keyword
https://read.qxmd.com/read/37162912/fission-yeast-ck1-promotes-dna-double-strand-break-repair-through-both-homologous-recombination-and-non-homologous-end-joining
#21
Sierra N Cullati, Eric Zhang, Yufan Shan, Rodrigo X Guillen, Jun-Song Chen, Jose Navarrete-Perea, Zachary C Elmore, Liping Ren, Steven P Gygi, Kathleen L Gould
The CK1 family are conserved serine/threonine kinases with numerous substrates and cellular functions. The fission yeast CK1 orthologues Hhp1 and Hhp2 were first characterized as regulators of DNA repair, but the mechanism(s) by which CK1 activity promotes DNA repair had not been investigated. Here, we found that deleting Hhp1 and Hhp2 or inhibiting CK1 catalytic activities in yeast or in human cells activated the DNA damage checkpoint due to persistent double-strand breaks (DSBs). The primary pathways to repair DSBs, homologous recombination and non-homologous end joining, were both less efficient in cells lacking Hhp1 and Hhp2 activity...
April 28, 2023: bioRxiv
https://read.qxmd.com/read/37126401/loops-and-the-activity-of-loop-extrusion-factors-constrain-chromatin-dynamics
#22
JOURNAL ARTICLE
Mary Lou P Bailey, Ivan Surovtsev, Jessica F Williams, Hao Yan, Tianyu Yuan, Kevin Li, Katherine Duseau, Simon G J Mochrie, Megan C King
The chromosomes - DNA polymers and their binding proteins - are compacted into a spatially organized, yet dynamic, three-dimensional structure. Recent genome-wide chromatin conformation capture experiments reveal a hierarchical organization of the DNA structure that is imposed, at least in part, by looping interactions arising from the activity of loop extrusion factors. The dynamics of chromatin reflects the response of the polymer to a combination of thermal fluctuations and active processes. However, how chromosome structure and enzymes acting on chromatin together define its dynamics remains poorly understood...
April 26, 2023: Molecular Biology of the Cell
https://read.qxmd.com/read/37043046/an-essential-role-for-the-ino80-chromatin-remodeling-complex-in-regulation-of-gene-expression-during-cellular-quiescence
#23
JOURNAL ARTICLE
Yasaman Zahedi, Shengyuan Zeng, Karl Ekwall
Cellular quiescence is an important physiological state both in unicellular and multicellular eukaryotes. Quiescent cells are halted for proliferation and stop the cell cycle at the G0 stage. Using fission yeast as a model organism, we have previously found that several subunits of a conserved chromatin remodeling complex, Ino80C (INOsitol requiring nucleosome remodeling factor), are required for survival in quiescence. Here, we demonstrate that Ino80C has a key function in the regulation of gene expression in G0 cells...
April 12, 2023: Chromosome Research
https://read.qxmd.com/read/37039545/transcriptional-regulation-of-autophagy-by-chromatin-remodeling-complex-and-histone-variant
#24
JOURNAL ARTICLE
Xin Li, Shanshan Wang, Xilan Yu, Shanshan Li
Autophagy is a catabolic process to maintain homeostasis, and involved in cell differentiation and development. Autophagy is tightly regulated in response to nutrient availability but the underlying mechanism is not completely understood. Recently, we identified the chromatin remodeling complex INO80 (inositol-requiring mutant 80) and histone variant H2A.Z as new autophagy regulators and uncover how histone deacetylase Rpd3L (reduced potassium dependency 3 large) complex represses autophagy by deacetylating Ino80 and H2A...
April 13, 2023: Autophagy
https://read.qxmd.com/read/37031881/swi-snf-complexes-and-cancers
#25
REVIEW
Liyuan Wang, Jinglong Tang
Epigenetics refers to the study of genetic changes that can affect gene expression without altering the underlying DNA sequence, including DNA methylation, histone modification, chromatin remodelling, X chromosome inactivation and non-coding RNA regulation. Of these, DNA methylation, histone modification and chromatin remodelling constitute the three classical modes of epigenetic regulation. These three mechanisms alter gene transcription by adjusting chromatin accessibility, thereby affecting cell and tissue phenotypes in the absence of DNA sequence changes...
April 7, 2023: Gene
https://read.qxmd.com/read/37020028/establishment-and-function-of-chromatin-organization-at-replication-origins
#26
JOURNAL ARTICLE
Erika Chacin, Karl-Uwe Reusswig, Jessica Furtmeier, Priyanka Bansal, Leonhard A Karl, Boris Pfander, Tobias Straub, Philipp Korber, Christoph F Kurat
The origin recognition complex (ORC) is essential for initiation of eukaryotic chromosome replication as it loads the replicative helicase-the minichromosome maintenance (MCM) complex-at replication origins1 . Replication origins display a stereotypic nucleosome organization with nucleosome depletion at ORC-binding sites and flanking arrays of regularly spaced nucleosomes2-4 . However, how this nucleosome organization is established and whether this organization is required for replication remain unknown. Here, using genome-scale biochemical reconstitution with approximately 300 replication origins, we screened 17 purified chromatin factors from budding yeast and found that the ORC established nucleosome depletion over replication origins and flanking nucleosome arrays by orchestrating the chromatin remodellers INO80, ISW1a, ISW2 and Chd1...
April 5, 2023: Nature
https://read.qxmd.com/read/36951681/mcrs1-regulates-g2-m-transition-and-spindle-assembly-during-mouse-oocyte-meiosis
#27
JOURNAL ARTICLE
Jia-Qian Ju, Zhen-Nan Pan, Kun-Huan Zhang, Yi-Ming Ji, Jing-Cai Liu, Shao-Chen Sun
Microspherule protein 1 (Mcrs1) is a component of the nonspecific lethal (NSL) complex and the chromatin remodeling INO80 complex, which participates in transcriptional regulation during mitosis. Here, we investigate the roles of Mcrs1 during female meiosis in mice. We demonstrate that Mcrs1 is a novel regulator of the meiotic G2/M transition and spindle assembly in mouse oocytes. Mcrs1 is present in the nucleus and associates with spindle poles and chromosomes of oocytes during meiosis I. Depletion of Mcrs1 alters HDAC2-mediated H4K16ac, H3K4me2, and H3K9me2 levels in nonsurrounded nucleolus (NSN)-type oocytes, and reduces CDK1 activity and cyclin B1 accumulation, leading to G2/M transition delay...
March 23, 2023: EMBO Reports
https://read.qxmd.com/read/36888706/the-torc1-activates-rpd3l-complex-to-deacetylate-ino80-and-h2a-z-and-repress-autophagy
#28
JOURNAL ARTICLE
Xin Li, Qianyun Mei, Qi Yu, Min Wang, Fei He, Duncheng Xiao, Huan Liu, Feng Ge, Xilan Yu, Shanshan Li
Autophagy is a critical process to maintain homeostasis, differentiation, and development. How autophagy is tightly regulated by nutritional changes is poorly understood. Here, we identify chromatin remodeling protein Ino80 and histone variant H2A.Z as the deacetylation targets for histone deacetylase Rpd3L complex and uncover how they regulate autophagy in response to nutrient availability. Mechanistically, Rpd3L deacetylates Ino80 K929, which protects Ino80 from being degraded by autophagy. The stabilized Ino80 promotes H2A...
March 10, 2023: Science Advances
https://read.qxmd.com/read/36831199/atp-dependent-chromatin-remodellers-in-inner-ear-development
#29
REVIEW
Ilyas Chohra, Keshi Chung, Subhajit Giri, Brigitte Malgrange
During transcription, DNA replication and repair, chromatin structure is constantly modified to reveal specific genetic regions and allow access to DNA-interacting enzymes. ATP-dependent chromatin remodelling complexes use the energy of ATP hydrolysis to modify chromatin architecture by repositioning and rearranging nucleosomes. These complexes are defined by a conserved SNF2-like, catalytic ATPase subunit and are divided into four families: CHD, SWI/SNF, ISWI and INO80. ATP-dependent chromatin remodellers are crucial in regulating development and stem cell biology in numerous organs, including the inner ear...
February 7, 2023: Cells
https://read.qxmd.com/read/36711658/ino80-regulates-chromatin-accessibility-to-facilitate-meiotic-sex-chromosome-inactivation
#30
Prabuddha Chakraborty, Terry Magnuson
The INO80 protein is the main catalytic subunit of the INO80-chromatin remodeling complex, which is critical for DNA repair and transcription regulation in murine spermatocytes. In this study, we explored the role of INO80 in silencing genes on meiotic sex chromosomes. Robust INO80 immunolocalization at the XY body in pachytene spermatocytes suggested a role for INO80 in the meiotic sex body. Subsequent deletion of Ino80 resulted in high expression of sex-linked genes. Furthermore, the active form of RNA polymerase II at the sex body of Ino80 -null pachytene spermatocytes indicates incomplete meiotic sex chromosome inactivation (MSCI)...
January 5, 2023: bioRxiv
https://read.qxmd.com/read/36647799/coordinated-histone-variant-h2a-z-eviction-and-h3-3-deposition-control-plant-thermomorphogenesis
#31
JOURNAL ARTICLE
Fengyue Zhao, Mande Xue, Huairen Zhang, Hui Li, Ting Zhao, Danhua Jiang
Plants can sense temperature changes and adjust their development and morphology accordingly in a process called thermomorphogenesis. This phenotypic plasticity implies complex mechanisms regulating gene expression reprogramming in response to environmental alteration. Histone variants often associate with specific chromatin states, yet how their deposition/eviction modulates transcriptional changes induced by environmental cues remains elusive. In Arabidopsis thaliana, temperature elevation-induced transcriptional activation at thermo-responsive genes entails the chromatin eviction of a histone variant H2A...
January 17, 2023: New Phytologist
https://read.qxmd.com/read/36647159/small-molecule-modulators-of-chromatin-remodeling-from-neurodevelopment-to-neurodegeneration
#32
REVIEW
Dongfang Jiang, Tingting Li, Caixia Guo, Tie-Shan Tang, Hongmei Liu
The dynamic changes in chromatin conformation alter the organization and structure of the genome and further regulate gene transcription. Basically, the chromatin structure is controlled by reversible, enzyme-catalyzed covalent modifications to chromatin components and by noncovalent ATP-dependent modifications via chromatin remodeling complexes, including switch/sucrose nonfermentable (SWI/SNF), inositol-requiring 80 (INO80), imitation switch (ISWI) and chromodomain-helicase DNA-binding protein (CHD) complexes...
January 16, 2023: Cell & Bioscience
https://read.qxmd.com/read/36563143/actr5-controls-cdkn2a-and-tumor-progression-in-an-ino80-independent-manner
#33
JOURNAL ARTICLE
Xiaobao Xu, Anthony K N Chan, Mingli Li, Qiao Liu, Nicole Mattson, Sheela Pangeni Pokharel, Wen-Han Chang, Yate-Ching Yuan, Jinhui Wang, Roger E Moore, Patrick Pirrotte, Jun Wu, Rui Su, Markus Müschen, Steven T Rosen, Jianjun Chen, Lu Yang, Chun-Wei Chen
Epigenetic dysregulation of cell cycle is a hallmark of tumorigenesis in multiple cancers, including hepatocellular carcinoma (HCC). Nonetheless, the epigenetic mechanisms underlying the aberrant cell cycle signaling and therapeutic response remain unclear. Here, we used an epigenetics-focused CRISPR interference screen and identified ACTR5 (actin-related protein 5), a component of the INO80 chromatin remodeling complex, to be essential for HCC tumor progression. Suppression of ACTR5 activated CDKN2A expression, ablated CDK/E2F-driven cell cycle signaling, and attenuated HCC tumor growth...
December 23, 2022: Science Advances
https://read.qxmd.com/read/36499727/ino80-is-required-for-the-cell-cycle-control-survival-and-differentiation-of-mouse-escs-by-transcriptional-regulation
#34
JOURNAL ARTICLE
Seonho Yoo, Eun Joo Lee, Nguyen Xuan Thang, Hyeonwoo La, Hyeonji Lee, Chanhyeok Park, Dong Wook Han, Sang Jun Uhm, Hyuk Song, Jeong Tae Do, Youngsok Choi, Kwonho Hong
Precise regulation of the cell cycle of embryonic stem cells (ESCs) is critical for their self-maintenance and differentiation. The cell cycle of ESCs differs from that of somatic cells and is different depending on the cell culture conditions. However, the cell cycle regulation in ESCs via epigenetic mechanisms remains unclear. Here, we showed that the ATP-dependent chromatin remodeler Ino80 regulates the cell cycle genes in ESCs under primed conditions. Ino80 loss led to a significantly extended length of the G1-phase in ESCs grown under primed culture conditions...
December 6, 2022: International Journal of Molecular Sciences
https://read.qxmd.com/read/36490333/structural-mechanism-of-extranucleosomal-dna-readout-by-the-ino80-complex
#35
JOURNAL ARTICLE
Franziska Kunert, Felix J Metzner, James Jung, Markus Höpfler, Stephan Woike, Kevin Schall, Dirk Kostrewa, Manuela Moldt, Jia-Xuan Chen, Susanne Bantele, Boris Pfander, Sebastian Eustermann, Karl-Peter Hopfner
The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding...
December 9, 2022: Science Advances
https://read.qxmd.com/read/36430148/the-emerging-role-of-chromatin-remodeling-complexes-in-ovarian-cancer
#36
REVIEW
Ieva Vaicekauskaitė, Rasa Sabaliauskaitė, Juozas Rimantas Lazutka, Sonata Jarmalaitė
Ovarian cancer (OC) is the fifth leading cause of women's death from cancers. The high mortality rate is attributed to the late presence of the disease and the lack of modern diagnostic tools, including molecular biomarkers. Moreover, OC is a highly heterogeneous disease, which contributes to early treatment failure. Thus, exploring OC molecular mechanisms could significantly enhance our understanding of the disease and provide new treatment options. Chromatin remodeling complexes (CRCs) are ATP-dependent molecular machines responsible for chromatin reorganization and involved in many DNA-related processes, including transcriptional regulation, replication, and reparation...
November 8, 2022: International Journal of Molecular Sciences
https://read.qxmd.com/read/36359878/identification-of-the-telomere-elongation-mutation-in-drosophila
#37
JOURNAL ARTICLE
Hemakumar M Reddy, Thomas A Randall, Francesca Cipressa, Antonella Porrazzo, Giovanni Cenci, Radmila Capkova Frydrychova, James M Mason
Telomeres in Drosophila melanogaster , which have inspired a large part of Sergio Pimpinelli work, are similar to those of other eukaryotes in terms of their function. Yet, their length maintenance relies on the transposition of the specialized retrotransposons Het-A , TART , and TAHRE , rather than on the activity of the enzyme telomerase as it occurs in most other eukaryotic organisms. The length of the telomeres in Drosophila thus depends on the number of copies of these transposable elements. Our previous work has led to the isolation of a dominant mutation, Tel1 , that caused a several-fold elongation of telomeres...
November 3, 2022: Cells
https://read.qxmd.com/read/36348125/nuclear-actin-dynamics-in-gene-expression-dna-repair-and-cancer
#38
JOURNAL ARTICLE
Yuanjian Huang, Shengzhe Zhang, Jae-Il Park
Actin is a highly conserved protein in mammals. The actin dynamics is regulated by actin-binding proteins and actin-related proteins. Nuclear actin and these regulatory proteins participate in multiple nuclear processes, including chromosome architecture organization, chromatin remodeling, transcription machinery regulation, and DNA repair. It is well known that the dysfunctions of these processes contribute to the development of cancer. Moreover, emerging evidence has shown that the deregulated actin dynamics is also related to cancer...
2022: Results and Problems in Cell Differentiation
https://read.qxmd.com/read/36140716/genome-wide-association-study-of-parasite-resistance-to-gastrointestinal-nematodes-in-corriedale-sheep
#39
JOURNAL ARTICLE
Beatriz Carracelas, Elly A Navajas, Brenda Vera, Gabriel Ciappesoni
Selection of genetically resistant animals is one alternative to reduce the negative impact of gastrointestinal nematodes (GIN) on sheep production. The aim of this study was to identify genomic regions associated with GIN resistance in Corriedale sheep by single-step genome-wide association studies (ssGWAS) using 170, 507 and 50K single nucleotide polymorphisms (SNPs). Analysis included 19,547 lambs with faecal egg counts (FEC) records, a pedigree file of 40,056 animals and 454, 711 and 383 genotypes from 170, 507 and 50K SNPs, respectively...
August 27, 2022: Genes
https://read.qxmd.com/read/36121211/microarray-and-in-silico-analysis-of-dna-repair-genes-between-human-testis-of-patients-with-nonobstructive-azoospermia-and-normal-cells
#40
JOURNAL ARTICLE
Danial Hashemi Karoii, Hossein Azizi, Thomas Skutella
DNA repair processes are critical to maintaining genomic integrity. As a result, dysregulation of repair genes is likely to be linked with health implications, such as an increased prevalence of infertility and an accelerated rate of aging. We evaluated all the DNA repair genes (322 genes) by microarray. This study has provided insight into the connection between DNA repair genes, including RAD23B, OBFC2A, PMS1, UBE2V1, ERCC5, SMUG1, RFC4, PMS2L5, MMS19, SHFM1, INO80, PMS2L1, CHEK2, TRIP13, and POLD4. The microarray analysis of six human cases with different nonobstructive azoospermia revealed that RAD23B, OBFC2A, PMS1, UBE2V1, ERCC5, SMUG1, RFC4, PMS2L5, MMS19, SHFM1, and INO80 were upregulated, and expression of PMS2L1, CHEK2, TRIP13, and POLD4 was downregulated versus the normal case...
September 19, 2022: Cell Biochemistry and Function
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