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Yeast epigenetics

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https://www.readbyqxmd.com/read/29760781/understanding-aneuploidy-in-cancer-through-the-lens-of-system-inheritance-fuzzy-inheritance-and-emergence-of-new-genome-systems
#1
REVIEW
Christine J Ye, Sarah Regan, Guo Liu, Sarah Alemara, Henry H Heng
Background: In the past 15 years, impressive progress has been made to understand the molecular mechanism behind aneuploidy, largely due to the effort of using various -omics approaches to study model systems (e.g. yeast and mouse models) and patient samples, as well as the new realization that chromosome alteration-mediated genome instability plays the key role in cancer. As the molecular characterization of the causes and effects of aneuploidy progresses, the search for the general mechanism of how aneuploidy contributes to cancer becomes increasingly challenging: since aneuploidy can be linked to diverse molecular pathways (in regards to both cause and effect), the chances of it being cancerous is highly context-dependent, making it more difficult to study than individual molecular mechanisms...
2018: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29739365/histone-methyltransferase-setdb1-promotes-cells-proliferation-and-migration-by-interacting-withtiam1-in-hepatocellular-carcinoma
#2
Yuqin Zhang, Jing Huang, Qisheng Li, Keli Chen, Yonghao Liang, Zetao Zhan, Feng Ye, Wen Ni, Longhua Chen, Yi Ding
BACKGROUND: SETDB1 is a histone H3K9 methyltransferase, which plays a significant role in the occurrence and progression of tumors. Previous studies have confirmed that T-lymphom invasion and metastasis gene (Tiam1) is a protein associated with the metastasis of hepatocellular carcinoma (HCC); however, we have not yet been successful in elucidating the specific mechanism of HCC. METHODS: Yeast two-hybrid test was conducted to screen proteins that interacted with Tiam1 gene...
May 8, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29729317/cellular-substrate-limitations-of-lysine-acetylation-turnover-by-sirtuins-investigated-with-engineered-futile-cycle-enzymes
#3
Svenja Heitmüller, Petra Neumann-Staubitz, Cornelia Herrfurth, Ivo Feussner, Heinz Neumann
Metabolic activity and epigenetic regulation of gene expression are intimately coupled. The mechanisms linking the two are incompletely understood. Sirtuins catalyse the removal of acetyl groups from lysine side chains of proteins using NAD+ as a stoichiometric cofactor, thereby connecting the acetylation state of histones to energy supply of the cell. Here, we investigate the impact of lysine acetylation turnover by sirtuins on cell physiology by engineering Sirtase, an enzyme that self-acetylates and deacetylates in futile cycles...
May 2, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29728458/the-epigenetic-regulator-sirt7-guards-against-mammalian-cellular-senescence-induced-by-ribosomal-dna-instability
#4
Silvana Paredes, Maria Angulo-Ibanez, Luisa Tasselli, Scott M Carlson, Wei Zheng, Tie-Mei Li, Katrin F Chua
In the yeast Saccharomyces cerevisiae, genomic instability in rDNA repeat sequences is an underlying cause of cell aging and is suppressed by the chromatin-silencing factor Sir2. In humans, rDNA instability is observed in cancers and premature aging syndromes, but its underlying mechanisms and functional consequences remain unclear. Here, we uncovered a pivotal role of sirtuin 7 (SIRT7), a mammalian Sir2 homolog, in guarding against rDNA instability and show that this function of SIRT7 protects against senescence in primary human cells...
May 4, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29726937/design-principles-for-nuclease-deficient-crispr-based-transcriptional-regulators
#5
Michael K Jensen
The engineering of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated proteins continues to expand the toolkit available for genome editing, reprogramming gene regulation, genome visualisation and epigenetic studies of living organisms. In this review, the emerging design principles on the use of nuclease-deficient CRISPR-based reprogramming of gene expression will be presented. The review will focus on the designs implemented in yeast both at the level of CRISPR proteins and guide RNA (gRNA), but will lend due credits to the seminal studies performed in other species where relevant...
June 1, 2018: FEMS Yeast Research
https://www.readbyqxmd.com/read/29724186/genome-wide-expert-annotation-of-the-epigenetic-machinery-of-the-plant-parasitic-nematodes-meloidogyne-spp-with-a-focus-on-the-asexually-reproducing-species
#6
Loris Pratx, Corinne Rancurel, Martine Da Rocha, Etienne G J Danchin, Philippe Castagnone-Sereno, Pierre Abad, Laetitia Perfus-Barbeoch
BACKGROUND: The renewed interest in epigenetics has led to the understanding that both the environment and individual lifestyle can directly interact with the epigenome to influence its dynamics. Epigenetic phenomena are mediated by DNA methylation, stable chromatin modifications and non-coding RNA-associated gene silencing involving specific proteins called epigenetic factors. Multiple organisms, ranging from plants to yeast and mammals, have been used as model systems to study epigenetics...
May 3, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29675464/heritable-stress-response-dynamics-revealed-by-single-cell-genealogy
#7
Meenakshi Chatterjee, Murat Acar
Cells often respond to environmental stimuli by activating specific transcription factors. Upon exposure to glucose limitation stress, it is known that yeast Saccharomyces cerevisiae cells dephosphorylate the general stress response factor Msn2, leading to its nuclear localization, which in turn activates the expression of many genes. However, the precise dynamics of Msn2 nucleocytoplasmic translocations and whether they are inherited over multiple generations in a stress-dependent manner are not well understood...
April 2018: Science Advances
https://www.readbyqxmd.com/read/29610759/molecular-signature-of-the-imprintosome-complex-at-the-mating-type-locus-in-fission-yeast
#8
Célia Raimondi, Bernd Jagla, Caroline Proux, Hervé Waxin, Serge Gangloff, Benoit Arcangioli
Genetic and molecular studies have indicated that an epigenetic imprint at mat1 , the sexual locus of fission yeast, initiates mating type switching. The polar DNA replication of mat1 generates an imprint on the Watson strand. The process by which the imprint is formed and maintained through the cell cycle remains unclear. To understand better the mechanism of imprint formation and stability, we characterized the recruitment of early players of mating type switching at the mat1 region. We found that the switch activating protein 1 (Sap1) is preferentially recruited inside the mat1M allele on a sequence ( SS13 ) that enhances the imprint...
January 16, 2018: Microbial Cell
https://www.readbyqxmd.com/read/29578371/extra-view-sirt1-acts-as-a-gatekeeper-of-replication-initiation-to-preserve-genomic-stability
#9
Koichi Utani, Mirit I Aladjem
Since the discovery of a yeast gene silencing modifier (Silent Information Modifier 2, SIR2) and its role in maintaining genomic stability more than two decades ago, SIR2 homologs (sirtuins) were identified in diverse species. Sirtuins are protein deacetylases that play diverse roles in proper cellular metabolism including cell cycle progression and maintenance of genomic stability. In yeast, SIR2 interacts with replication origins and protein complexes that affect both replication origin usage and gene silencing...
March 26, 2018: Nucleus
https://www.readbyqxmd.com/read/29577419/an-optimized-faire-procedure-for-low-cell-numbers-in-yeast
#10
David Segorbe, Derek Wilkinson, Alexandru Mizeranschi, Timothy Hughes, Ragnhild Aaløkken, Libuse Vachova, Zdena Palkova, Gregor D Gilfillan
We report an optimised low-input FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements-sequencing) procedure to assay chromatin accessibility from limited amounts of yeast cells. We demonstrate that the method performs well on as little as 4 mg cells scraped directly from a few colonies. Sensitivity, specificity and reproducibility of the scaled-down method are comparable to that of regular, higher input amounts, and allows the use of 100-fold fewer cells than existing procedures. The method enables epigenetic analysis of chromatin structure without the need for cell multiplication of exponentially growing cells in liquid culture, thus opening the possibility to study colony cell subpopulations, or those that can be isolated directly from environmental samples...
March 25, 2018: Yeast
https://www.readbyqxmd.com/read/29540259/histone-tail-cleavage-as-a-novel-epigenetic-regulatory-mechanism-for-gene-expression
#11
Sun-Ju Yi, Kyunghwan Kim
Chromatin is an intelligent building block that can express either external or internal needs through structural changes. To date, three methods to change chromatin structure and regulate gene expression have been well-documented: histone modification, histone exchange, and ATP-dependent chromatin remodeling. Recently, a growing body of literature has suggested that histone tail cleavage is related to various cellular processes including stem cell differentiation, osteoclast differentiation, granulocyte differentiation, mammary gland differentiation, viral infection, aging, and yeast sporulation...
March 15, 2018: BMB Reports
https://www.readbyqxmd.com/read/29527415/identification-and-characterization-of-the-cytosine-5-dna-methyltransferase-gene-family-in-salvia-miltiorrhiza
#12
Jiang Li, Caili Li, Shanfa Lu
Cytosine DNA methylation is highly conserved epigenetic modification involved in a wide range of biological processes in eukaryotes. It was established and maintained by cytosine-5 DNA methyltransferases (C5-MTases) in plants. Through genome-wide identification, eight putative SmC5-MTase genes were identified from the genome of Salvia miltiorrhiza , a well-known traditional Chinese medicine material and an emerging model medicinal plant. Based on conserved domains and phylogenetic analysis, eight SmC5-MTase genes were divided into four subfamilies, including MET , CMT , DRM and DNMT2 ...
2018: PeerJ
https://www.readbyqxmd.com/read/29514099/muscle-specific-histone-h3k36-dimethyltransferase-set-18-shortens-lifespan-of-caenorhabditis-elegans-by-repressing-daf-16a-expression
#13
Liangping Su, Hongyuan Li, Cheng Huang, Tingting Zhao, Yongjun Zhang, Xueqing Ba, Zhongwei Li, Yu Zhang, Baiqu Huang, Jun Lu, Yanmei Zhao, Xiaoxue Li
Mounting evidence shows that histone methylation, a typical epigenetic mark, is crucial for gene expression regulation during aging. Decreased trimethylation of Lys 36 on histone H3 (H3K36me3) in worms and yeast is reported to shorten lifespan. The function of H3K36me2 in aging remains unclear. In this study, we identified Caenorhabditis elegans SET-18 as a histone H3K36 dimethyltransferase. SET-18 deletion extended lifespan and increased oxidative stress resistance, dependent on daf-16 activity in the insulin/IGF pathway...
March 6, 2018: Cell Reports
https://www.readbyqxmd.com/read/29500261/plant-homeodomain-genes-play-important-roles-in-cryptococcal-yeast-hypha-transition
#14
Yunfang Meng, Yumeng Fan, Wanqing Liao, Xiaorong Lin
Cryptococcus neoformans is a major opportunistic fungal pathogen. Like many dimorphic fungal pathogens, C. neoformans can undergo morphological transition from the yeast form to the hypha form, and its morphotype is tightly linked to its virulence. Although some genetic factors controlling morphogenesis have been identified, little is known about the epigenetic regulation in this process. Proteins with the plant homeodomain (PHD) finger, a structurally conserved domain in eukaryotes, were first identified in plants and are known to be involved in reading and effecting chromatin modification...
May 1, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29492790/gene-expression-hallmarks-of-cellular-ageing
#15
Stephen Frenk, Jonathan Houseley
Ageing leads to dramatic changes in the physiology of many different tissues resulting in a spectrum of pathology. Nonetheless, many lines of evidence suggest that ageing is driven by highly conserved cell intrinsic processes, and a set of unifying hallmarks of ageing has been defined. Here, we survey reports of age-linked changes in basal gene expression across eukaryotes from yeast to human and identify six gene expression hallmarks of cellular ageing: downregulation of genes encoding mitochondrial proteins; downregulation of the protein synthesis machinery; dysregulation of immune system genes; reduced growth factor signalling; constitutive responses to stress and DNA damage; dysregulation of gene expression and mRNA processing...
February 28, 2018: Biogerontology
https://www.readbyqxmd.com/read/29371397/transcriptional-and-post-transcriptional-regulation-of-autophagy-in-the-yeast-saccharomyces-cerevisiae
#16
REVIEW
Elizabeth Delorme-Axford, Daniel J Klionsky
Autophagy is a highly conserved catabolic pathway that is vital for development, cell survival, and the degradation of dysfunctional organelles and potentially toxic aggregates. Dysregulation of autophagy is associated with cancer, neurodegeneration, and lysosomal storage diseases. Accordingly, autophagy is precisely regulated at multiple levels (transcriptional, post-transcriptional, translational, and post-translational) to prevent aberrant activity. Various model organisms are used to study autophagy, but the baker's yeast Saccharomyces cerevisiae continues to be advantageous for genetic and biochemical analysis of non-selective and selective autophagy...
April 13, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29365171/epigenomics-in-3d-importance-of-long-range-spreading-and-specific-interactions-in-epigenomic-maintenance
#17
Daniel Jost, Cédric Vaillant
Recent progresses of genome-wide chromatin conformation capture techniques have shown that the genome is segmented into hierarchically organized spatial compartments. However, whether this non-random 3D organization only reflects or indeed contributes-and how-to the regulation of genome function remain to be elucidated. The observation in many species that 3D domains correlate strongly with the 1D epigenomic information along the genome suggests a dynamic coupling between chromatin organization and epigenetic regulation...
March 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29243911/neurodegenerative-disease-proteinopathies-are-connected-to-distinct-histone-post-translational-modification-landscapes
#18
Karen Chen, Seth A Bennett, Navin Rana, Huda Yousuf, Mohamed Said, Sadiqa Taaseen, Natalie Mendo, Steven M Meltser, Mariana P Torrente
Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) are devastating neurodegenerative diseases involving the progressive degeneration of neurons. No cure is available for patients diagnosed with these diseases. A prominent feature of both ALS and PD is the accumulation of protein inclusions in the cytoplasm of degenerating neurons; however, the particular proteins constituting these inclusions vary: the RNA-binding proteins TDP-43 and FUS are most notable in ALS, while α-synuclein aggregates into Lewy bodies in PD...
January 8, 2018: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29228701/a-systematic-assessment-of-chemical-genetic-and-epigenetic-factors-influencing-the-activity-of-anticancer-drug-kp1019-ffc14a
#19
Upendarrao Golla, Swati Swagatika, Sakshi Chauhan, Raghuvir Singh Tomar
KP1019 ([trans-RuCl4 (1H-indazole)2 ]; FFC14A) is one of the promising ruthenium-based anticancer drugs undergoing clinical trials. Despite the pre-clinical and clinical success of KP1019, the mode of action and various factors capable of modulating its effects are largely unknown. Here, we used transcriptomics and genetic screening approaches in budding yeast model and deciphered various genetic targets and plethora of cellular pathways including cellular signaling, metal homeostasis, vacuolar transport, and lipid homeostasis that are primarily targeted by KP1019...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29187422/dependency-of-heterochromatin-domains-on-replication-factors
#20
Leonie Johanna Jahn, Bethany Mason, Peter Brøgger, Tea Toteva, Dennis Kim Nielsen, Genevieve Thon
Chromatin structure regulates both genome expression and dynamics in eukaryotes, where large heterochromatic regions are epigenetically silenced through the methylation of histone H3K9, histone deacetylation, and the assembly of repressive complexes. Previous genetic screens with the fission yeast Schizosaccharomyces pombe have led to the identification of key enzymatic activities and structural constituents of heterochromatin. We report here on additional factors discovered by screening a library of deletion mutants for silencing defects at the edge of a heterochromatic domain bound by its natural boundary-the IR-R + element-or by ectopic boundaries...
February 2, 2018: G3: Genes—Genomes—Genetics
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