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Kainth AS, Zhang H, Gross DS. A critical role for Pol II CTD phosphorylation in heterochromatic gene activation. Gene 2024; 918:148473. [PMID: 38615982 DOI: 10.1016/j.gene.2024.148473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
How gene activation works in heterochromatin, and how the mechanism might differ from the one used in euchromatin, has been largely unexplored. Previous work has shown that in SIR-regulated heterochromatin of Saccharomyces cerevisiae, gene activation occurs in the absence of covalent histone modifications and other alterations of chromatin commonly associated with transcription.Here we demonstrate that such activation occurs in a substantial fraction of cells, consistent with frequent transcriptional bursting, and this raises the possibility that an alternative activation pathway might be used. We address one such possibility, Pol II CTD phosphorylation, and explore this idea using a natural telomere-linked gene, YFR057w, as a model. Unlike covalent histone modifications, we find that Ser2, Ser5 and Ser7 CTD phosphorylated Pol II is prevalent at the drug-induced heterochromatic gene. Particularly enriched relative to the euchromatic state is Ser2 phosphorylation. Consistent with a functional role for Ser2P, YFR057w is negligibly activated in cells deficient in the Ser2 CTD kinases Ctk1 and Bur1 even though the gene is strongly stimulated when it is placed in a euchromatic context. Collectively, our results are consistent with a critical role for Ser2 CTD phosphorylation in driving Pol II recruitment and transcription of a natural heterochromatic gene - an activity that may supplant the need for histone epigenetic modifications.
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Affiliation(s)
- Amoldeep S Kainth
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, United States
| | - Hesheng Zhang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, United States
| | - David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, United States.
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2
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Erlendson AA, Freitag M. Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases. Methods Mol Biol 2022; 2529:3-40. [PMID: 35733008 DOI: 10.1007/978-1-0716-2481-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the "histone code," and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies.
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Affiliation(s)
- Allyson A Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
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3
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Abstract
Irregularities in nuclear shape and/or alterations to nuclear size are a hallmark of malignancy in a broad range of cancer types. Though these abnormalities are commonly used for diagnostic purposes and are often used to assess cancer progression in the clinic, the mechanisms through which they occur are not well understood. Nuclear size alterations in cancer could potentially arise from aneuploidy, changes in osmotic coupling with the cytoplasm, and perturbations to nucleocytoplasmic transport. Nuclear shape changes may occur due to alterations to cell-generated mechanical stresses and/or alterations to nuclear structural components, which balance those stresses, such as the nuclear lamina and chromatin. A better understanding of the mechanisms underlying abnormal nuclear morphology and size may allow the development of new therapeutics to target nuclear aberrations in cancer.
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Affiliation(s)
- Ishita Singh
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Tanmay P. Lele
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA,Department of Chemical Engineering, University of Florida, Gainesville, FL, USA,Department of Translational Medical Sciences, Texas A&M University, Houston, TX, USA
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4
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Zaib S, Rana N, Khan I. Histone modifications and their role in epigenetics of cancer. Curr Med Chem 2021; 29:2399-2411. [PMID: 34749606 DOI: 10.2174/0929867328666211108105214] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/19/2021] [Accepted: 08/25/2021] [Indexed: 11/22/2022]
Abstract
Epigenetic regulations play a crucial role in the expression of various genes that are important in the normal cell function. Any alteration in these epigenetic mechanisms can lead to the modification of histone and DNA resulting in the silencing or enhanced expression of some genes causing various diseases. Acetylation, methylation, ribosylation or phosphorylation of histone proteins modifies its interaction with the DNA, consequently changing the ratio of heterochromatin and euchromatin. Terminal lysine residues of histone proteins serve as potential targets of such epigenetic modifications. The current review focuses on the histone modifications, their contributing factors, role of these modifications on metabolism leading to cancer and methylation of histone in cancer affects the DNA repair mechanisms.
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Affiliation(s)
- Sumera Zaib
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore-54590. Pakistan
| | - Nehal Rana
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore-54590. Pakistan
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN. United Kingdom
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5
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Feliciello I, Pezer Ž, Sermek A, Bruvo Mađarić B, Ljubić S, Ugarković Đ. Satellite DNA-Mediated Gene Expression Regulation: Physiological and Evolutionary Implication. Prog Mol Subcell Biol 2021; 60:145-167. [PMID: 34386875 DOI: 10.1007/978-3-030-74889-0_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Satellite DNAs are tandemly repeated sequences organized in large clusters within (peri)centromeric and/or subtelomeric heterochromatin. However, in many species, satellite DNAs are not restricted to heterochromatin but are also dispersed as short arrays within euchromatin. Such genomic organization together with transcriptional activity seems to be a prerequisite for the gene-modulatory effect of satellite DNAs which was first demonstrated in the beetle Tribolium castaneum upon heat stress. Namely, enrichment of a silent histone mark at euchromatic repeats of a major beetle satellite DNA results in epigenetic silencing of neighboring genes. In addition, human satellite III transcripts induced by heat shock contribute to genome-wide gene silencing, providing protection against stress-induced cell death. Gene silencing mediated by satellite RNA was also shown to be fundamental for the early embryonic development of the mosquito Aedes aegypti. Apart from a physiological role during embryogenesis and heat stress response, activation of satellite DNAs in terms of transcription and proliferation can have an evolutionary impact. Spreading of satellite repeats throughout euchromatin promotes the variation of epigenetic landscapes and gene expression diversity, contributing to the evolution of gene regulatory networks and to genome adaptation in fluctuating environmental conditions.
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Affiliation(s)
- Isidoro Feliciello
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.,Dipartimento di Medicina Clinica e Chirurgia, Universita' degli Studi di Napoli Federico II, Naples, Italy
| | - Željka Pezer
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antonio Sermek
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Sven Ljubić
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Đurđica Ugarković
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
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6
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Abstract
The nucleus is the organelle in the cell that contains the genome and its associate proteins which is collectively called chromatin. New work has shown that chromatin and its compaction level, dictated largely through histone modification state, provides rigidity to protect and stabilize the nucleus. Alterations in chromatin, its mechanics, and downstream loss of nuclear shape and stability are hallmarks of human disease. Weakened nuclear mechanics and abnormal morphology have been shown to cause rupturing of the nucleus which results in nuclear dysfunction including DNA damage. Thus, the rigidity provided by chromatin to maintain nuclear mechanical stability also provides its own protection from DNA damage via compartmentalization maintenance.
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Affiliation(s)
- Andrew D Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, United States.
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7
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Burette AC, Judson MC, Li AN, Chang EF, Seeley WW, Philpot BD, Weinberg RJ. Subcellular organization of UBE3A in human cerebral cortex. Mol Autism 2018; 9:54. [PMID: 30364390 PMCID: PMC6194692 DOI: 10.1186/s13229-018-0238-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/03/2018] [Indexed: 12/04/2022] Open
Abstract
Background Loss of UBE3A causes Angelman syndrome, whereas excess UBE3A activity appears to increase the risk for autism. Despite this powerful association with neurodevelopmental disorders, there is still much to be learned about UBE3A, including its cellular and subcellular organization in the human brain. The issue is important, since UBE3A’s localization is integral to its function. Methods We used light and electron microscopic immunohistochemistry to study the cellular and subcellular distribution of UBE3A in the adult human cerebral cortex. Experiments were performed on multiple tissue sources, but our results focused on optimally preserved material, using surgically resected human temporal cortex of high ultrastructural quality from nine individuals. Results We demonstrate that UBE3A is expressed in both glutamatergic and GABAergic neurons, and to a lesser extent in glial cells. We find that UBE3A in neurons has a non-uniform subcellular distribution. In somata, UBE3A preferentially concentrates in euchromatin-rich domains within the nucleus. Electron microscopy reveals that labeling concentrates in the head and neck of dendritic spines and is excluded from the PSD. Strongest labeling within the neuropil was found in axon terminals. Conclusions By highlighting the subcellular compartments in which UBE3A is likely to function in the human neocortex, our data provide insight into the diverse functional capacities of this E3 ligase. These anatomical data may help to elucidate the role of UBE3A in Angelman syndrome and autism spectrum disorder.
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Affiliation(s)
- Alain C Burette
- 1Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, 314 Taylor Hall, Campus, Box 7545, Chapel Hill, NC 27599-7545 USA
| | - Matthew C Judson
- 2Department of Cell Biology and Physiology and Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Alissa N Li
- 3Department of Neurology, University of California, San Francisco, CA USA.,4Department of Pathology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA USA
| | - Edward F Chang
- 5Department of Neurological Surgery, University of California, 505 Parnassus Avenue, Box 0112, San Francisco, CA 94143-0112 USA
| | - William W Seeley
- 3Department of Neurology, University of California, San Francisco, CA USA.,4Department of Pathology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA USA
| | - Benjamin D Philpot
- 2Department of Cell Biology and Physiology and Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599 USA.,6Neuroscience Curriculum, Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Richard J Weinberg
- 2Department of Cell Biology and Physiology and Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599 USA
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8
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Sun Z, Chadwick BP. Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene. Epigenetics Chromatin 2018; 11:45. [PMID: 30103804 PMCID: PMC6088404 DOI: 10.1186/s13072-018-0218-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/10/2018] [Indexed: 01/04/2023] Open
Abstract
Background The product of dosage compensation in female mammals is the inactive X chromosome (Xi). Xi facultative heterochromatin is organized into two different types, one of which is defined by histone H3 trimethylated at lysine 9 (H3K9me3). The rationale for this study was to assess SET domain bifurcated 1 (SETDB1) as a candidate for maintaining this repressive modification at the human Xi. Results Here, we show that loss of SETDB1 does not result in large-scale H3K9me3 changes at the Xi, but unexpectedly we observed striking decompaction of the Xi territory. Close examination revealed a 0.5 Mb region of the Xi that transitioned from H3K9me3 heterochromatin to euchromatin within the 3′ end of the IL1RAPL1 gene that is part of a common chromosome fragile site that is frequently deleted or rearranged in patients afflicted with intellectual disability and other neurological ailments. Centrally located within this interval is a powerful enhancer adjacent to an ERVL-MaLR element. In the absence of SETDB1, the enhancer is reactivated on the Xi coupled with bidirectional transcription from the ERVL-MaLR element. Xa deletion of the enhancer/ERVL-MaLR resulted in loss of full-length IL1RAPL1 transcript in cis, coupled with trans decompaction of the Xi chromosome territory, whereas Xi deletion increased detection of full-length IL1RAPL1 transcript in trans, but did not impact Xi compaction. Conclusions These data support a critical role for SETDB1 in maintaining the ERVL-MaLR element and adjacent enhancer in the 3′ end of the IL1RAPL1 gene in a silent state to facilitate Xi compaction. Electronic supplementary material The online version of this article (10.1186/s13072-018-0218-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhuo Sun
- Department of Biological Science, Florida State University, 319 Stadium Drive, King 3076, Tallahassee, FL, 32306-4295, USA
| | - Brian P Chadwick
- Department of Biological Science, Florida State University, 319 Stadium Drive, King 3076, Tallahassee, FL, 32306-4295, USA.
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9
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Winnicki K, Żabka A, Polit JT, Maszewski J. Mitogen-activated protein kinases concentrate in the vicinity of chromosomes and may regulate directly cellular patterning in Vicia faba embryos. Planta 2018; 248:307-322. [PMID: 29721610 DOI: 10.1007/s00425-018-2905-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
Mitogen-activated protein kinases seem to mark genes which are set up to be activated in daughter cells and thus they may play a direct role in cellular patterning during embryogenesis. Embryonic patterning starts very early and after the first division of zygote different genes are expressed in apical and basal cells. However, there is an ongoing debate about the way these different transcription patterns are established during embryogenesis. The presented data indicate that mitogen-activated protein kinases (MAPKs) concentrate in the vicinity of chromosomes and form visible foci there. Cells in the apical and basal regions differ in number of foci observed during the metaphase which suggests that cellular patterning may be determined by activation of diverse MAPK-dependent genes. Different number of foci in each group of separating chromatids and the specified direction of these mitoses in apical-basal axis indicate that the unilateral auxin accumulation in a single cell may regulate the number of foci in each group of chromatids. Thus, we put forward a hypothesis that MAPKs localized in the vicinity of chromosomes during mitosis mark those genes which are set up to be activated in daughter cells after division. It implies that the chromosomal localization of MAPKs may be one of the mechanisms involved in establishment of cellular patterns in some plant species.
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Affiliation(s)
- Konrad Winnicki
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143, 90-236, Lodz, Poland.
| | - Aneta Żabka
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143, 90-236, Lodz, Poland
| | - Justyna Teresa Polit
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143, 90-236, Lodz, Poland
| | - Janusz Maszewski
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143, 90-236, Lodz, Poland
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10
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Fabrice TN, Cherkezyan L, Ringli C, Baroux C. Transmission Electron Microscopy Imaging to Analyze Chromatin Density Distribution at the Nanoscale Level. Methods Mol Biol 2018; 1675:633-51. [PMID: 29052215 DOI: 10.1007/978-1-4939-7318-7_34] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Transmission electron microscopy (TEM) is used to study the fine ultrastructural organization of cells. Delicate specimen preparation is required for results to reflect the "native" ultrastructural organization of subcellular features such as the nucleus. Despite the advent of high-resolution, fluorescent imaging of chromatin components, TEM still provides a unique and complementary level of resolution capturing chromatin organization at the nanoscale level. Here, we describe the workflow, from tissue preparation, TEM image acquisition and image processing, for obtaining a quantitative description of chromatin density distribution in plant cells, informing on local fluctuations and periodicity. Comparative analyses then allow to elucidate the structural changes induced by developmental or environmental cues, or by mutations affecting specific chromatin modifiers at the nanoscale level. We argue that this approach remains affordable and merits a renewed interest by the plant chromatin community.
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11
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Rakhshandehroo F, Rezaee S, Palukaitis P. Silencing the tobacco gene for RNA-dependent RNA polymerase 1 and infection by potato virus Y cause remodeling of cellular organelles. Virology 2017; 510:127-136. [PMID: 28719835 DOI: 10.1016/j.virol.2017.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 01/13/2023]
Abstract
RNA-dependent RNA polymerase 1 (RDR1) has been shown to be involved in DNA methylation, RNA silencing and regulating expression of other genes. RDR1 gene expression is stimulated by infection with potato virus Y° (PVY). Transgenic Nicotiana tabacum plants silenced for RDR1 gene expression showed morphological changes in mesophyll cells, associated with remodeling of the nuclei, chloroplasts and mitochondria. RDR1 silencing led to decreased nuclear size, increased heterochromatin content and aggregation, decreased numbers of chloroplasts, plus changes in shape, internal structures and integrity of chloroplasts and mitochondria. RDR1-silenced transgenic plants showed increased PVY accumulation and ultrastructural remodeling was intensified in both chloroplasts and mitochondria of PVY-infected, RDR1-silenced plants. By contrast, heterochromatin condensation was reduced by PVY infection, and in non-transgenic plants the nuclei were translucent and lacked morphology after PVY infection. Thus, RDR1 regulates gene expression leading to remodeling of chromosomes, and PVY infection counteracts these effects on chromosomal remodeling.
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Affiliation(s)
- Farshad Rakhshandehroo
- Department of Plant Pathology, College of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Tehran 14515-775, Iran; James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Saeed Rezaee
- Department of Plant Pathology, College of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Tehran 14515-775, Iran
| | - Peter Palukaitis
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; Department of Horticultural Sciences, Seoul Women's University, Nowon-gu, Seoul 01797, Republic of Korea.
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12
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Gupta AP, Bozdech Z. Epigenetic landscapes underlining global patterns of gene expression in the human malaria parasite, Plasmodium falciparum. Int J Parasitol 2017; 47:399-407. [PMID: 28414071 DOI: 10.1016/j.ijpara.2016.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/15/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022]
Abstract
The dynamic chromatin landscape displaying combinatorial complexity of the epigenome impacts gene expression that underlies many events of differentiation and cell cycle progression. In the past few years, epigenetic mechanisms have emerged as important processes involved in the tight gene regulation in malaria parasites, Plasmodium spp. Focusing predominantly on Plasmodium falciparum, the species associated with the most severe form of the disease, many advances have been made in our understanding of the interaction between transcriptional regulation and epigenetic mechanisms as the pivotal processes in regulating life cycle progression, host parasite interactions and parasite adaptation to the host environment. This review focuses on the epigenome and its effect on transcriptional regulation in P. falciparum, highlighting its unique, evolutionary diverse features.
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Affiliation(s)
- Archana P Gupta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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13
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Pantic I, Petrovic D, Paunovic J, Vucevic D, Radosavljevic T, Pantic S. Age-related reduction of chromatin fractal dimension in toluidine blue - stained hepatocytes. Mech Ageing Dev 2016; 157:30-4. [PMID: 27412950 DOI: 10.1016/j.mad.2016.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/26/2016] [Accepted: 07/06/2016] [Indexed: 02/05/2023]
Abstract
In this study, we proposed a hypothesis that chromatin of mouse hepatocytes exhibits age-related reduction of fractal dimension. This hypothesis was based on previously published works demonstrating that complexity of biological systems such as tissues, decreases during the process of physiological aging. Liver tissue was obtained from 24 male mice divided into 3 age groups: 10-days-old (young, juvenile), 210-days-old (adult) and 390-days-old. The tissue was stained using a modification of toluidine blue (nucleic acid - specific) staining method. A total of 480 chromatin structures (20 for each animal) were analyzed. For each structure, the values of fractal dimension, lacunarity, textural angular second moment and inverse difference moment were calculated using ImageJ software and its plugins. The results indicated the age-related reduction in fractal dimension and increase in lacunarity (p<0.01). Fractal dimension is a potentially good indicator of age associated changes in chromatin structure. To our knowledge, this is the first study to show that fractal complexity of hepatocyte chromatin decreases during the process of physiological aging. Fractal analysis as a method could be useful in detection of small age-related changes in chromatin distribution not otherwise visible with naked eye on conventional tissue micrographs.
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Affiliation(s)
- Igor Pantic
- Laboratory for Cellular Physiology, Institute of Medical Physiology, Faculty of Medicine University of Belgrade, Visegradska 26/II, RS-11129, Belgrade, Serbia.
| | - Danica Petrovic
- Health Center Studenica, Kraljevo, Jug Bogdanova 112, RS-36000, Kraljevo, Serbia
| | - Jovana Paunovic
- Laboratory for Cellular Physiology, Institute of Medical Physiology, Faculty of Medicine University of Belgrade, Visegradska 26/II, RS-11129, Belgrade, Serbia
| | - Danijela Vucevic
- Institute of pathological physiology, School of Medicine, University of Belgrade, Dr Subotica 9, RS-11129, Belgrade, Serbia
| | - Tatjana Radosavljevic
- Institute of pathological physiology, School of Medicine, University of Belgrade, Dr Subotica 9, RS-11129, Belgrade, Serbia
| | - Senka Pantic
- Institute of Histology and Embryology, School of Medicine, University of Belgrade Visegradska 26/II, RS-11129, Belgrade, Serbia
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14
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Termolino P, Cremona G, Consiglio MF, Conicella C. Insights into epigenetic landscape of recombination-free regions. Chromosoma 2016; 125:301-8. [PMID: 26801812 PMCID: PMC4830869 DOI: 10.1007/s00412-016-0574-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 01/10/2016] [Accepted: 01/12/2016] [Indexed: 11/29/2022]
Abstract
Genome architecture is shaped by gene-rich and repeat-rich regions also known as euchromatin and heterochromatin, respectively. Under normal conditions, the repeat-containing regions undergo little or no meiotic crossover (CO) recombination. COs within repeats are risky for the genome integrity. Indeed, they can promote non-allelic homologous recombination (NAHR) resulting in deleterious genomic rearrangements associated with diseases in humans. The assembly of heterochromatin is driven by the combinatorial action of many factors including histones, their modifications, and DNA methylation. In this review, we discuss current knowledge dealing with the epigenetic signatures of the major repeat regions where COs are suppressed. Then we describe mutants for epiregulators of heterochromatin in different organisms to find out how chromatin structure influences the CO rate and distribution.
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Affiliation(s)
- Pasquale Termolino
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy
| | - Gaetana Cremona
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy
| | - Maria Federica Consiglio
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy
| | - Clara Conicella
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy.
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15
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George P, Jensen S, Pogorelcnik R, Lee J, Xing Y, Brasset E, Vaury C, Sharakhov IV. Increased production of piRNAs from euchromatic clusters and genes in Anopheles gambiae compared with Drosophila melanogaster. Epigenetics Chromatin 2015; 8:50. [PMID: 26617674 PMCID: PMC4662822 DOI: 10.1186/s13072-015-0041-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/04/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Specific genomic loci, termed Piwi-interacting RNA (piRNA) clusters, manufacture piRNAs that serve as guides for the inactivation of complementary transposable elements (TEs). The piRNA pathway has been accurately detailed in Drosophila melanogaster, while it remains poorly examined in other insects. This pathway is increasingly recognized as critical for germline development and reproduction. Understanding of the piRNA functions in mosquitoes could offer an opportunity for disease vector control by the reduction of their reproductive potential. RESULTS To analyze the similarities and differences in this pathway between Drosophila and mosquito, we performed an in-depth analysis of the genomic loci producing piRNAs and their targets in the African malaria vector Anopheles gambiae. We identified 187 piRNA clusters in the An. gambiae genome and 155 piRNA clusters in the D. melanogaster genome. We demonstrate that many more piRNA clusters in the mosquito compared with the fruit fly are uni-directionally transcribed and are located outside pericentromeric heterochromatin. About 11 % of the An. gambiae piRNA population map to gene transcripts. This is a noticeable increase compared with the ~6 % of the piRNA population mapped to genes in D. melanogaster. A subset of the piRNA-enriched genes in An. gambiae has functions related to reproduction and development. At least 24 and 65 % of the mapped piRNAs correspond to genomic TE sequences in An. gambiae and D. melanogaster, respectively. DNA transposons and non-LTR retrotransposons are more abundant in An. gambiae, while LTR retrotransposons are more abundant in D. melanogaster. Yet, piRNAs predominantly target LTR retrotransposons in both species, which may point to a distinct feature of these elements compared to the other classes of TEs concerning their silencing by the piRNA pathway. CONCLUSIONS Here, we demonstrate that piRNA-producing loci have more ubiquitous distribution in the An. gambiae genome than in the genome of D. melanogaster. Also, protein-coding genes have an increased role in production of piRNAs in the germline of this mosquito. Genes involved in germline and embryonic development of An. gambiae generate a substantial portion of piRNAs, suggesting a role of the piRNA pathway in the epigenetic regulation of the reproductive processes in the African malaria vector.
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Affiliation(s)
- Phillip George
- />Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Silke Jensen
- />Laboratoire Génétique, Reproduction, et Développement, Clermont Université, Université d’Auvergne, BP 38, 63001 Clermont-Ferrand, France
- />Institut National de la Santé et de la Recherche Médicale, U 1103, BP 38, 63001 Clermont-Ferrand, France
- />Centre National de Recherche Scientifique, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Romain Pogorelcnik
- />Laboratoire Génétique, Reproduction, et Développement, Clermont Université, Université d’Auvergne, BP 38, 63001 Clermont-Ferrand, France
- />Institut National de la Santé et de la Recherche Médicale, U 1103, BP 38, 63001 Clermont-Ferrand, France
- />Centre National de Recherche Scientifique, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Jiyoung Lee
- />The PhD Program in Genomics Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Yi Xing
- />The PhD Program in Genomics Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Emilie Brasset
- />Laboratoire Génétique, Reproduction, et Développement, Clermont Université, Université d’Auvergne, BP 38, 63001 Clermont-Ferrand, France
- />Institut National de la Santé et de la Recherche Médicale, U 1103, BP 38, 63001 Clermont-Ferrand, France
- />Centre National de Recherche Scientifique, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Chantal Vaury
- />Laboratoire Génétique, Reproduction, et Développement, Clermont Université, Université d’Auvergne, BP 38, 63001 Clermont-Ferrand, France
- />Institut National de la Santé et de la Recherche Médicale, U 1103, BP 38, 63001 Clermont-Ferrand, France
- />Centre National de Recherche Scientifique, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Igor V. Sharakhov
- />Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
- />The PhD Program in Genomics Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
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Cabrera JR, Olcese U, Horabin JI. A balancing act: heterochromatin protein 1a and the Polycomb group coordinate their levels to silence chromatin in Drosophila. Epigenetics Chromatin 2015; 8:17. [PMID: 25954320 PMCID: PMC4423169 DOI: 10.1186/s13072-015-0010-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The small non-histone protein Heterochromatin protein 1a (HP1a) plays a vital role in packaging chromatin, most notably in forming constitutive heterochromatin at the centromeres and telomeres. A second major chromatin regulating system is that of the Polycomb/trithorax groups of genes which, respectively, maintain the repressed/activated state of euchromatin. Recent analyses suggest they affect the expression of a multitude of genes, beyond the homeotics whose alteration in expression lead to their initial discovery. RESULTS Our data suggest that early in Drosophila development, HP1a collaborates with the Polycomb/trithorax groups of proteins to regulate gene expression and that the two chromatin systems do not act separately as convention describes. HP1a affects the levels of both the Polycomb complexes and RNA polymerase II at promoters, as assayed by chromatin immunoprecipitation analysis. Deposition of both the repressive (H3K27me3) and activating (H3K4me3) marks promoted by the Polycomb/trithorax group genes at gene promoters is affected. Additionally, depending on which parent contributes the null mutation of the HP1a gene, the levels of the H3K27me3 and H3K9me3 silencing marks at both promoters and heterochromatin are different. Changes in levels of the H3K27me3 and H3K9me3 repressive marks show a mostly reciprocal nature. The time around the mid-blastula transition, when the zygotic genome begins to be actively transcribed, appears to be a transition/decision point for setting the levels. CONCLUSIONS We find that HP1a, which is normally critical for the formation of constitutive heterochromatin, also affects the generation of the epigenetic marks of the Polycomb/trithorax groups of proteins, chromatin modifiers which are key to maintaining gene expression in euchromatin. At gene promoters, deposition of both the repressive H3K27me3 and activating H3K4me3 marks of histone modifications shows a dependence on HP1a. Around the mid-blastula transition, when the zygotic genome begins to be actively transcribed, a pivotal decision for the level of silencing appears to take place. This is also when the embryo organizes its genome into heterochromatin and euchromatin. A balance between the HP1a and Polycomb group silencing systems appears to be set for the chromatin types that each system will primarily regulate.
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Affiliation(s)
- Janel R Cabrera
- Department of Biomedical Sciences, College of Medicine, Florida State University, Rm 3300-G, 1115 W, Call St., Tallahassee, FL 32306 USA ; Current Address: Center for Life Sciences, Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Rm 917, 3 Blackfan Circle, Boston, MA 02215 USA
| | - Ursula Olcese
- Department of Biomedical Sciences, College of Medicine, Florida State University, Rm 3300-G, 1115 W, Call St., Tallahassee, FL 32306 USA
| | - Jamila I Horabin
- Department of Biomedical Sciences, College of Medicine, Florida State University, Rm 3300-G, 1115 W, Call St., Tallahassee, FL 32306 USA
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