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https://www.readbyqxmd.com/read/28441589/nutrient-stress-induced-chromatin-changes-in-plants
#1
REVIEW
David Secco, James Whelan, Hatem Rouached, Ryan Lister
The ability of plants to appropriately respond to the soil nutrient availability is of primary importance for their development and to complete their life cycle. Deciphering these multifaceted adaptive mechanisms remains a major challenge for scientists to date. Recent technological breakthroughs now enable to assess the dynamism and complexity of these processes at unprecedented resolution. In this review, we present some of the most recent findings on the involvement of histone modifications, histone variants and DNA methylation in response to nutrient stresses as well as discussing the potential roles these chromatin changes could serve as priming or as trans-generational stress memory mechanisms...
April 22, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28441415/pax7-remodels-the-chromatin-landscape-in-skeletal-muscle-stem-cells
#2
Karin C Lilja, Nan Zhang, Alessandro Magli, Volkan Gunduz, Christopher J Bowman, Robert W Arpke, Radbod Darabi, Michael Kyba, Rita Perlingeiro, Brian D Dynlacht
Pluripotent stem cells (PSC) hold great promise for the treatment of human skeletal muscle diseases. However, it remains challenging to convert PSC to skeletal muscle cells, and the mechanisms by which the master regulatory transcription factor, Pax7, promotes muscle stem (satellite) cell identity are not yet understood. We have taken advantage of PSC-derived skeletal muscle precursor cells (iPax7), wherein the induced expression of Pax7 robustly initiates the muscle program and enables the in vitro generation of precursors that seed the satellite cell compartment upon transplantation...
2017: PloS One
https://www.readbyqxmd.com/read/28441353/matrix-metalloproteinase-gene-activation-resulting-from-disordred-epigenetic-mechanisms-in-rheumatoid-arthritis
#3
REVIEW
Yasuto Araki, Toshihide Mimura
Matrix metalloproteinases (MMPs) are implicated in the degradation of extracellular matrix (ECM). Rheumatoid arthritis (RA) synovial fibroblasts (SFs) produce matrix-degrading enzymes, including MMPs, which facilitate cartilage destruction in the affected joints in RA. Epigenetic mechanisms contribute to change in the chromatin state, resulting in an alteration of gene transcription. Recently, MMP gene activation has been shown to be caused in RASFs by the dysregulation of epigenetic changes, such as histone modifications, DNA methylation, and microRNA (miRNA) signaling...
April 25, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28441146/epigenetic-regulation-of-glucose-metabolism
#4
Sapna Sharma, Jennifer Kriebel, Harald Grallert
PURPOSE OF REVIEW: Glucose metabolism is a central process in mammalian energy homeostasis. Its deregulation is a key factor in development of metabolic disease like diabetes and cancer. In recent decades, our understanding of gene regulation at the signaling, chromatin and posttranscriptional levels has seen dramatic developments. RECENT FINDINGS: A number of epigenetic mechanisms that do not affect the genetic code can be assessed with new technologies. However, increasing complexity becomes a major challenge for translation into clinical application...
April 24, 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/28440894/chromatin-sumoylation-in-heat-stress-to-protect-pause-and-organise-sumo-stress-response-on-chromatin
#5
REVIEW
Einari A Niskanen, Jorma J Palvimo
Post-translational modifications, e.g. SUMO modifications (SUMOylation), provide a mechanism for swiftly changing a protein's activity. Various stress conditions trigger a SUMO stress response (SSR) - a stress-induced rapid change in the conjugation of SUMO to multiple proteins, which predominantly targets nuclear proteins. The SSR has been postulated to protect stressed cells by preserving the functionality of crucial proteins. However, it is unclear how it exerts its protective functions. Interestingly, heat stress (HS) increases SUMOylation of proteins at active promoters and enhancers...
April 25, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28440495/relationship-between-epigenetic-changes-in-wnt-antagonists-and-acute-leukemia
#6
Hua-Rong Zhou, Hai-Ying Fu, Dan-Sen Wu, Yuan-Yuan Zhang, Si-Han Huang, Cong-Jie Chen, Jian-Guo Yan, Jin-Long Huang, Jian-Zhen Shen
The present study was designed to investigate the relationship among epigenetic changes in Wnt antagonists, histone H4K20me1 and the expression of tumor-suppressor genes in acute leukemia (AL) to better understand the pathogenesis of leukemia. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to detect messenger RNA (mRNA) expression levels of Wnt antagonists (Wnt5a, HDPR1, DKK1 and DKK3) in patients with AL and in normal controls; pyrophosphate sequencing was performed to detect the methylation status of the Wnt5a promoter; and western blotting was performed to detect the overall expression levels of Wnt5a protein and histone H4K20me1 in patients with acute myeloid leukemia (AML) and in normal controls...
May 2017: Oncology Reports
https://www.readbyqxmd.com/read/28440397/hypermethylation-of-mirna-589-promoter-leads-to-upregulation-of-hdac5-which-promotes-malignancy-in-non-small-cell-lung-cancer
#7
Changhong Liu, Desheng Lv, Mo Li, Xuefei Zhang, Ge Sun, Yu Bai, Dongmin Chang
Histone deacetylases (HDACs) are crucial for regulating chromatin activity, which plays a critical role in cell proliferation, differentiation, and apoptosis of various cancers. Therefore, HDAC inhibitors have been applied as effective therapeutic agents for cancer treatment. However, the expression profiles and regulatory mechanisms of histone deacetylases in lung cancer are not well understood. In the present study, aberrant high levels of HDAC5 were observed in non-small cell lung cancer (NSCLC) and further analysis indicated a negative relationship between HDAC5 and a tumor suppressor, miR‑589‑5p, in NSCLC specimens...
April 20, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28440310/klf5-mediates-odontoblastic-differentiation-through-regulating-dentin-specific-extracellular-matrix-gene-expression-during-mouse-tooth-development
#8
Zhuo Chen, Qi Zhang, Han Wang, Wentong Li, Feng Wang, Chunyan Wan, Shuli Deng, Hui Chen, Yixin Yin, Xiaoyan Li, Zhijian Xie, Shuo Chen
Klf5, a member of the Krüppel-like transcription factor family, has essential roles during embryonic development, cell proliferation, differentiation, migration and apoptosis. This study was to define molecular mechanism of Klf5 during the odontoblastic differentiation. The expression of Klf5, odontoblast-differentiation markers, Dspp and Dmp1 was co-localized in odontoblastic cells at different stages of mouse tooth development and mouse dental papilla mesenchymal cells. Klf5 was able to promote odontoblastic differentiation and enhance mineral formation of mouse dental papilla mesenchymal cells...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28440295/kdm3-epigenetically-controls-tumorigenic-potentials-of-human-colorectal-cancer-stem-cells-through-wnt-%C3%AE-catenin-signalling
#9
Jiong Li, Bo Yu, Peng Deng, Yingduan Cheng, Yongxin Yu, Kareena Kevork, Sivakumar Ramadoss, Xiangming Ding, Xinmin Li, Cun-Yu Wang
Human colorectal cancer stem cells (CSCs) are tumour initiating cells that can self-renew and are highly tumorigenic and chemoresistant. While genetic mutations associated with human colorectal cancer development are well-known, little is known about how and whether epigenetic factors specifically contribute to the functional properties of human colorectal CSCs. Here we report that the KDM3 family of histone demethylases plays an important role in tumorigenic potential and survival of human colorectal CSCs by epigenetically activating Wnt target gene transcription...
April 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28439859/genome-wide-profiling-of-histone-modifications-and-histone-variants-in-arabidopsis-thaliana-and-marchantia-polymorpha
#10
Ramesh Yelagandula, Akihisa Osakabe, Elin Axelsson, Frederic Berger, Tomokazu Kawashima
Histone modifications and histone variants barcode the genome and play major roles in epigenetic regulations. Chromatin immunoprecipitation (ChIP) coupled with next-generation sequencing (NGS) is a well-established method to investigate the landscape of epigenetic marks at a genomic level. Here, we describe procedures for conducting ChIP, subsequent NGS library construction, and data analysis on histone modifications and histone variants in Arabidopsis thaliana. We also describe an optimized nuclear isolation procedure to prepare chromatin for ChIP in the liverwort, Marchantia polymorpha, which is the emerging model plant ideal for evolutionary studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439570/epigenomics-of-human-cd8-t-cell-differentiation-and-aging
#11
David M Moskowitz, David W Zhang, Bin Hu, Sabine Le Saux, Rolando E Yanes, Zhongde Ye, Jason D Buenrostro, Cornelia M Weyand, William J Greenleaf, Jörg J Goronzy
The efficacy of the adaptive immune response declines dramatically with age, but the cell-intrinsic mechanisms driving immune aging in humans remain poorly understood. Immune aging is characterized by a loss of self-renewing naïve cells and the accumulation of differentiated but dysfunctional cells within the CD8 T cell compartment. Using ATAC-seq, we inferred the transcription factor binding activities correlated with naive and central and effector memory CD8 T cell states in young adults. Integrating our results with RNA-seq, we identified transcription networks associated with CD8 T cell differentiation, with prominent roles implicated for BATF, ETS1, Eomes, and Sp1...
February 2017: Science Immunology
https://www.readbyqxmd.com/read/28438793/brassinosteroid-biosynthesis-is-modulated-via-a-transcription-factor-cascade-of-cog1-pif4-and-pif5
#12
Zhuoyun Wei, Tong Yuan, Danuše Tarkowská, Jeongsik Kim, Hong Gil Nam, Ondřej Novák, Kai He, Xiaoping Gou, Jia Li
Brassinosteroids (BRs) are essential phytohormones regulating various developmental and physiological processes during normal growth and development. cog1-3D (cogwheel 1-3D) was identified as an activation-tagged genetic modifier of bri1-5, an intermediate BR receptor mutant. COG1 encodes a Dof-type transcription factor previously found to act as a negative regulator of the phytochrome signaling pathway. cog1-3D single mutants show an elongated hypocotyl phenotype under light conditions. Loss-of-function by ethylmethanoesulfonate (EMS) mutation or inducible expression of a dominant-negative form of COG1 results in an opposite phenotype...
April 24, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28438634/structural-insights-into-baf47-and-baf155-complex-formation
#13
Li Yan, Si Xie, Yongming Du, Chengmin Qian
Mammalian BAF complexes are a subfamily of SWI/SNF ATP-dependent chromatin remodelers that dynamically modulate chromatin structure to regulate fundamental cellular processes including gene transcription, cell cycle control and DNA damage response. So far many distinct BAF complexes have been identified with polymorphic assemblies of up to 15 subunits from 29 genes. The evolutionarily conserved BRG1/BRM, BAF47 and BAF155/BAF170 form a stable complex that carries out essential chromatin remodeling activity and therefore have been regarded as the core components of BAF complex...
April 21, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28438576/arabidopsis-mads-box-transcription-factor-agl21-acts-as-environmental-surveillance-for-seed-germination-by-regulating-abi5-expression
#14
Lin-Hui Yu, Jie Wu, Zi-Sheng Zhang, Zi-Qing Miao, Ping-Xia Zhao, Zhen Wang, Cheng-Bin Xiang
Seed germination is a crucial checkpoint for plant survival under unfavorable environmental conditions. Abscisic acid (ABA) and its signaling play a vital role in integrating environmental information to regulate seed germination. MCM1/AGAMOUS/DEFICIENS/SRF (MADS)-box transcription factors are mainly known as key regulators of seed and flower development in Arabidopsis. However, little is known about their functions in seed germination. Here we report that MADS-box transcription factor AGL21 negatively modulates seed germination and post-germination growth by controlling the expression of ABA-INSENSITIVE 5 (ABI5) in Arabidopsis...
April 21, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28438565/improvements-in-oocyte-competence-in-superovulated-mice-following-treatment-with-cilostazol-ovulation-of-immature-oocytes-with-high-developmental-rates
#15
Ahmed M Taiyeb, Saeeda A Muhsen-Alanssari, William L Dees, Jill Hiney, Michael E Kjelland, Duane C Kraemer, Mundhir T Ridha-Albarzanchi
Exogenous administration of superovulatory hormones negatively affects oocyte competence in mammals. Phosphodiesterase 3A inhibitors were found to improve competence of oocytes matured in vitro in several species, including humans. This study was therefore designed to define oocyte maturation synchronization and competence in superovulated mice treated with cilostazol, a selective phosphodiesterase 3A inhibitor. Swiss Webster mice were superovulated and treated orally with 7.5mg cilostazol once or twice to result in ovulation of immature oocytes at the metaphase I (MI) or germinal vesicle (GV) stage, respectively...
April 21, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28438527/the-baf-brg1-brm-associated-factor-chromatin-remodeling-complex-exhibits-ethanol-sensitivity-in-fetal-neural-progenitor-cells-and-regulates-transcription-at-the-mir-9-2-encoding-gene-locus
#16
Sasha G Burrowes, Nihal A Salem, Alexander M Tseng, Sridevi Balaraman, Marisa R Pinson, Cadianna Garcia, Rajesh C Miranda
Fetal alcohol spectrum disorders are a leading cause of intellectual disability worldwide. Previous studies have shown that developmental ethanol exposure results in loss of microRNAs (miRNAs), including miR-9, and loss of these miRNAs, in turn, mediates some of ethanol's teratogenic effects in the developing brain. We previously found that ethanol increased methylation at the miR-9-2 encoding gene locus in mouse fetal neural stem cells (NSC), advancing a mechanism for epigenetic silencing of this locus and consequently, miR-9 loss in NSCs...
April 7, 2017: Alcohol
https://www.readbyqxmd.com/read/28438174/exercise-attenuates-neurological-deficits-by-stimulating-a-critical-hsp70-nf-%C3%AE%C2%BAb-il-6-synapsin-i-axis-in-traumatic-brain-injury-rats
#17
Chung-Ching Chio, Hung-Jung Lin, Yu-Feng Tian, Yu-Chieh Chen, Mao-Tsun Lin, Cheng-Hsien Lin, Ching-Ping Chang, Chien-Chin Hsu
BACKGROUND: Despite previous evidence for a potent inflammatory response after a traumatic brain injury (TBI), it is unknown whether exercise preconditioning (EP) improves outcomes after a TBI by modulating inflammatory responses. METHODS: We performed quantitative real-time PCR (qPCR) to quantify the genes encoding 84 cytokines and chemokines in the peripheral blood and used ELISA to determine both the cerebral and blood levels of interleukin-6 (IL-6). We also performed the chromatin immunoprecipitation (ChIP) assay to evaluate the extent of nuclear factor kappa-B (NF-κB) binding to the DNA elements in the IL-6 promoter regions...
April 24, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28437481/firemaster%C3%A2-550-and-its-components-isopropylated-triphenyl-phosphate-and-triphenyl-phosphate-enhance-adipogenesis-and-transcriptional-activity-of-peroxisome-proliferator-activated-receptor-ppar%C3%AE-on-the-adipocyte-protein-2-ap2-promoter
#18
Emily W Y Tung, Shaimaa Ahmed, Vian Peshdary, Ella Atlas
Firemaster® 550 (FM550) is a chemical mixture currently used as an additive flame retardant in commercial products, and is comprised of 2-ethylhexyl-2,3,4,5-tertrabromobenzoate (TBB), bis(2-ethylhexyl) tetrabromophthalate (TBPH), triphenyl phosphate (TPP), and isopropylated triphenyl phosphate (IPTP). Animal and in vitro studies suggest that FM550, TPP and IPTP may have adipogenic effects and may exert these effects through PPARγ activation. Using murine 3T3-L1 preadipocytes, we investigated the detailed expression of transcription factors and adipogenic markers in response to FM550 and its components...
2017: PloS One
https://www.readbyqxmd.com/read/28436983/stable-polycomb-dependent-transgenerational-inheritance-of-chromatin-states-in-drosophila
#19
Filippo Ciabrelli, Federico Comoglio, Simon Fellous, Boyan Bonev, Maria Ninova, Quentin Szabo, Anne Xuéreb, Christophe Klopp, Alexei Aravin, Renato Paro, Frédéric Bantignies, Giacomo Cavalli
Transgenerational epigenetic inheritance (TEI) describes the transmission of alternative functional states through multiple generations in the presence of the same genomic DNA sequence. Very little is known about the principles and the molecular mechanisms governing this type of inheritance. Here, by transiently enhancing 3D chromatin interactions, we established stable and isogenic Drosophila epilines that carry alternative epialleles, as defined by differential levels of Polycomb-dependent trimethylation of histone H3 Lys27 (forming H3K27me3)...
April 24, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28436955/vitamin-a-mediates-conversion-of-monocyte-derived-macrophages-into-tissue-resident-macrophages-during-alternative-activation
#20
Uma Mahesh Gundra, Natasha M Girgis, Michael A Gonzalez, Mei San Tang, Hendrik J P Van Der Zande, Jian-Da Lin, Mireille Ouimet, Lily J Ma, Jordan Poles, Nikollaq Vozhilla, Edward A Fisher, Kathryn J Moore, P'ng Loke
It remains unclear whether activated inflammatory macrophages can adopt features of tissue-resident macrophages, or what mechanisms might mediate such a phenotypic conversion. Here we show that vitamin A is required for the phenotypic conversion of interleukin 4 (IL-4)-activated monocyte-derived F4/80(int)CD206(+)PD-L2(+)MHCII(+) macrophages into macrophages with a tissue-resident F4/80(hi)CD206(-)PD-L2(-)MHCII(-)UCP1(+) phenotype in the peritoneal cavity of mice and during the formation of liver granulomas in mice infected with Schistosoma mansoni...
April 24, 2017: Nature Immunology
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