation sequencing showed alterations of these epigenetic marks and extensive transcription inhibition in sperm. These differential repressive marks were mainly distributed at intergenic regions and introns. According to results by Gene Ontology enrichment analysis, both differentially methylated and expressed genes were mainly enriched in pathways related to synapse organization. Subtle differences in genomic imprinting were also observed between the two groups. These results suggested that GLA predominantly impaired sperm epigenome and transcriptome in mice, with little effect on fertility, testis histology or semen quality. Further studies on human sperm using similar strategies need to be conducted for a better understanding of the male reproductive toxicity of GLA.
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Affiliation(s)
- Xuan Ma
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Bingqian Wang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhe Li
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xingwang Ding
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Ya Wen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Wenqi Shan
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Weiyue Hu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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Bodelón A, Fablet M, Veber P, Vieira C, García Guerreiro MP. OUP accepted manuscript. Genome Biol Evol 2022; 14:6526395. [PMID: 35143649 PMCID: PMC8872975 DOI: 10.1093/gbe/evac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
Interspecific hybridization is often seen as a genomic stress that may lead to new gene expression patterns and deregulation of transposable elements (TEs). The understanding of expression changes in hybrids compared with parental species is essential to disentangle their putative role in speciation processes. However, to date we ignore the detailed mechanisms involved in genomic deregulation in hybrids. We studied the ovarian transcriptome and epigenome of the Drosophila buzzatii and Drosophila koepferae species together with their F1 hybrid females. We found a trend toward underexpression of genes and TE families in hybrids. The epigenome in hybrids was highly similar to the parental epigenomes and showed intermediate histone enrichments between parental species in most cases. Differential gene expression in hybrids was often associated only with changes in H3K4me3 enrichments, whereas differential TE family expression in hybrids may be associated with changes in H3K4me3, H3K9me3, or H3K27me3 enrichments. We identified specific genes and TE families, which their differential expression in comparison with the parental species was explained by their differential chromatin mark combination enrichment. Finally, cis–trans compensatory regulation could also contribute in some way to the hybrid deregulation. This work provides the first study of histone content in Drosophila interspecific hybrids and their effect on gene and TE expression deregulation.
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Affiliation(s)
- Alejandra Bodelón
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Spain
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
- Institut universitaire de France, France
| | - Philippe Veber
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Maria Pilar García Guerreiro
- Grup de Genòmica, Bioinformática i Biologia Evolutiva, Departament de Genètica i Microbiologia (Edifici C), Universitat Autònoma de Barcelona, Spain
- Corresponding author: E-mail:
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Amabis JM, Gorab E. Dramatic nucleolar dispersion in the salivary gland of Schwenkfeldina sp. (Diptera: Sciaridae). Sci Rep 2021; 11:8347. [PMID: 33863925 PMCID: PMC8052372 DOI: 10.1038/s41598-021-87012-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
Micronucleoli are among the structures composing the peculiar scenario of the nucleolus in salivary gland nuclei of dipterans representative of Sciaridae. Micronucleolar bodies contain ribosomal DNA and RNA, are transcriptionally active and may appear free in the nucleoplasm or associated with specific chromosome regions in salivary gland nuclei. This report deals with an extreme case of nucleolar fragmentation/dispersion detected in the salivary gland of Schwenkfeldina sp. Such a phenomenon in this species was found to be restricted to cell types undergoing polyteny and seems to be differentially controlled according to the cell type. Furthermore, transcriptional activity was detected in virtually all the micronucleolar bodies generated in the salivary gland. The relative proportion of the rDNA in polytene and diploid tissues showed that rDNA under-replication did not occur in polytene nuclei suggesting that the nucleolar and concomitant rDNA dispersion in Schwenkfeldina sp. may reflect a previously hypothesised process in order to counterbalance the rDNA loss due to the under-replication. The chromosomal distribution of epigenetic markers for the heterochromatin agreed with early cytological observations in this species suggesting that heterochromatin is spread throughout the chromosome length of Schwenkfeldina sp. A comparison made with results from another sciarid species argues for a role played by the heterochromatin in the establishment of the rDNA topology in polytene nuclei of Sciaridae.
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Affiliation(s)
- José Mariano Amabis
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Eduardo Gorab
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil.
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Hoyer-Fender S. Transgenerational effect of drug-mediated inhibition of LSD1 on eye pigment expression in Drosophila. BMC Ecol 2020; 20:62. [PMID: 33228645 PMCID: PMC7684728 DOI: 10.1186/s12898-020-00330-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 11/11/2020] [Indexed: 11/25/2022] Open
Abstract
Background The Drosophila melanogaster mutant white-mottled is a well-established model for position-effect variegation (PEV). Transposition of the euchromatic white gene into the vicinity of the pericentric heterochromatin caused variegated expression of white due to heterochromatin spreading. The establishment of the euchromatin-heterochromatin boundary and spreading of silencing is regulated by mutually exclusive histone modifications, i.e. the methylations of histone H3 at lysine 9 and lysine 4. Demethylation of H3K4, catalysed by lysine-specific demethylase LSD1, is required for subsequent methylation of H3K9 to establish heterochromatin. LSD1 is therefore essential for heterochromatin formation and spreading. We asked whether drug-mediated inhibition of LSD affects the expression of white and if this induced change can be transmitted to those generations that have never been exposed to the triggering signal, i.e. transgenerational epigenetic inheritance. Results We used the lysine-specific demethylase 1 (LSD1)-inhibitor Tranylcypromine to investigate its effect on eye colour expression in consecutive generations by feeding the parental and F1 generations of the Drosophila melanogaster mutant white-mottled. Quantitative Western blotting revealed that Tranylcypromine inhibits H3K4-demethylation both in vitro in S2 cells as well as in embryos when used as feeding additive. Eye colour expression in male flies was determined by optical measurement of pigment extracts and qRT-PCR of white gene expression. Flies raised in the presence of Tranylcypromine and its solvent DMSO showed increased eye pigment expression. Beyond that, eye pigment expression was also affected in consecutive generations including F3, which is the first generation without contact with the inhibitor. Conclusions Our results show that feeding of Tranylcypromine and DMSO caused desilencing of white in treated flies of generation F1. Consecutive generations, raised on standard food without further supplements, are also affected by the drug-induced alteration of histone modifications. Although eye pigment expression eventually returned to the basal state, the observed long-lasting effect points to a memory capacity of previous epigenomes. Furthermore, our results indicate that food compounds potentially affect chromatin modification and hence gene expression and that the alteration is putatively inherited not only parentally but transgenerationally.
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Affiliation(s)
- Sigrid Hoyer-Fender
- Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology-Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, Göttingen, Germany.
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10
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Das P, Bhadra MP. Histone deacetylase (Rpd3) regulates Drosophila early brain development via regulation of Tailless. Open Biol 2020; 10:200029. [PMID: 32873153 PMCID: PMC7536075 DOI: 10.1098/rsob.200029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/29/2020] [Indexed: 11/29/2022] Open
Abstract
Tailless is a committed transcriptional repressor and principal regulator of the brain and eye development in Drosophila. Rpd3, the histone deacetylase, is an established repressor that interacts with co-repressors like Sin3a, Prospero, Brakeless and Atrophin. This study aims at deciphering the role of Rpd3 in embryonic segmentation and larval brain development in Drosophila. It delineates the mechanism of Tailless regulation by Rpd3, along with its interacting partners. There was a significant reduction in Tailless in Rpd3 heteroallelic mutant embryos, substantiating that Rpd3 is indispensable for the normal Tailless expression. The expression of the primary readout, Tailless was correlative to the expression of the neural cell adhesion molecule homologue, Fascilin2 (Fas2). Rpd3 also aids in the proper development of the mushroom body. Both Tailless and Fas2 expression are reported to be antagonistic to the epidermal growth factor receptor (EGFR) expression. The decrease in Tailless and Fas2 expression highlights that EGFR is upregulated in the larval mutants, hindering brain development. This study outlines the axis comprising Rpd3, dEGFR, Tailless and Fas2, which interact to fine-tune the early segmentation and larval brain development. Therefore, Rpd3 along with Tailless has immense significance in early embryogenesis and development of the larval brain.
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Affiliation(s)
- Paromita Das
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR) Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai 600 113, India
| | - Manika Pal Bhadra
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR) Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai 600 113, India
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11
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Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay. PLoS Genet 2019; 15:e1008502. [PMID: 31738748 PMCID: PMC6897423 DOI: 10.1371/journal.pgen.1008502] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/06/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022] Open
Abstract
Male Drosophila typically have achiasmatic meiosis, and fusions between autosomes and the Y chromosome have repeatedly created non-recombining neo-Y chromosomes that degenerate. Intriguingly, Drosophila nasuta males recombine, but their close relative D. albomicans reverted back to achiasmy after evolving neo-sex chromosomes. Here we use genome-wide polymorphism data to reconstruct the complex evolutionary history of neo-sex chromosomes in D. albomicans and examine the effect of recombination and its cessation on the initiation of neo-Y decay. Population and phylogenomic analyses reveal three distinct neo-Y types that are geographically restricted. Due to ancestral recombination with the neo-X, overall nucleotide diversity on the neo-Y is similar to the neo-X but severely reduced within neo-Y types. Consistently, the neo-Y chromosomes fail to form a monophyletic clade in sliding window trees outside of the region proximal to the fusion. Based on tree topology changes, we inferred the recombination breakpoints that produced haplotypes specific to each neo-Y type. We show that recombination became suppressed at different time points for the different neo-Y haplotypes. Haplotype age correlates with onset of neo-Y decay, and older neo-Y haplotypes show more fixed gene disruption via frameshift indels and down-regulation of neo-Y alleles. Genes are downregulated independently on the different neo-Ys, but are depleted of testes-expressed genes across all haplotypes. This indicates that genes important for male function are initially shielded from degeneration. Our results offer a time course of the early progression of Y chromosome evolution, showing how the suppression of recombination, through the reversal to achiasmy in D. albomicans males, initiates the process of degeneration.
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12
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Benner L, Castro EA, Whitworth C, Venken KJT, Yang H, Fang J, Oliver B, Cook KR, Lerit DA. Drosophila Heterochromatin Stabilization Requires the Zinc-Finger Protein Small Ovary. Genetics 2019; 213:877-895. [PMID: 31558581 PMCID: PMC6827387 DOI: 10.1534/genetics.119.302590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/21/2019] [Indexed: 02/04/2023] Open
Abstract
Heterochromatin-mediated repression is essential for controlling the expression of transposons and for coordinated cell type-specific gene regulation. The small ovary (sov) locus was identified in a screen for female-sterile mutations in Drosophila melanogaster, and mutants show dramatic ovarian morphogenesis defects. We show that the null sov phenotype is lethal and map the locus to the uncharacterized gene CG14438, which encodes a nuclear zinc-finger protein that colocalizes with the essential Heterochromatin Protein 1 (HP1a). We demonstrate Sov functions to repress inappropriate gene expression in the ovary, silence transposons, and suppress position-effect variegation in the eye, suggesting a central role in heterochromatin stabilization.
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Affiliation(s)
- Leif Benner
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218
| | - Elias A Castro
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Cale Whitworth
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology
- McNair Medical Institute at the Robert and Janice McNair Foundation
- Dan L. Duncan Cancer Center, Center for Drug Discovery
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Haiwang Yang
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Junnan Fang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Kevin R Cook
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Dorothy A Lerit
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia 30322
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13
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Saravanan K, Kumar H, Chhotaray S, Preethi AL, Talokar AJ, Natarajan A, Parida S, Bhushan B, Panigrahi M. Drosophila melanogaster: a promising model system for epigenetic research. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1685216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- K.A. Saravanan
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Supriya Chhotaray
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - A. Latha Preethi
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Amol J. Talokar
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - A. Natarajan
- Division of Animal Nutrition, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Subhashree Parida
- Division of Pharmacology and Toxicology, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics and Breeding, ICAR - Indian Veterinary Research Institute, Bareilly, India
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14
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Han X, Zhang P, Shen W, Zhao Y, Zhang H. Estrogen Receptor-Related DNA and Histone Methylation May Be Involved in the Transgenerational Disruption in Spermatogenesis by Selective Toxic Chemicals. Front Pharmacol 2019; 10:1012. [PMID: 31572187 PMCID: PMC6749155 DOI: 10.3389/fphar.2019.01012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022] Open
Abstract
Air pollution is a global threat to human health especially spermatogenesis. Animal and epidemiological studies suggest that epigenetic factors can transmit the pathologies transgenerationally. Paternal epigenetic effects can greatly impact offspring health. In this study and together with our previous report, we found that H2S donor Na2S and/or NH3 donor NH4Cl diminished mouse fertility, decreased spermatozoa concentration and motility, and impaired spermatogenesis in three consequent generations (F0, F1, and F2). In the current study, we found that DNA methylation, histone methylation, and estrogen receptor alpha (ERα) were impaired by NH4Cl and/or Na2S in F0, F1, and F2 mouse testes. Moreover, NH4Cl and/or Na2S might act as environmental endocrine-disrupting chemicals to decrease estrogen and testosterone in mouse blood. It has been reported that ERα signaling is intertwined together with DNA methylation and histone methylation, which plays very important roles in spermatogenesis. These data together indicate that the transgenerational disruption in spermatogenesis by NH4Cl and/or Na2S may be through ERα-related DNA methylation and histone methylation pathways. Therefore, we strongly recommend that greater attention should be paid to NH3 and/or H2S contamination to minimize their impact on human health especially spermatogenesis.
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Affiliation(s)
- Xiao Han
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.,College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Pengfei Zhang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yong Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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15
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Xavier MJ, Roman SD, Aitken RJ, Nixon B. Transgenerational inheritance: how impacts to the epigenetic and genetic information of parents affect offspring health. Hum Reprod Update 2019; 25:518-540. [DOI: 10.1093/humupd/dmz017] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/19/2019] [Accepted: 04/04/2019] [Indexed: 12/18/2022] Open
Abstract
Abstract
BACKGROUND
A defining feature of sexual reproduction is the transmission of genomic information from both parents to the offspring. There is now compelling evidence that the inheritance of such genetic information is accompanied by additional epigenetic marks, or stable heritable information that is not accounted for by variations in DNA sequence. The reversible nature of epigenetic marks coupled with multiple rounds of epigenetic reprogramming that erase the majority of existing patterns have made the investigation of this phenomenon challenging. However, continual advances in molecular methods are allowing closer examination of the dynamic alterations to histone composition and DNA methylation patterns that accompany development and, in particular, how these modifications can occur in an individual’s germline and be transmitted to the following generation. While the underlying mechanisms that permit this form of transgenerational inheritance remain unclear, it is increasingly apparent that a combination of genetic and epigenetic modifications plays major roles in determining the phenotypes of individuals and their offspring.
OBJECTIVE AND RATIONALE
Information pertaining to transgenerational inheritance was systematically reviewed focusing primarily on mammalian cells to the exclusion of inheritance in plants, due to inherent differences in the means by which information is transmitted between generations. The effects of environmental factors and biological processes on both epigenetic and genetic information were reviewed to determine their contribution to modulating inheritable phenotypes.
SEARCH METHODS
Articles indexed in PubMed were searched using keywords related to transgenerational inheritance, epigenetic modifications, paternal and maternal inheritable traits and environmental and biological factors influencing transgenerational modifications. We sought to clarify the role of epigenetic reprogramming events during the life cycle of mammals and provide a comprehensive review of how the genomic and epigenomic make-up of progenitors may determine the phenotype of its descendants.
OUTCOMES
We found strong evidence supporting the role of DNA methylation patterns, histone modifications and even non-protein-coding RNA in altering the epigenetic composition of individuals and producing stable epigenetic effects that were transmitted from parents to offspring, in both humans and rodent species. Multiple genomic domains and several histone modification sites were found to resist demethylation and endure genome-wide reprogramming events. Epigenetic modifications integrated into the genome of individuals were shown to modulate gene expression and activity at enhancer and promoter domains, while genetic mutations were shown to alter sequence availability for methylation and histone binding. Fundamentally, alterations to the nuclear composition of the germline in response to environmental factors, ageing, diet and toxicant exposure have the potential to become hereditably transmitted.
WIDER IMPLICATIONS
The environment influences the health and well-being of progeny by working through the germline to introduce spontaneous genetic mutations as well as a variety of epigenetic changes, including alterations in DNA methylation status and the post-translational modification of histones. In evolutionary terms, these changes create the phenotypic diversity that fuels the fires of natural selection. However, rather than being adaptive, such variation may also generate a plethora of pathological disease states ranging from dominant genetic disorders to neurological conditions, including spontaneous schizophrenia and autism.
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Affiliation(s)
- Miguel João Xavier
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Shaun D Roman
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Chemical Biology and Clinical Pharmacology, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - R John Aitken
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Brett Nixon
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
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16
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Bhattacharjee S, Roche B, Martienssen RA. RNA-induced initiation of transcriptional silencing (RITS) complex structure and function. RNA Biol 2019; 16:1133-1146. [PMID: 31213126 DOI: 10.1080/15476286.2019.1621624] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Heterochromatic regions of the genome are epigenetically regulated to maintain a heritable '"silent state"'. In fission yeast and other organisms, epigenetic silencing is guided by nascent transcripts, which are targeted by the RNA interference pathway. The key effector complex of the RNA interference pathway consists of small interfering RNA molecules (siRNAs) associated with Argonaute, assembled into the RNA-induced transcriptional silencing (RITS) complex. This review focuses on our current understanding of how RITS promotes heterochromatin formation, and in particular on the role of Argonaute-containing complexes in many other functions such as quelling, release of RNA polymerases, cellular quiescence and genome defense.
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Affiliation(s)
- Sonali Bhattacharjee
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Benjamin Roche
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Robert A Martienssen
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
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17
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Smurova K, De Wulf P. Centromere and Pericentromere Transcription: Roles and Regulation … in Sickness and in Health. Front Genet 2018; 9:674. [PMID: 30627137 PMCID: PMC6309819 DOI: 10.3389/fgene.2018.00674] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/04/2018] [Indexed: 12/26/2022] Open
Abstract
The chromosomal loci known as centromeres (CEN) mediate the equal distribution of the duplicated genome between both daughter cells. Specifically, centromeres recruit a protein complex named the kinetochore, that bi-orients the replicated chromosome pairs to the mitotic or meiotic spindle structure. The paired chromosomes are then separated, and the individual chromosomes segregate in opposite direction along the regressing spindle into each daughter cell. Erroneous kinetochore assembly or activity produces aneuploid cells that contain an abnormal number of chromosomes. Aneuploidy may incite cell death, developmental defects (including genetic syndromes), and cancer (>90% of all cancer cells are aneuploid). While kinetochores and their activities have been preserved through evolution, the CEN DNA sequences have not. Hence, to be recognized as sites for kinetochore assembly, CEN display conserved structural themes. In addition, CEN nucleosomes enclose a CEN-exclusive variant of histone H3, named CENP-A, and carry distinct epigenetic labels on CENP-A and the other CEN histone proteins. Through the cell cycle, CEN are transcribed into non-coding RNAs. After subsequent processing, they become key components of the CEN chromatin by marking the CEN locus and by stably anchoring the CEN-binding kinetochore proteins. CEN transcription is tightly regulated, of low intensity, and essential for differentiation and development. Under- or overexpression of CEN transcripts, as documented for myriad cancers, provoke chromosome missegregation and aneuploidy. CEN are genetically stable and fully competent only when they are insulated from the surrounding, pericentromeric chromatin, which must be silenced. We will review CEN transcription and its contribution to faithful kinetochore function. We will further discuss how pericentromeric chromatin is silenced by RNA processing and transcriptionally repressive chromatin marks. We will report on the transcriptional misregulation of (peri)centromeres during stress, natural aging, and disease and reflect on whether their transcripts can serve as future diagnostic tools and anti-cancer targets in the clinic.
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Affiliation(s)
- Ksenia Smurova
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Peter De Wulf
- Centre for Integrative Biology, University of Trento, Trento, Italy
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18
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Abstract
Gametogenesis represents the most dramatic cellular differentiation pathways in both female and male flies. At the genome level, meiosis ensures that diploid germ cells become haploid gametes. At the epigenome level, extensive changes are required to turn on and shut off gene expression in a precise spatiotemporally controlled manner. Research applying conventional molecular genetics and cell biology, in combination with rapidly advancing genomic tools have helped us to investigate (1) how germ cells maintain lineage specificity throughout their adult reproductive lifetime; (2) what molecular mechanisms ensure proper oogenesis and spermatogenesis, as well as protect genome integrity of the germline; (3) how signaling pathways contribute to germline-soma communication; and (4) if such communication is important. In this chapter, we highlight recent discoveries that have improved our understanding of these questions. On the other hand, restarting a new life cycle upon fertilization is a unique challenge faced by gametes, raising questions that involve intergenerational and transgenerational epigenetic inheritance. Therefore, we also discuss new developments that link changes during gametogenesis to early embryonic development-a rapidly growing field that promises to bring more understanding to some fundamental questions regarding metazoan development.
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19
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Dubey A, Jeon J. Epigenetic regulation of development and pathogenesis in fungal plant pathogens. MOLECULAR PLANT PATHOLOGY 2017; 18:887-898. [PMID: 27749982 PMCID: PMC6638268 DOI: 10.1111/mpp.12499] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 10/10/2016] [Accepted: 10/12/2016] [Indexed: 05/08/2023]
Abstract
Evidently, epigenetics is at forefront in explaining the mechanisms underlying the success of human pathogens and in the identification of pathogen-induced modifications within host plants. However, there is a lack of studies highlighting the role of epigenetics in the modulation of the growth and pathogenicity of fungal plant pathogens. In this review, we attempt to highlight and discuss the role of epigenetics in the regulation of the growth and pathogenicity of fungal phytopathogens using Magnaporthe oryzae, a devastating fungal plant pathogen, as a model system. With the perspective of wide application in the understanding of the development, pathogenesis and control of other fungal pathogens, we attempt to provide a synthesized view of the epigenetic studies conducted on M. oryzae to date. First, we discuss the mechanisms of epigenetic modifications in M. oryzae and their impact on fungal development and pathogenicity. Second, we highlight the unexplored epigenetic mechanisms and areas of research that should be considered in the near future to construct a holistic view of epigenetic functioning in M. oryzae and other fungal plant pathogens. Importantly, the development of a complete understanding of the modulation of epigenetic regulation in fungal pathogens can help in the identification of target points to combat fungal pathogenesis.
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Affiliation(s)
- Akanksha Dubey
- Department of BiotechnologyCollege of Life and Applied Sciences, Yeungnam UniversityGyeongsanGyeongbuk38541South Korea
| | - Junhyun Jeon
- Department of BiotechnologyCollege of Life and Applied Sciences, Yeungnam UniversityGyeongsanGyeongbuk38541South Korea
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20
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Aldrich JC, Ferree PM. Genome Silencing and Elimination: Insights from a "Selfish" B Chromosome. Front Genet 2017; 8:50. [PMID: 28487723 PMCID: PMC5403880 DOI: 10.3389/fgene.2017.00050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/10/2017] [Indexed: 02/04/2023] Open
Abstract
B chromosomes are non-essential components of numerous plant and animal genomes. Because many of these "extra" chromosomes enhance their own transmission in ways that are detrimental to the rest of the genome, they can be thought of as genome parasites. An extreme example is a paternally inherited B chromosome known as paternal sex ratio (PSR), which is found in natural populations of the jewel wasp Nasonia vitripennis. In order to ensure its own propagation, PSR severely biases the wasp sex ratio by converting diploid female-destined embryos into transmitting haploid males. This action occurs at the expense of the other paternally inherited chromosomes, which fail to resolve during the first round of division and are thus eliminated. Recent work has revealed that paternal genome elimination by PSR occurs through the disruption of a number of specific histone post-translational modifications, suggesting a central role for chromatin regulation in this phenomenon. In this review, we describe these recent advances in the light of older ones and in the context of what is currently understood about the molecular mechanisms of targeted genome silencing and elimination in other systems.
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Affiliation(s)
| | - Patrick M. Ferree
- W.M. Keck Science Department, Claremont McKenna College, Pitzer College and Scripps College, ClaremontCA, USA
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21
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Yu D, Shi W, Zhang YE. Underrepresentation of active histone modification marks in evolutionarily young genes. INSECT SCIENCE 2017; 24:174-186. [PMID: 26607206 DOI: 10.1111/1744-7917.12299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
It is known that evolutionarily new genes can rapidly evolve essential roles in fundamental biological processes. Nevertheless, the underlying molecular mechanism of how they acquire their novel transcriptional pattern is less characterized except for the role of cis-regulatory evolution. Epigenetic modification offers an alternative possibility. Here, we examined how histone modifications have changed among different gene age groups in Drosophila melanogaster by integrative analyses of an updated new gene dataset and published epigenomic data. We found a robust pattern across various datasets where both the coverage and intensity of active histone modifications, histone 3 lysine 4 trimethylation and lysine 36 trimethylation, increased with evolutionary age. Such a temporal correlation is negative and much weaker for the repressive histone mark, lysine 9 trimethylation, which is expected given its major association with heterochromatin. By further comparison with neighboring old genes, the depletion of active marks of new genes could be only partially explained by the local epigenetic context. All these data are consistent with the observation that older genes bear relatively higher expression levels and suggest that the evolution of histone modifications could be implicated in transcriptional evolution after gene birth.
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Affiliation(s)
- Daqi Yu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenwen Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong E Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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22
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Wu F, Ma C, Tan C. Network motifs modulate druggability of cellular targets. Sci Rep 2016; 6:36626. [PMID: 27824147 PMCID: PMC5100546 DOI: 10.1038/srep36626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/17/2016] [Indexed: 01/02/2023] Open
Abstract
Druggability refers to the capacity of a cellular target to be modulated by a small-molecule drug. To date, druggability is mainly studied by focusing on direct binding interactions between a drug and its target. However, druggability is impacted by cellular networks connected to a drug target. Here, we use computational approaches to reveal basic principles of network motifs that modulate druggability. Through quantitative analysis, we find that inhibiting self-positive feedback loop is a more robust and effective treatment strategy than inhibiting other regulations, and adding direct regulations to a drug-target generally reduces its druggability. The findings are explained through analytical solution of the motifs. Furthermore, we find that a consensus topology of highly druggable motifs consists of a negative feedback loop without any positive feedback loops, and consensus motifs with low druggability have multiple positive direct regulations and positive feedback loops. Based on the discovered principles, we predict potential genetic targets in Escherichia coli that have either high or low druggability based on their network context. Our work establishes the foundation toward identifying and predicting druggable targets based on their network topology.
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Affiliation(s)
- Fan Wu
- Department of Biomedical Engineering, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Cong Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
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23
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Badaracco A, Gorab E. Unusual chromatin state in Rhynchosciara americana (Diptera: Sciaridae). Chromosome Res 2016; 23:781-90. [PMID: 26490538 DOI: 10.1007/s10577-015-9497-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 11/26/2022]
Abstract
Euchromatin and heterochromatin are usually defined by the degree of DNA compaction, gene content and combinations of histone and non-histone proteins. More recent studies on protein location have been able to specify a variety of chromatin types thus adding chromatin configurations other than the two basic reference states. Chromatin research exploiting non-model organisms has the potential to provide novel information related to epigenetic modifications and their impact on chromosome structure and function. Polytene chromosomes of Rhynchosciara americana display a particular region within the A9 sub-section characterised by lack of DNA compaction as well as an usual polytene banding pattern. DNA content in the sub-section seems to be low as deduced by DAPI staining. Antibodies to H3K4me, a conserved epigenetic transcription marker,labelled the A9 sub-section strongly. In contrast,transcriptional activity in the region, if any, seems to be low as inferred by detection of RNA polymerase II and RNA. Histone markers related to heterochromatin formation such as H3K9me and H3K27me are underrepresented in the A9 sub-section. However, a chromodomain-containing sciarid protein was detected in the region, displaying levels of fluorescence very close to those observed in pericentric heterochromatin.A plasmid micro-library constructed with microdissected DNA from the A9 sub-section was screened for repetitive DNA. The proportion of inserts containing repeats was found to be similar to that contained in another micro-library made with DNA from a single chromosome end of this species. The data suggest an unusual "chromatin colour" indicating that high levels of histone markers related to transcription coexist with a significant presence of chromodomain-containing proteins and the virtual absence of histone modifications observed in heterochromatin formation.
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24
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Guo S, Jiang F, Yang P, Liu Q, Wang X, Kang L. Characteristics and expression patterns of histone-modifying enzyme systems in the migratory locust. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 76:18-28. [PMID: 27343382 DOI: 10.1016/j.ibmb.2016.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/15/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Abstract
The density-dependent phase polyphenism in locusts offers an excellent model to investigate the epigenetic regulatory mechanisms underlying phenotypic plasticity. In this study, we identified histone-modifying enzymes mediating histone post-translational modifications, which serve as a major regulatory mechanism of epigenetic processes, on the basis of the whole genome sequence of the migratory locust, Locusta migratoria. We confirmed the existence of various functional histone modifications in the locusts. Compared with other sequenced insect genomes, the locust genome contains a richer repertoire of histone-modifying enzymes. Several locust histone-modifying enzymes display vertebrate-like characteristics, such as the presence of a Sirt3-like gene and multiple alternative splicing of GCN5 gene. Most histone-modifying enzymes are highly expressed in the eggs or in the testis tissues of male adults. Several histone deacetylases and H3K4-specific methyltransferases exhibit differential expression patterns in brain tissues between solitarious and gregarious locusts. These results reveal the main characteristics of histone-modifying enzymes and provide important cues for understanding the epigenetic mechanisms underlying phase polyphenism in locusts.
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Affiliation(s)
- Siyuan Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Jiang
- Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Pengcheng Yang
- Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
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25
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Abstract
Trans-inactivation is the repression of genes on a normal chromosome under the influence of a rearranged homologous chromosome demonstrating the position effect variegation (PEV). This phenomenon was studied in detail on the example of brownDominant allele causing the repression of wild-type brown gene on the opposite chromosome. We have investigated another trans-inactivation-inducing chromosome rearrangement, In(2)A4 inversion. In both cases, brownDominant and In(2)A4, the repression seems to be the result of dragging of the euchromatic region of the normal chromosome into the heterochromatic environment. It was found that cis-inactivation (classical PEV) and trans-inactivation show different patterns of distribution along the chromosome and respond differently to PEV modifying genes. It appears that the causative mechanism of trans-inactivation is de novo heterochromatin assembly on euchromatic sequences dragged into the heterochromatic nuclear compartment. Trans-inactivation turns out to be the result of a combination of heterochromatin-induced position effect and the somatic interphase chromosome pairing that is widespread in Diptera.
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Affiliation(s)
- Aleksei S Shatskikh
- a Department of Molecular Genetics of the Cell , Institute of Molecular Genetics, Russian Academy of Science , Moscow , Russia
| | - Yuriy A Abramov
- a Department of Molecular Genetics of the Cell , Institute of Molecular Genetics, Russian Academy of Science , Moscow , Russia
| | - Sergey A Lavrov
- a Department of Molecular Genetics of the Cell , Institute of Molecular Genetics, Russian Academy of Science , Moscow , Russia
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26
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Parry AJ, Narita M. Old cells, new tricks: chromatin structure in senescence. Mamm Genome 2016; 27:320-31. [PMID: 27021489 PMCID: PMC4935760 DOI: 10.1007/s00335-016-9628-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/16/2016] [Indexed: 12/20/2022]
Abstract
Cellular senescence is a stable form of cell cycle arrest with roles in many pathophysiological processes including development, tissue repair, cancer, and aging. Senescence does not represent a single entity but rather a heterogeneous phenotype that depends on the trigger and cell type of origin. Such heterogeneous features include alterations to chromatin structure and epigenetic states. New technologies are beginning to unravel the distinct mechanisms regulating chromatin structure during senescence. Here, we describe the multiple levels of chromatin organization associated with senescence: global and focal, linear, and higher order.
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Affiliation(s)
- Aled John Parry
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE UK
| | - Masashi Narita
- Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE UK
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27
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Long Y, Nie J. Homocysteine in Renal Injury. KIDNEY DISEASES 2016; 2:80-7. [PMID: 27536696 DOI: 10.1159/000444900] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/23/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Homocysteine (Hcy) is an intermediate of methionine metabolism. Hyperhomocysteinemia (HHcy) can result from a deficiency in the enzymes or vitamin cofactors required for Hcy metabolism. Patients with renal disease tend to be hyperhomocysteinemic, particularly as renal function declines, although the underlying cause of HHcy in renal disease is not entirely understood. SUMMARY HHcy is considered a risk or pathogenic factor in the progression of chronic kidney disease (CKD) as well as the cardiovascular complications. KEY MESSAGES In this review, we summarize both clinical and experimental findings that reveal the contribution of Hcy as a pathogenic factor to the development of CKD. In addition, we discuss several important mechanisms mediating the pathogenic action of Hcy in the kidney, such as local oxidative stress, endoplasmic reticulum stress, inflammation and hypomethylation.
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Affiliation(s)
- Yanjun Long
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guiyang, PR China; Division of Nephrology, Guizhou Provincial People's Hospital, Guizhou Provincial Institute of Nephritic and Urinary Disease, Guiyang, PR China
| | - Jing Nie
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, Guiyang, PR China
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28
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Coulthard AB, Taylor-Kamall RW, Hallson G, Axentiev A, Sinclair DA, Honda BM, Hilliker AJ. Meiotic recombination is suppressed near the histone-defined border of euchromatin and heterochromatin on chromosome 2L of Drosophila melanogaster. Genome 2016; 59:289-94. [DOI: 10.1139/gen-2015-0171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Drosophila melanogaster, the borders between pericentric heterochromatin and euchromatin on the major chromosome arms have been defined in various ways, including chromatin-specific histone modifications, the binding patterns of heterochromatin-enriched chromosomal proteins, and various cytogenetic techniques. Elucidation of the genetic properties that independently define the different chromatin states associated with heterochromatin and euchromatin should help refine the boundary. Since meiotic recombination is present in euchromatin, but absent in heterochromatin, it constitutes a key genetic property that can be observed transitioning between chromatin states. Using P element insertion lines marked with a su(Hw) insulated mini-white gene, meiotic recombination was found to transition in a region consistent with the H3K9me2 transition observed in ovaries.
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Affiliation(s)
| | | | - Graham Hallson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Anna Axentiev
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - Don A. Sinclair
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Barry M. Honda
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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29
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Uchino R, Sugiyama S, Katagiri M, Chuman Y, Furukawa K. Non-farnesylated B-type lamin can tether chromatin inside the nucleus and its chromatin interaction requires the Ig-fold region. Chromosoma 2016; 126:125-144. [PMID: 26892013 DOI: 10.1007/s00412-016-0581-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/06/2016] [Accepted: 02/10/2016] [Indexed: 11/27/2022]
Abstract
Lamins are thought to direct heterochromatin to the nuclear lamina (NL); however, this function of lamin has not been clearly demonstrated in vivo. To address this, we analyzed polytene chromosome morphology when artificial lamin variants were expressed in Drosophila endoreplicating cells. We found that the CaaX-motif-deleted B-type lamin Dm0, but not A-type lamin C, was able to form a nuclear envelope-independent layer that was closely associated with chromatin. Other nuclear envelope proteins were not detected in this "ectopic lamina," and the associated chromatin showed a repressive histone modification maker but not a permissive histone modification marker nor RNA polymerase II proteins. Furthermore, deletion of the C-terminal lamin-Ig-fold domain prevents chromatin association with this ectopic lamina. Thus, non-farnesylated B-type lamin Dm0 can form an ectopic lamina and induce changes to chromatin structure and status inside the interphase nucleus.
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Affiliation(s)
- Ryo Uchino
- Department of Chemistry, Faculty of Science, Niigata University, Niigata, 950-2181, Japan
| | - Shin Sugiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Motoi Katagiri
- Department of Chemistry, Faculty of Science, Niigata University, Niigata, 950-2181, Japan
| | - Yoshiro Chuman
- Department of Chemistry, Faculty of Science, Niigata University, Niigata, 950-2181, Japan
| | - Kazuhiro Furukawa
- Department of Chemistry, Faculty of Science, Niigata University, Niigata, 950-2181, Japan.
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30
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Heidor R, de Conti A, Ortega JF, Furtado KS, Silva RC, Tavares PELM, Purgatto E, Ract JNR, de Paiva SAR, Gioielli LA, Pogribny IP, Moreno FS. The chemopreventive activity of butyrate-containing structured lipids in experimental rat hepatocarcinogenesis. Mol Nutr Food Res 2015; 60:420-9. [PMID: 26548572 DOI: 10.1002/mnfr.201500643] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/15/2015] [Accepted: 10/26/2015] [Indexed: 12/26/2022]
Abstract
SCOPE Emerging evidence indicates that the use of bioactive food components is a promising strategy to prevent the development of liver cancer. The goal of this study was to examine the chemopreventive effect of butyrate-containing structured lipids (STLs) produced by an enzymatic interesterification of tributyrin and flaxseed oil on rat hepatocarcinogenesis. METHODS AND RESULTS Male Wistar rats were subjected to a classic "resistant hepatocyte" model of liver carcinogenesis and treated with STLs, tributyrin or flaxseed oil during the initial phases of hepatocarcinogenesis. Treatment with STLs and tributyrin strongly inhibited the development of preneoplastic liver lesions. The chemopreventive activity of tributyrin was associated with the induction of apoptosis and reduction of the expression of major activated hepatocarcinogenesis-related oncogenes. Treatment with STLs caused substantially greater inhibitory effects than tributyrin on oncogene expression. CONCLUSION These results demonstrate that the tumor-suppressing activity of butyrate-containing STLs is associated with its ability to prevent and inhibit activation of major hepatocarcinogenesis-related oncogenes. Enrichment of histone H3K9me3 and H3K27me3 at the promoter of Myc and Ccnd1 genes may be related to the inhibitory effect on oncogene expression in the livers of STL-treated rats.
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Affiliation(s)
- Renato Heidor
- Laboratory of Diet, Nutrition and Cancer, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Advanced Research Center in Food Science and Nutrition (NAPAN), Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil.,Food Research Center (FORC), Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
| | - Aline de Conti
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | - Juliana F Ortega
- Laboratory of Diet, Nutrition and Cancer, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Kelly S Furtado
- Laboratory of Diet, Nutrition and Cancer, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Advanced Research Center in Food Science and Nutrition (NAPAN), Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
| | - Roberta C Silva
- Department of Biochemical and Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paulo E L M Tavares
- Laboratory of Diet, Nutrition and Cancer, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Eduardo Purgatto
- Laboratory of Food Chemistry and Biochemistry, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil.,Advanced Research Center in Food Science and Nutrition (NAPAN), Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil.,Food Research Center (FORC), Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
| | - Juliana N R Ract
- Department of Biochemical and Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sérgio A R de Paiva
- Department of Internal Medicine, Botucatu Medical School, UNESP - São Paulo State University, Botucatu, Brazil.,Food Research Center (FORC), Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
| | - Luiz A Gioielli
- Department of Biochemical and Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Igor P Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | - Fernando S Moreno
- Laboratory of Diet, Nutrition and Cancer, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Advanced Research Center in Food Science and Nutrition (NAPAN), Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil.,Food Research Center (FORC), Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
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31
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Abstract
Differentiated sex chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated sex chromosomes share the problems of the unequal expression of the genes borne on sex chromosomes, both between the sexes and with respect to autosomes. Dosage compensation of genes on sex chromosomes is surprisingly variable - and can even be absent - in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.
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32
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Regional centromeres in the yeast Candida lusitaniae lack pericentromeric heterochromatin. Proc Natl Acad Sci U S A 2015; 112:12139-44. [PMID: 26371315 DOI: 10.1073/pnas.1508749112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Point centromeres are specified by a short consensus sequence that seeds kinetochore formation, whereas regional centromeres lack a conserved sequence and instead are epigenetically inherited. Regional centromeres are generally flanked by heterochromatin that ensures high levels of cohesin and promotes faithful chromosome segregation. However, it is not known whether regional centromeres require pericentromeric heterochromatin. In the yeast Candida lusitaniae, we identified a distinct type of regional centromere that lacks pericentromeric heterochromatin. Centromere locations were determined by ChIP-sequencing of two key centromere proteins, Cse4 and Mif2, and are consistent with bioinformatic predictions. The centromeric DNA sequence was unique for each chromosome and spanned 4-4.5 kbp, consistent with regional epigenetically inherited centromeres. However, unlike other regional centromeres, there was no evidence of pericentromeric heterochromatin in C. lusitaniae. In particular, flanking genes were expressed at a similar level to the rest of the genome, and a URA3 reporter inserted adjacent to a centromere was not repressed. In addition, regions flanking the centromeric core were not associated with hypoacetylated histones or a sirtuin deacetylase that generates heterochromatin in other yeast. Interestingly, the centromeric chromatin had a distinct pattern of histone modifications, being enriched for methylated H3K79 and H3R2 but lacking methylation of H3K4, which is found at other regional centromeres. Thus, not all regional centromeres require flanking heterochromatin.
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33
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Qin T, Si J, Raynal NJM, Wang X, Gharibyan V, Ahmed S, Hu X, Jin C, Lu Y, Shu J, Estecio MR, Jelinek J, Issa JPJ. Epigenetic synergy between decitabine and platinum derivatives. Clin Epigenetics 2015; 7:97. [PMID: 26366234 PMCID: PMC4567801 DOI: 10.1186/s13148-015-0131-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/01/2015] [Indexed: 01/25/2023] Open
Abstract
Background Aberrant epigenetic silencing of tumor suppressor genes has been recognized as a driving force in cancer. Epigenetic drugs such as the DNA methylation inhibitor decitabine reactivate genes and are effective in myeloid leukemia, but resistance often develops and efficacy in solid tumors is limited. To improve their clinical efficacy, we searched among approved anti-cancer drugs for an epigenetic synergistic combination with decitabine. Results We used the YB5 cell line, a clonal derivative of the SW48 colon cancer cell line that contains a single copy of a hypermethylated cytomegalovirus (CMV) promoter driving green fluorescent protein (GFP) to screen for drug-induced gene reactivation and synergy with decitabine. None of the 16 anti-cancer drugs tested had effects on their own. However, in combination with decitabine, platinum compounds showed striking synergy in activating GFP. This was dose dependent, observed both in concurrent and sequential combinations, and also seen with other alkylating agents. Clinically achievable concentrations of carboplatin at (25 μM) and decitabine reactivated GFP in 28 % of the YB5 cells as compared to 15 % with decitabine alone. Epigenetic synergy was also seen at endogenously hypermethylated tumor suppressor genes such as MLH1 and PDLIM4. Genome-wide studies showed that reactivation of hypermethylated genes by the combination was significantly better than that induced by decitabine alone or carboplatin alone. Platinum compounds did not enhance decitabine-induced hypomethylation. Rather, we found significantly inhibited HP1α expression by carboplatin and the combination. This was accompanied by increased histone H3 lysine 4 (H3K4) trimethylation and histone H3 lysine 9 (H3K9) acetylation at reactivated genes (P < 0.0001) and reduced occupancy by methyl-binding proteins including MeCP2 and methyl-CpG-binding domain protein 2 (MBD2) (P < 0.0001). Conclusions Our results suggest that the combination of decitabine with platinum analogs shows epigenetic synergy that might be exploited in the treatment of different cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0131-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taichun Qin
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jiali Si
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Noël J-M Raynal
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Fels Institute for Cancer Research and Molecular Biology, Temple University, 3307 North Broad Street, Rm 154, PAHB, Philadelphia, PA 19140 USA
| | - Xiaodan Wang
- Harbin Institute of Hematology & Oncology, Harbin, 150010 China
| | - Vazganush Gharibyan
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Saira Ahmed
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Xin Hu
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Chunlei Jin
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Yue Lu
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jingmin Shu
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Marcos Rh Estecio
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jaroslav Jelinek
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Fels Institute for Cancer Research and Molecular Biology, Temple University, 3307 North Broad Street, Rm 154, PAHB, Philadelphia, PA 19140 USA
| | - Jean-Pierre J Issa
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA.,Fels Institute for Cancer Research and Molecular Biology, Temple University, 3307 North Broad Street, Rm 154, PAHB, Philadelphia, PA 19140 USA
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34
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Homocysteine Induces Collagen I Expression by Downregulating Histone Methyltransferase G9a. PLoS One 2015; 10:e0130421. [PMID: 26192994 PMCID: PMC4508059 DOI: 10.1371/journal.pone.0130421] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
Hyperhomocysteinemia (HHcy) leads to several clinical manifestations including hepatic fibrosis. Excess deposition of extracellular matrix (ECM) components including collagen is the eponymous lesion of liver fibrosis. In this study, we demonstrated that elevated concentration of Hcy induced the expression of collagen type I in cultured human liver cells as well as in liver tissue of HHcy mice. Meanwhile, Hcy inhibited the expression of histone methyltransferase G9a. Mechanistically, silencing endogenous G9a by siRNA enhanced the promoter activity of COL1A1 in LO2 cells. Conversely, overexpressing G9a inhibited the promoter activity of COL1A1. CHIP assay demonstrated that G9a binds to the neuron-restrictive silencer element (NRSE) on the promoter of COL1A1. Hcy treatment decreased the binding of G9a on NRSE, which in turn decreased the level of H3K9me2 on the promoter of COL1A1, led to upregulation of COL1A1. Taken together, these results provide a novel mechanism on explaining how HHcy promotes ECM production.
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35
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Dolgushin KV, Iudinkova ES, Petrova NV, Razin SV, Iarovaia OV. Joint locus of a/b-globin genes in Danio rerio is segregated into structural subdomains active at different stages of development. Mol Biol 2015. [DOI: 10.1134/s0026893315030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Yu Z, Liu J, Deng WM, Jiao R. Histone chaperone CAF-1: essential roles in multi-cellular organism development. Cell Mol Life Sci 2015; 72:327-37. [PMID: 25292338 PMCID: PMC11114026 DOI: 10.1007/s00018-014-1748-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 09/16/2014] [Accepted: 09/29/2014] [Indexed: 01/01/2023]
Abstract
More and more studies have shown chromatin remodelers and histone modifiers play essential roles in regulating developmental patterns by organizing specific chromosomal architecture to establish programmed transcriptional profiles, with implications that histone chaperones execute a coordinating role in these processes. Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved three-subunit protein complex, was identified as a histone chaperone coupled with DNA replication and repair in cultured mammalian cells and yeasts. Interestingly, recent findings indicate CAF-1 may have important regulatory roles during development by interacting with specific transcription factors and epigenetic regulators. In this review, we focus on the essential roles of CAF-1 in regulating heterochromatin organization, asymmetric cell division, and specific signal transduction through epigenetic modulations of the chromatin. In the end, we aim at providing a current image of facets of CAF-1 as a histone chaperone to orchestrate cell proliferation and differentiation during multi-cellular organism development.
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Affiliation(s)
- Zhongsheng Yu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100080 China
| | - Jiyong Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- Guangzhou Hoffmann Institute of Immunology, School of Basic Sciences, Guangzhou Medical University, Dongfengxi Road 195, Guangzhou, 510182 China
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295 USA
| | - Renjie Jiao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100080 China
- Guangzhou Hoffmann Institute of Immunology, School of Basic Sciences, Guangzhou Medical University, Dongfengxi Road 195, Guangzhou, 510182 China
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37
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An updated insight into the Sialotranscriptome of Triatoma infestans: developmental stage and geographic variations. PLoS Negl Trop Dis 2014; 8:e3372. [PMID: 25474469 PMCID: PMC4256203 DOI: 10.1371/journal.pntd.0003372] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/25/2014] [Indexed: 01/06/2023] Open
Abstract
Background Triatoma infestans is the main vector of Chagas disease in South America. As in all hematophagous arthropods, its saliva contains a complex cocktail that assists blood feeding by preventing platelet aggregation and blood clotting and promoting vasodilation. These salivary components can be immunologically recognized by their vector's hosts and targeted with antibodies that might disrupt blood feeding. These antibodies can be used to detect vector exposure using immunoassays. Antibodies may also contribute to the fast evolution of the salivary cocktail. Methodology Salivary gland cDNA libraries from nymphal and adult T. infestans of breeding colonies originating from different locations (Argentina, Chile, Peru and Bolivia), and cDNA libraries originating from F1 populations of Bolivia, were sequenced using Illumina technology. Coding sequences (CDS) were extracted from the assembled reads, the numbers of reads mapped to these CDS, sequences were functionally annotated and polymorphisms determined. Main findings/Significance Over five thousand CDS, mostly full length or near full length, were publicly deposited on GenBank. Transcripts that were over 10-fold overexpressed from different geographical regions, or from different developmental stages were identified. Polymorphisms were mapped to derived coding sequences, and found to vary between developmental instars and geographic origin of the biological material. This expanded sialome database from T. infestans should be of assistance in future proteomic work attempting to identify salivary proteins that might be used as epidemiological markers of vector exposure, or proteins of pharmacological interest. Triatoma infestans is the main vector of Chagas disease in South America. As in all hematophagous arthropods, its saliva contains a complex cocktail that assists blood feeding by preventing platelet aggregation and blood clotting and promoting vasodilation. These salivary components can be immunologically recognized by their hosts and targeted with antibodies that might disrupt blood feeding. The respective antibodies can be used to detect vector exposure using immunoassays. On the other hand, antibodies may also contribute to the fast evolution of the salivary cocktail. In this work, we attempted to identify variations in the salivary proteins of T. infestans using Illumina technology that allowed identification of over five thousand proteins based on over 300 million sequences obtained from ten salivary gland libraries. This expanded sialome database from T. infestans should be of assistance in future work attempting to identify salivary proteins that might be used as epidemiological markers of vector exposure, or proteins of pharmacological interest.
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38
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Topoisomerase II is required for the proper separation of heterochromatic regions during Drosophila melanogaster female meiosis. PLoS Genet 2014; 10:e1004650. [PMID: 25340780 PMCID: PMC4207608 DOI: 10.1371/journal.pgen.1004650] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/21/2014] [Indexed: 01/03/2023] Open
Abstract
Heterochromatic homology ensures the segregation of achiasmate chromosomes during meiosis I in Drosophila melanogaster females, perhaps as a consequence of the heterochromatic threads that connect achiasmate homologs during prometaphase I. Here, we ask how these threads, and other possible heterochromatic entanglements, are resolved prior to anaphase I. We show that the knockdown of Topoisomerase II (Top2) by RNAi in the later stages of meiosis results in a specific defect in the separation of heterochromatic regions after spindle assembly. In Top2 RNAi-expressing oocytes, heterochromatic regions of both achiasmate and chiasmate chromosomes often failed to separate during prometaphase I and metaphase I. Heterochromatic regions were stretched into long, abnormal projections with centromeres localizing near the tips of the projections in some oocytes. Despite these anomalies, we observed bipolar spindles in most Top2 RNAi-expressing oocytes, although the obligately achiasmate 4th chromosomes exhibited a near complete failure to move toward the spindle poles during prometaphase I. Both achiasmate and chiasmate chromosomes displayed defects in biorientation. Given that euchromatic regions separate much earlier in prophase, no defects were expected or observed in the ability of euchromatic regions to separate during late prophase upon knockdown of Top2 at mid-prophase. Finally, embryos from Top2 RNAi-expressing females frequently failed to initiate mitotic divisions. These data suggest both that Topoisomerase II is involved in the resolution of heterochromatic DNA entanglements during meiosis I and that these entanglements must be resolved in order to complete meiosis. Proper chromosome segregation during egg and sperm development is crucial to prevent birth defects and miscarriage. During chromosome replication, DNA entanglements are created that must be resolved before chromosomes can fully separate. In the oocytes of the fruit fly Drosophila melanogaster, DNA entanglements persist between heterochromatic regions of the chromosomes until after spindle assembly and may facilitate the proper segregation of chromosomes during meiosis. Topoisomerase II enzymes can resolve DNA entanglements by cutting and untwisting tangled DNA. Decreasing Topoisomerase II (Top2) levels in the ovaries of fruit flies led to sterility. RNAi knockdown of the Top2 gene in oocytes resulted in chromosomes that failed to fully separate their heterochromatic regions during meiosis I and caused oocytes to arrest in meiosis I. These studies demonstrate that the Top2 enzyme is required for releasing DNA entanglements between homologous chromosomes before the onset of chromosome segregation during Drosophila female meiosis.
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Lonardo F, Di Natale P, Lualdi S, Acquaviva F, Cuoco C, Scarano F, Maioli M, Pavone LM, Di Gregorio G, Filocamo M, Scarano G. Mucopolysaccharidosis type II in a female patient with a reciprocal X;9 translocation and skewed X chromosome inactivation. Am J Med Genet A 2014; 164A:2627-32. [PMID: 25044788 DOI: 10.1002/ajmg.a.36667] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 06/09/2014] [Indexed: 11/08/2022]
Abstract
Mucopolysaccharidosis type II (MPS II or Hunter syndrome) is a rare X-linked disorder caused by deficient activity of the lysosomal enzyme, iduronate-2-sulfatase (IDS). Phenotypic expression of MPS II in female patients rarely occurs and may be the result of (i) structural abnormalities of the X chromosome, (ii) homozygosity for disease-causing mutations, or (iii) skewed X-chromosome inactivation, in which the normal IDS allele is preferentially inactivated and the abnormal IDS allele is active. We report here on a female patient with clinical MPS II manifestations, deficiency of IDS enzyme activity and a de novo balanced reciprocal X;9 translocation. As our patient has a skewed XCI pattern, but neither genomic IDS mutations nor abnormal IDS transcripts were detected, we speculate about the possible role of the chromosomal rearrangement in reducing the IDS translation efficiency.
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Rivière G. Epigenetic features in the oyster Crassostrea gigas suggestive of functionally relevant promoter DNA methylation in invertebrates. Front Physiol 2014; 5:129. [PMID: 24778620 PMCID: PMC3985014 DOI: 10.3389/fphys.2014.00129] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/14/2014] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is evolutionarily conserved. Vertebrates exhibit high, widespread DNA methylation whereas invertebrate genomes are less methylated, predominantly within gene bodies. DNA methylation in invertebrates is associated with transcription level, alternative splicing, and genome evolution, but functional outcomes of DNA methylation remain poorly described in lophotrochozoans. Recent genome-wide approaches improve understanding in distant taxa such as molluscs, where the phylogenetic position, and life traits of Crassostrea gigas make this bivalve an ideal model to study the physiological and evolutionary implications of DNA methylation. We review the literature about DNA methylation in invertebrates and focus on DNA methylation features in the oyster. Indeed, though our MeDIP-seq results confirm predominant intragenic methylation, the profiles depend on the oyster's developmental and reproductive stage. We discuss the perspective that oyster DNA methylation could be biased toward the 5'-end of some genes, depending on physiological status, suggesting important functional outcomes of putative promoter methylation from cell differentiation during early development to sustained adaptation of the species to the environment.
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Affiliation(s)
- Guillaume Rivière
- Institute for Fundamental and Applied Biology, Normandy UniversityCaen, France
- UMR BOREA ‘Biologie des Organismes et Ecosystèmes Aquatiques’ Université de Caen Basse-Normandie, MNHN, UPMC, CNRS-7208, IRD-207Caen, France
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Greer EL, Beese-Sims SE, Brookes E, Spadafora R, Zhu Y, Rothbart SB, Aristizábal-Corrales D, Chen S, Badeaux AI, Jin Q, Wang W, Strahl BD, Colaiácovo MP, Shi Y. A histone methylation network regulates transgenerational epigenetic memory in C. elegans. Cell Rep 2014; 7:113-26. [PMID: 24685137 DOI: 10.1016/j.celrep.2014.02.044] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/30/2014] [Accepted: 02/27/2014] [Indexed: 01/03/2023] Open
Abstract
How epigenetic information is transmitted from generation to generation remains largely unknown. Deletion of the C. elegans histone H3 lysine 4 dimethyl (H3K4me2) demethylase spr-5 leads to inherited accumulation of the euchromatic H3K4me2 mark and progressive decline in fertility. Here, we identified multiple chromatin-modifying factors, including H3K4me1/me2 and H3K9me3 methyltransferases, an H3K9me3 demethylase, and an H3K9me reader, which either suppress or accelerate the progressive transgenerational phenotypes of spr-5 mutant worms. Our findings uncover a network of chromatin regulators that control the transgenerational flow of epigenetic information and suggest that the balance between euchromatic H3K4 and heterochromatic H3K9 methylation regulates transgenerational effects on fertility.
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Affiliation(s)
- Eric L Greer
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Sara E Beese-Sims
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Emily Brookes
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Ruggero Spadafora
- Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Yun Zhu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Scott B Rothbart
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - David Aristizábal-Corrales
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Shuzhen Chen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Aimee I Badeaux
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Qiuye Jin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | | | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA.
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Krassovsky K, Henikoff S. Distinct chromatin features characterize different classes of repeat sequences in Drosophila melanogaster. BMC Genomics 2014; 15:105. [PMID: 24498936 PMCID: PMC3922421 DOI: 10.1186/1471-2164-15-105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 01/30/2014] [Indexed: 11/15/2022] Open
Abstract
Background Repeat sequences are abundant in eukaryotic genomes but many are excluded from genome assemblies. In Drosophila melanogaster classical studies of repeat content suggested variability between individuals, but they lacked the precision of modern high throughput sequencing technologies. Genome-wide profiling of chromatin features such as histone tail modifications and DNA-binding proteins relies on alignment to the reference genome and hence excludes highly repetitive sequences. Results By analyzing repeat libraries, sequence complexity and k-mer counts we determined the abundances of different D. melanogaster repeat classes in flies in two public datasets, DGRP and modENCODE. We found that larval DNA was depleted of all repeat classes relative to adult and embryonic DNA, as expected from the known depletion of repeat-rich pericentromeric regions during polytenization of larval tissues. By applying a method that is independent of alignment to the genome assembly, we found that satellite repeats associate with distinct H3 tail modifications, such as H3K9me2 and H3K9me3 for short repeats and H3K9me1 for 359 bp repeats. Short AT-rich repeats however are depleted of nucleosomes and hence all histone modifications and associated chromatin proteins. Conclusions The total repeat content and association of repeat sequences with chromatin modifications can be determined despite repeats being excluded from genome assemblies, revealing unexpected distinctions in chromatin features based on sequence composition.
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Affiliation(s)
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.
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Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster. Chromosoma 2013; 123:253-64. [DOI: 10.1007/s00412-013-0445-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 08/09/2013] [Accepted: 11/18/2013] [Indexed: 12/30/2022]
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Rezaei-Ghaleh N, Klama F, Munari F, Zweckstetter M. Vorhersage der Rotationskorrelationszeit in dynamischen Mehrdomänenproteinen und supramolekularen Komplexen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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45
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Min H, Lee JY, Kim MH. Hoxc gene collinear expression and epigenetic modifications established during embryogenesis are maintained until after birth. Int J Biol Sci 2013; 9:960-5. [PMID: 24155669 PMCID: PMC3805901 DOI: 10.7150/ijbs.6739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/12/2013] [Indexed: 11/05/2022] Open
Abstract
The Hox genes, which are organized into clusters on different chromosomes, are key regulators of embryonic anterior-posterior (A-P) body pattern formation and are expressed at specific times and in specific positions in developing vertebrate embryos. Previously, we have shown that histone methylation patterns are closely correlated with collinear Hox gene expression patterns along the A-P axis of E14.5 mouse embryos. Since histone modification is thought to play a crucial mechanistic role in the highly coordinated pattern of collinear Hox gene expression, we examined the maintenance of the spatial collinear expression pattern of Hoxc genes and the corresponding histone modifications during embryogenesis and in early postnatal mice. Hox expression patterns and histone modifications were analyzed by semi-quantitative RT-PCR and chromatin immunoprecipitation (ChIP)-PCR analyses, respectively. The spatiotemporal expression patterns of Hoxc genes in a cluster were maintained until the early postnatal stage (from E8.5 through P5). Examination of histone modifications in E14.5 and P5 tissues revealed that level of H3K27me3 is only a weak correlation with collinear Hoxc gene expression in the trunk regions although diminished in general, however the enrichment of H3K4me3 is strongly correlated with the gene expression in both stages. In summary, the initial spatiotemporal collinear expression pattern of Hoxc genes and epigenetic modifications are maintained after birth, likely contributing to the establishment of the gene expression code for position in the anatomic body axis throughout the entire life of the organism.
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Affiliation(s)
- Hyehyun Min
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Korea
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Rezaei-Ghaleh N, Klama F, Munari F, Zweckstetter M. Predicting the Rotational Tumbling of Dynamic Multidomain Proteins and Supramolecular Complexes. Angew Chem Int Ed Engl 2013; 52:11410-4. [DOI: 10.1002/anie.201305094] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Indexed: 01/10/2023]
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47
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Rothbart SB, Dickson BM, Ong MS, Krajewski K, Houliston S, Kireev DB, Arrowsmith CH, Strahl BD. Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation. Genes Dev 2013; 27:1288-98. [PMID: 23752590 DOI: 10.1101/gad.220467.113] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Histone post-translational modifications regulate chromatin structure and function largely through interactions with effector proteins that often contain multiple histone-binding domains. While significant progress has been made characterizing individual effector domains, the role of paired domains and how they function in a combinatorial fashion within chromatin are poorly defined. Here we show that the linked tandem Tudor and plant homeodomain (PHD) of UHRF1 (ubiquitin-like PHD and RING finger domain-containing protein 1) operates as a functional unit in cells, providing a defined combinatorial readout of a heterochromatin signature within a single histone H3 tail that is essential for UHRF1-directed epigenetic inheritance of DNA methylation. These findings provide critical support for the "histone code" hypothesis, demonstrating that multivalent histone engagement plays a key role in driving a fundamental downstream biological event in chromatin.
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Affiliation(s)
- Scott B Rothbart
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Elgin SCR, Reuter G. Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila. Cold Spring Harb Perspect Biol 2013; 5:a017780. [PMID: 23906716 DOI: 10.1101/cshperspect.a017780] [Citation(s) in RCA: 309] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Position-effect variegation (PEV) results when a gene normally in euchromatin is juxtaposed with heterochromatin by rearrangement or transposition. When heterochromatin packaging spreads across the heterochromatin/euchromatin border, it causes transcriptional silencing in a stochastic pattern. PEV is intensely studied in Drosophila using the white gene. Screens for dominant mutations that suppress or enhance white variegation have identified many conserved epigenetic factors, including the histone H3 lysine 9 methyltransferase SU(VAR)3-9. Heterochromatin protein HP1a binds H3K9me2/3 and interacts with SU(VAR)3-9, creating a core memory system. Genetic, molecular, and biochemical analysis of PEV in Drosophila has contributed many key findings concerning establishment and maintenance of heterochromatin with concomitant gene silencing.
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Affiliation(s)
- Sarah C R Elgin
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
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Abstract
Cre/LoxP has broad utility for studying the function, development, and oncogenic transformation of pancreatic cells in mice. Here we provide an overview of the Cre driver lines that are available for such studies. We discuss how variegated expression, transgene silencing, and recombination in undesired cell types have conspired to limit the performance of these lines, sometimes leading to serious experimental concerns. We also discuss preferred strategies for achieving high-fidelity driver lines and remind investigators of the continuing need for caution when interpreting results obtained from any Cre/LoxP-based experiment performed in mice.
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Affiliation(s)
- Mark A Magnuson
- Center for Stem Cell Biology and Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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De Loof A, Boerjan B, Ernst UR, Schoofs L. The mode of action of juvenile hormone and ecdysone: towards an epi-endocrinological paradigm? Gen Comp Endocrinol 2013; 188:35-45. [PMID: 23454668 DOI: 10.1016/j.ygcen.2013.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/07/2013] [Accepted: 02/12/2013] [Indexed: 12/20/2022]
Abstract
In some insect species, two sites of juvenile hormone (JH) synthesis have been reported: the very well documented corpora allata that secrete JH for "general use", and the reproductive system, in particular the male accessory glands, in which the function of the sometimes huge amounts of JH (e.g. in Hyalophora cecropia) remains to be clarified. A recent finding in Schistocerca gregaria, namely that suppression of the ecdysteroid peak preceding a molt by RNAi of the Halloween genes spook, phantom and shade does not impede normal molting, challenges the (never experimentally proven) classical concept that such a peak is causally linked to a molt. Recent developments in epigenetic control of gene expression in both the honey bee and in locusts suggest that, in addition to the classical scheme of hormone-receptor (membrane- and/or nuclear) mode of action, there may be a third way. Upon combining these and other orphan data that do not fit in the commonly accepted textbook schemes, we here advance the working hypothesis that both JH and ecdysone might be important but overlooked players in epigenetic control of gene expression, in particular at extreme concentrations (peak values or total absence). In this review, we put forward how epi-endocrinology can complement classical arthropod endocrinology.
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Affiliation(s)
- Arnold De Loof
- Research Group of Functional Genomics and Proteomics, KU Leuven, Naamsestraat 59, Bus 2465, 3000 Leuven, Belgium.
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