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Amélie Bonnet-Garnier, Kiên Kiêu, Tiphaine Aguirre-Lavin, Krisztina Tar, Pierre Flores, Zichuan Liu, Nathalie Peynot, Martine Chebrout, András Dinnyés, Véronique Duranthon, Nathalie Beaujean
Changes to the spatial organization of specific chromatin domains such as constitutive heterochromatin have been studied extensively in somatic cells. During early embryonic development, drastic epigenetic reprogramming of both the maternal and paternal genomes, followed by chromatin remodeling at the time of embryonic genome activation (EGA), have been observed in the mouse. Very few studies have been performed in other mammalian species (human, bovine, or rabbit) and the data are far from complete. During this work, we studied the three-dimensional organization of pericentromeric regions during the preimplantation period in the rabbit using specific techniques (3D-FISH) and tools (semi-automated image analysis)...
April 18, 2018: Chromosoma
Kyohei Oyama, Danny El-Nachef, Chen Fang, Hidemi Kajimoto, Jeremy P Brown, Prim B Singh, W Robb MacLellan
BACKGROUND: Heterochromatin, which is formed when tri-methyl lysine 9 of histone H3 (H3K9me3) is bound by heterochromatin 1 proteins (HP1s), plays an important role in differentiation and senescence by silencing cell cycle genes. Cardiac myocytes (CMs) accumulate heterochromatin during differentiation and demethylation of H3K9me3 inhibits cell cycle gene silencing and cell cycle exit in CMs; however, it is unclear if this process is mediated by HP1s. In this study, we created a conditional CM-specific HP1 gamma (HP1γ) knockout (KO) mouse model and tested whether HP1γ is required for cell cycle gene silencing and cardiac growth...
April 17, 2018: Epigenetics & Chromatin
Lin Guo, Xiuwei Cao, Yuhao Liu, Jun Li, Yongpeng Li, Dongming Li, Ke Zhang, Caixia Gao, Aiwu Dong, Xigang Liu
WUSCHEL (WUS) is critical for plant meristem maintenance and determinacy in Arabidopsis, and the regulation of its spatiotemporal expression patterns is complex. We previously found that AGAMOUS (AG), a key MADS-domain transcription factor in floral organ identity and floral meristem determinacy, can directly suppress WUS expression through the recruitment of the Polycomb group (PcG) protein TERMINAL FLOWER2 (TFL2, also known as LIKE HETEROCHROMATIN PROTEIN1, LHP1) at the WUS locus. However, the mechanism by which WUS is repressed remains unclear...
April 16, 2018: Plant Journal: for Cell and Molecular Biology
A L Caldeira-Brant, L Eras-Garcia, D Alves-Freitas, F R C L Almeida, H Chiarini-Garcia
STUDY QUESTION: Could a more detailed evaluation of marmoset spermatogonial morphology, kinetics, and niches using high-resolution light microscopy (HRLM) lead to new findings? SUMMARY ANSWER: Three new classes of marmoset spermatogonia, which were not evenly distributed in terms of number and position along the basal membrane, and an extra premeiotic cell division not present in humans were identified using HRLM. WHAT IS KNOWN ALREADY: The seminiferous epithelium cycle (SEC) of marmosets is divided into nine stages when based on the acrosome system, and several spermatogenic stages can usually be recognized within the same tubular cross-section...
April 11, 2018: Molecular Human Reproduction
Guillaume Velasco, Giacomo Grillo, Nizar Touleimat, Laure Ferry, Ivana Ivkovic, Florence Ribierre, Jean-François Deleuze, Sophie Chantalat, Capucine Picard, Claire Francastel
Alterations of DNA methylation landscapes and machinery are a hallmark of many human diseases. A prominent case is the ICF syndrome, a rare autosomal recessive immunological/neurological disorder diagnosed by the loss of DNA methylation at (peri)centromeric repeats and its associated chromosomal instability. It is caused by mutations in the de novo DNA methyltransferase DNMT3B in about half of the patients (ICF1). In the remainder, the striking identification of mutations in factors devoid of DNA methyltransferase activity, ZBTB24 (ICF2), CDCA7 (ICF3) or HELLS (ICF4), raised key questions about common or distinguishing DNA methylation alterations downstream of these mutations and hence, about the functional link between the four factors...
April 12, 2018: Human Molecular Genetics
Luyang Sun, Ruofan Yu, Weiwei Dang
Chromatin 3D structure is highly dynamic and associated with many biological processes, such as cell cycle progression, cellular differentiation, cell fate reprogramming, cancer development, cellular senescence, and aging. Recently, by using chromosome conformation capture technologies, tremendous findings have been reported about the dynamics of genome architecture, their associated proteins, and the underlying mechanisms involved in regulating chromatin spatial organization and gene expression. Cellular senescence and aging, which involve multiple cellular and molecular functional declines, also undergo significant chromatin structural changes, including alternations of heterochromatin and disruption of higher-order chromatin structure...
April 16, 2018: Genes
Laura Avogaro, Emmanuelle Querido, Myriam Dalachi, Michael F Jantsch, Pascal Chartrand, Emilio Cusanelli
Telomeres cap the ends of eukaryotic chromosomes, protecting them from degradation and erroneous recombination events which may lead to genome instability. Telomeres are transcribed giving rise to telomeric repeat-containing RNAs, called TERRA. The TERRA long noncoding RNAs have been proposed to play important roles in telomere biology, including heterochromatin formation and telomere length homeostasis. While TERRA RNAs are predominantly nuclear and localize at telomeres, little is known about the dynamics and function of TERRA molecules expressed from individual telomeres...
April 16, 2018: RNA Biology
Anna M Chiarella, Austin L Quimby, Marjan Mehrab-Mohseni, Brian Velasco, Sandeep K Kasoji, Ian Davis, Paul A Dayton, Nathaniel A Hathaway, Samantha Pattenden
One of the most sensitive, time consuming, and variable steps of chromatin immunoprecipitation (ChIP) is chromatin sonication. Traditionally, this process can take hours to properly sonicate enough chromatin for multiple ChIP assays. Further, the length of sheared DNA is often inconsistent. In order to faithfully measure chemical and structural changes at the chromatin level, sonication needs to be reliable. Thus, chromatin fragmentation by sonication represents a significant bottleneck to downstream quantitative analysis...
April 16, 2018: Biochemistry
Zhe Liang, Lisha Shen, Xuean Cui, Shengjie Bao, Yuke Geng, Guoliang Yu, Fan Liang, Shang Xie, Tiegang Lu, Xiaofeng Gu, Hao Yu
DNA methylation on N6 -adenine (6mA) has recently been found to be a potentially epigenetic mark in several unicellular and multicellular eukaryotes. However, its distribution patterns and potential functions in land plants, which are primary producers for most ecosystems, remain largely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genome of Arabidopsis thaliana at different developmental stages using single-molecule real-time sequencing. 6mA sites are widely distributed across the Arabidopsis genome and enriched over the pericentromeric heterochromatin regions...
April 12, 2018: Developmental Cell
Suman Abhishek, M Angel Nivya, Naveen Kumar Nakarakanti, Waghela Deeksha, Sanjeev Khosla, Eerappa Rajakumara
UHRF1 is a multi-domain protein comprising of a tandem tudor (UHRF1 TTD), a PHD finger, and a SET and RING-associated domain. It is required for the maintenance of CG methylation, heterochromatin formation and DNA repair. Isothermal titration calorimetry binding studies of unmodified and methylated lysine histone peptides establish that the UHRF1 TTD binds dimethylated Lys9 on histone H3 (H3K9me2). Further, MD simulation and binding studies reveal that TTD-PHD of UHRF1 (UHRF1 TTD-PHD) preferentially recognizes dimethyl-lysine status...
April 12, 2018: Biochimie
Lucas Baumgärtner, Leonardo Marcel Paiz, Fabio Hiroshi Takagui, Roberto Laridondo Lui, Orlando Moreira Filho, Lucia Giuliano-Caetano, Ana Luiza de Brito Portela-Castro, Vladimir Pavan Margarido
Doradidae has been a target of phylogenetic studies over the last few years, but chromosomal information about the family is still scarce. Therefore, new cytogenetic data are provided herein and they are correlated with phylogenetic proposals to contribute to the knowledge of chromosomal evolution within doradids. Cytogenetic studies were performed on Trachydoras paraguayensis, Anadoras sp. "araguaia," Ossancora eigenmanni, Platydoras armatulus, and Rhinodoras dorbignyi. O. eigenmanni, P. armatulus, and R...
March 13, 2018: Zebrafish
Geeta J Narlikar, Adam G Larson
In eukaryotic cells, structures called heterochromatin play critical roles in nuclear processes ranging from gene repression to chromosome segregation. Biochemical and in vivo studies over the past several decades have implied that the diverse functions of heterochromatin rely on the ability of these structures to spread across large regions of the genome, to compact the underlying DNA, and to recruit different types of activities. Recent observations have suggested that heterochromatin may possess liquid droplet like properties...
April 12, 2018: Biochemistry
Polliana Silva Rodrigues, Margarete Magalhães Souza, Cláusio Antônio Ferreira Melo, Telma Nair Santana Pereira, Ronan Xavier Corrêa
BACKGROUND: The Leguminosae family is the third-largest family of angiosperms, and Caesalpinioideae is its second-largest subfamily. A great number of species (approximately 205) are found in the Caesalpinia group within this subfamily; together with these species' phenotypic plasticity and the similarities in their morphological descriptors, make this a complex group for taxonomic and phylogenetic studies. The objective of the present work was to evaluate the karyotypic diversity and the 2C DNA content variation in 10 species of the Caesalpinia group, representing six genera: Paubrasilia, Caesalpinia, Cenostigma, Poincianella, Erythrostemon and Libidibia...
April 11, 2018: BMC Genetics
O I Podgornaya, D I Ostromyshenskii, N I Enukashvily
Centromeres (CEN), pericentromeric regions (periCEN), and subtelomeric regions (subTel) comprise the areas of constitutive heterochromatin (HChr). Tandem repeats (TRs or satellite DNA) are the main components of HChr forming no less than 10% of the mouse and human genome. HChr is assembled within distinct structures in the interphase nuclei of many species - chromocenters. In this review, the main classes of HChr repeat sequences are considered in the order of their number increase in the sequencing reads of the mouse chromocenters (ChrmC)...
April 2018: Biochemistry. Biokhimii︠a︡
Karine Nozeret, François Loll, Gildas Mouta Cardoso, Christophe Escudé, Alexandre S Boutorine
Pericentromeric heterochromatin plays important roles in controlling gene expression and cellular differentiation. Fluorescent pyrrole-imidazole polyamides targeting murine pericentromeric DNA (major satellites) can be used for the visualization of pericentromeric heterochromatin foci in live mouse cells. New derivatives targeting human repeated DNA sequences (α-satellites) were synthesized and their interaction with target DNA was characterized. The possibility to use major satellite and α -satellite binding polyamides as tools for staining pericentromeric heterochromatin was further investigated in fixed and living mouse and human cells...
April 4, 2018: Biochimie
Ho-Jun Jeon, Young-Shin Kim, Joong-Gook Kim, Kyu Heo, Jung-Hoon Pyo, Masamitsu Yamaguchi, Joung-Sun Park, Mi-Ae Yoo
Chromatin change is one of the crucial causes of aging. Specifically, maintenance of heterochromatin stability is critical for cellular integrity, and its loss induces genomic instability and cellular aging. However, the causes and effects of heterochromatin instability in multicellular tissue aging still remain unclear. Here, in the adult Drosophila midgut, we report age-related loss of heterochromatin stability in enterocytes (ECs) due to the loss and dispersion of tri-methylated histone H3 Lys9 (H3K9me3) and heterochromatin protein 1 (HP1)...
April 3, 2018: Mechanisms of Ageing and Development
Lili Gong, Fangyuan Liu, Zhen Xiong, Ruili Qi, Zhongwen Luo, Xiaodong Gong, Qian Nie, Qian Sun, Yun-Fei Liu, Wenjie Qing, Ling Wang, Lan Zhang, Xiangcheng Tang, Shan Huang, Gen Li, Hong Ouyang, Mengqing Xiang, Quan Dong Nguyen, Yizhi Liu, David Wan-Cheng Li
Oxidative stress (OS)-induced retinal pigment epithelium (RPE) cell apoptosis is critically implicated in the pathogenesis of age-related macular degeneration (AMD), a leading cause of blindness in the elderly. Heterochromatin, a compact and transcriptional inert chromatin structure, has been recently shown to be dynamically regulated in response to stress stimuli. The functional mechanism of heterochromatin on OS exposure is unclear, however. Here we show that OS increases heterochromatin formation both in vivo and in vitro, which is essential for protecting RPE cells from oxidative damage...
April 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
Beth R Watts, Sina Wittmann, Maxime Wery, Camille Gautier, Krzysztof Kus, Adrien Birot, Dong-Hyuk Heo, Cornelia Kilchert, Antonin Morillon, Lidia Vasiljeva
It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains...
March 29, 2018: Nucleic Acids Research
Guo-Hua Qiu, Cuiqin Huang, Xintian Zheng, Xiaoyan Yang
Peripheral and abundant noncoding DNA has been hypothesized to protect the genome and the central protein-coding sequences against DNA damage in somatic genome. In the cytosol, invading exogenous nucleic acids may first be deactivated by small RNAs encoded by noncoding DNA via mechanisms similar to the prokaryotic CRISPR-Cas system. In the nucleus, the radicals generated by radiation in the cytosol, radiation energy and invading exogenous nucleic acids are absorbed, blocked and/or reduced by peripheral heterochromatin, and damaged DNA in heterochromatin is removed and excluded from the nucleus to the cytoplasm through nuclear pore complexes...
April 4, 2018: Epigenomics
Inrok Oh, Saehyun Choi, YounJoon Jung, Jun Soo Kim
Sharp increase in macromolecular crowding induces abnormal chromatin compaction in the cell nucleus, suggesting its non-negligible impact on chromatin structure and function. However, the details of the crowding-induced chromatin compaction remain poorly understood. In this work, we present a computer simulation study on the entropic effect of macromolecular crowding on the interaction between chromatin structural units called nucleosome clutches. Nucleosome clutches were modeled by a chain of nucleosomes collapsed by harmonic restraints implicitly mimicking the nucleosome association mediated by histone tails and linker histones...
April 3, 2018: Scientific Reports
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