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https://www.readbyqxmd.com/read/29052191/histone-h1-purification-and-post-translational-modification-profiling-by-high-resolution-mass-spectrometry
#1
Maciej Kotliński, Andrzej Jerzmanowski
It has proven particularly difficult to purify Linker (H1) histones from the model plant Arabidopsis thaliana. This is most likely due to its low nuclear DNA content and the abundance of substances that interfere with protein isolation. These problems have hindered the use of Arabidopsis for in-depth characterization of nuclear proteins by modern techniques based on mass spectrometry (MS). Here, we describe an improved methodology for preparing pure Arabidopsis H1s and separating them by HPLC into fractions corresponding to nonallelic variants...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052186/a-rapid-and-efficient-chip-protocol-to-profile-chromatin-binding-proteins-and-epigenetic-modifications-in-arabidopsis
#2
Bénédicte Desvoyes, Zaida Vergara, Joana Sequeira-Mendes, Sofia Madeira, Crisanto Gutierrez
Chromatin immunoprecipitation (ChIP) is a widely used and very powerful procedure to identify the proteins that are associated with the DNA to regulate developmental processes. These proteins can be transcription factors, or specific histone variants and modified histones, which are all crucial for gene regulation. In order to obtain reliable results, ChIP must be carried out under highly reproducible conditions. Here, we describe a simple and fast ChIP protocol adapted for Arabidopsis seedlings, which can serve as a basis for other species, organs or more sophisticated procedures, such as the sequential ChIP...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29045007/chromatin-remodeling-factor-osino80-is-involved-in-regulation-of-gibberellin-biosynthesis-and-is-crucial-for-rice-plant-growth-and-development
#3
Chao Li, Yuhao Liu, Wen-Hui Sun, Yu Yu, Aiwu Dong
The phytohormone gibberellin (GA) plays essential roles in plant growth and development. Here, we report that OsINO80, a conserved ATP-dependent chromatin-remodeling factor in rice (Oryza sativa), functions in diverse biological processes and GA biosynthesis. OsINO80-knockdown mutants, derived from either T-DNA insertion or RNA interference, display typical GA-deficient phenotypes, including dwarfism, reduced cell length, late flowering, retarded seed germination and impaired reproductive development. Consistently, transcriptome analyses reveal that OsINO80 knockdown results in down-regulation by more than two-fold of over 1000 genes, including the GA biosynthesis genes CPS1 and GA3ox2, and the dwarf phenotype of OsINO80-knockdown mutants can be rescued by the application of exogenous GA3...
October 17, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/29044188/the-histone-variant-h3-3-g34w-substitution-in-giant-cell-tumor-of-the-bone-link-chromatin-and-rna-processing
#4
Jinyeong Lim, Joo Hyun Park, Annika Baude, Yeongran Yoo, Yeon Kyu Lee, Christopher R Schmidt, Jong Bae Park, Jörg Fellenberg, Josef Zustin, Florian Haller, Irene Krücken, Hyun Guy Kang, Yoon Jung Park, Christoph Plass, Anders M Lindroth
While transcription as regulated by histones and their post-translational modifications has been well described, the function of histone variants in this process remains poorly characterized. Potentially important insight into this process pertain to the frequently occurring mutations of H3.3, leading to G34 substitutions in childhood glioblastoma and giant cell tumor of the bone (GCTB). In this study, we have established primary cell lines from GCTB patients and used them to uncover the influence of H3.3 G34W substitutions on cellular growth behavior, gene expression, and chromatin compaction...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29036702/a-hyperdynamic-h3-3-nucleosome-marks-promoter-regions-in-pluripotent-embryonic-stem-cells
#5
Sharon Schlesinger, Binyamin Kaffe, Shai Melcer, Jose D Aguilera, Divya M Sivaraman, Tommy Kaplan, Eran Meshorer
Histone variants and their chaperones are key regulators of eukaryotic transcription, and are critical for normal development. The histone variant H3.3 has been shown to play important roles in pluripotency and differentiation, and although its genome-wide patterns have been investigated, little is known about the role of its dynamic turnover in transcriptional regulation. To elucidate the role of H3.3 dynamics in embryonic stem cell (ESC) biology, we generated mouse ESC lines carrying a single copy of a doxycycline (Dox)-inducible HA-tagged version of H3...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036442/global-inhibition-of-transcription-causes-an-increase-in-histone-h2a-z-incorporation-within-gene-bodies
#6
Anahita Lashgari, Jean-François Millau, Pierre-Étienne Jacques, Luc Gaudreau
H2A.Z histone variant is an important regulator of gene transcription, which is enriched at regulatory regions but is also found within gene bodies. Recent evidence suggests that active recruitment of H2A.Z within gene bodies is required to induce gene repression. In contrast to this view, we show that global inhibition of transcription results in H2A.Z accumulation at gene transcription start sites, as well as within gene bodies. Our results indicate that accumulation of H2A.Z within repressed genes can also be a consequence of the repression of gene transcription rather than an active mechanism required to establish the repression...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29035139/novel-17-bp-deletion-in-kdm1b-gene-is-significantly-associated-with-testis-weight-in-male-piglet
#7
Yang Cui, Tao Hu, Rui Chen, Shuai Yu, Wuzi Dong, Xiaoyan Lv, Chuanying Pan
Lysine-specific demethylase 1B (KDM1B) which plays a crucial role in regulating methylation status at lysine 4 of histone 3 is important for male fertility. The aim of this study was to explore the KDM1B mRNA expression profiles and to identify novel genetic variants of the pig KDM1B gene, as well as to determine the association between these variants and testis measurement traits in male piglets. The KDM1B mRNA expression profiles indicated that this gene widely expressed in all tested organs. In addition, a novel 17-bp deletion (NC_010449...
October 16, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/29034626/-sequence-analysis-and-expression-patterns-of-histone-h2a-variants-in-phytophthora-infestans
#8
Xiaowen Wang, Liyun Guo
In eukaryotic cells, DNA is packaged inside the nucleus together with histones to form nucleosomes. Each histone molecule contains two of each core histone subunits H2A, H2B, H3 and H4. Among core histones, the H2A family is of great interest due to the high diversity of specialized variants. These variants have shown important role in critical cellular processes. Epigenetic mechanism in oomycetes is barely known. Phytophthora infestans is a severe pathogen and a model species in oomycetes. In this study, we studied the sequence and expression pattern of H2A variants of P...
November 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29023412/post-translational-modification-of-human-histone-by-wide-tolerance-of-acetylation
#9
Cuiling Li, Han-Pil Choi, Xiaoyue Wang, Fei Wu, Xinjun Chen, Xin Lü, Ruirui Jing, Hoon Ryu, Xingyuan Wang, Kazem M Azadzoi, Jing-Hua Yang
Histone acetylation adds an acetyl group on the lysine residue commonly found within the N-terminal tail protruding from the histone core of the nucleosome, and is important for chromosome structure and function in gene transcription and chromatin remodeling. Acetylation may also occur on other residues additional to lysine, but have not been thoroughly investigated at the proteomics level. Here we report a wide tolerance acetylation study mimicking the addition of 42 ± 0.5 Da delta mass modification on undefined amino acid residues of histones by shotgun proteomics using liquid chromatography-tandem mass spectrometry...
October 12, 2017: Cells
https://www.readbyqxmd.com/read/29021892/catching-global-interactions-in-vivo
#10
Yi Qiu, Suming Huang
Histone proteins and transcription factors (TFs) play critical roles in gene transcription and development of multicellular organisms. Although antibody mediated protein isolation couple with mass spectrometry approach has been a standard method to identify TF interacting partners and characterize their functional molecular complexes, it becomes urge to develop a robust method to functional characterize how these transcription factors act during biological process in the post-human genome project era. Here, Dr...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/29016894/diffuse-high-grade-gliomas-with-h3-k27m-mutations-carry-a-dismal-prognosis-independent-of-tumor-location
#11
Michael Karremann, Gerrit H Gielen, Marion Hoffmann, Maria Wiese, Niclas Colditz, Monika Warmuth-Metz, Brigitte Bison, Alexander Claviez, Dannis G van Vuurden, André O von Bueren, Marco Gessi, Ingrid Kühnle, Volkmar H Hans, Martin Benesch, Dominik Sturm, Rolf-Dieter Kortmann, Andreas Waha, Torsten Pietsch, Christof M Kramm
Background: The novel entity of "diffuse midline glioma, H3 K27M-mutant" has been defined in the 2016 revision of the World Health Organization (WHO) classification of tumors of the central nervous system (CNS). Tumors of this entity arise in CNS midline structures of predominantly pediatric patients and are associated with an overall dismal prognosis. They are defined by K27M mutations in H3F3A or HIST1H3B/C, encoding for histone 3 variants H3.3 and H3.1, respectively, which are considered hallmark events driving gliomagenesis...
August 4, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28992292/macroh2a1-1-cooperates-with-ezh2-to-promote-adipogenesis-by-regulating-wnt-signaling
#12
Danyang Wan, Chengyu Liu, Y Sun, Wenjun Wang, Kun Huang, Ling Zheng
White adipocytes play important roles in many physiological processes, including energy storage, endocrine signaling, and inflammatory responses. Understanding the molecular mechanisms of adipocyte formation (adipogenesis) provides insights into therapeutic approaches against obesity and its related diseases. Many transcriptional factors and epigenetic enzymes are known to regulate adipogenesis; however, whether histone variants play a role in this process is unknown. Here we found that macroH2A1.1 (mH2A1.1), a variant of histone H2A, was upregulated during adipocyte differentiation in 3T3-L1 cells and in the white adipose tissue of obese mice...
August 1, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28991266/macroh2a1-1-regulates-mitochondrial-respiration-by-limiting-nuclear-nad-consumption
#13
Melanija Posavec Marjanović, Sarah Hurtado-Bagès, Maximilian Lassi, Vanesa Valero, Roberto Malinverni, Hélène Delage, Miriam Navarro, David Corujo, Iva Guberovic, Julien Douet, Pau Gama-Perez, Pablo M Garcia-Roves, Ivan Ahel, Andreas G Ladurner, Oscar Yanes, Philippe Bouvet, Mònica Suelves, Raffaele Teperino, J Andrew Pospisilik, Marcus Buschbeck
Histone variants are structural components of eukaryotic chromatin that can replace replication-coupled histones in the nucleosome. The histone variant macroH2A1.1 contains a macrodomain capable of binding NAD(+)-derived metabolites. Here we report that macroH2A1.1 is rapidly induced during myogenic differentiation through a switch in alternative splicing, and that myotubes that lack macroH2A1.1 have a defect in mitochondrial respiratory capacity. We found that the metabolite-binding macrodomain was essential for sustained optimal mitochondrial function but dispensable for gene regulation...
October 9, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28985495/mendelian-randomization-analysis-identifies-cpg-sites-as-putative-mediators-for-genetic-influences-on-cardiovascular-disease-risk
#14
Tom G Richardson, Jie Zheng, George Davey Smith, Nicholas J Timpson, Tom R Gaunt, Caroline L Relton, Gibran Hemani
The extent to which genetic influences on cardiovascular disease risk are mediated by changes in DNA methylation levels has not been systematically explored. We developed an analytical framework that integrates genetic fine mapping and Mendelian randomization with epigenome-wide association studies to evaluate the causal relationships between methylation levels and 14 cardiovascular disease traits. We identified ten genetic loci known to influence proximal DNA methylation which were also associated with cardiovascular traits after multiple-testing correction...
October 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28982979/a-simple-and-versatile-system-for-the-atp-dependent-assembly-of-chromatin
#15
Mai T Khuong, Jia Fei, Grisel Cruz-Becerra, James T Kadonaga
Chromatin is the natural form of DNA in the eukaryotic nucleus, and is the substrate for diverse biological phenomena. The functional analysis of these processes would ideally be carried out with nucleosomal templates that are assembled with customized core histones, DNA sequences, and chromosomal proteins. Here we report a simple, reliable, and versatile method for the ATP-dependent assembly of evenly-spaced nucleosome arrays. This minimal chromatin assembly system comprises the Drosophila nucleoplasmin-like protein (dNLP) histone chaperone, the imitation switch (ISWI) ATP-driven motor protein, core histones, template DNA, and ATP...
October 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28980861/budding-yeast-cenp-a-cse4-interacts-with-the-n-terminus-of-sgo1-and-regulates-its-association-with-centromeric-chromatin
#16
Prashant K Mishra, Kriti S Thapa, Panyue Chen, Suyu Wang, Tony R Hazbun, Munira A Basrai
Shugoshin is an evolutionarily conserved protein, which is involved in tension sensing on mitotic chromosomes, kinetochore biorientation, and protection of centromeric (CEN) cohesin for faithful chromosome segregation. Interaction of the C-terminus of Sgo1 with phosphorylated histone H2A regulates its association with CEN and pericentromeric (peri-CEN) chromatin, whereas mutations in histone H3 selectively compromise the association of Sgo1 with peri-CEN but not CEN chromatin. Given that histone H3 is absent from CEN and is replaced by a histone H3 variant CENP-A(Cse4), we investigated if CENP-A(Cse4) interacts with Sgo1 and promotes its association with the CEN chromatin...
October 5, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28977426/histone-h1-depletion-triggers-an-interferon-response-in-cancer-cells-via-activation-of-heterochromatic-repeats
#17
Andrea Izquierdo-Bouldstridge, Alberto Bustillos, Carles Bonet-Costa, Patricia Aribau-Miralbés, Daniel García-Gomis, Marc Dabad, Anna Esteve-Codina, Laura Pascual-Reguant, Sandra Peiró, Manel Esteller, Matthew Murtha, Lluís Millán-Ariño, Albert Jordan
Histone H1 has seven variants in human somatic cells and contributes to chromatin compaction and transcriptional regulation. Knock-down (KD) of each H1 variant in breast cancer cells results in altered gene expression and proliferation differently in a variant specific manner with H1.2 and H1.4 KDs being most deleterious. Here we show combined depletion of H1.2 and H1.4 has a strong deleterious effect resulting in a strong interferon (IFN) response, as evidenced by an up-regulation of many IFN-stimulated genes (ISGs) not seen in individual nor in other combinations of H1 variant KDs...
August 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28968821/sinopsis-single-nucleotide-polymorphisms-selection-and-promoter-profiling
#18
Daniel Boloc, Natalia Rodríguez, Patricia Gassó, Josep F Abril, Miquel Bernardo, Amalia Lafuente, Sergi Mas
Motivation: The selection of a Single Nucleotide Polymorphism (SNP) using bibliographic methods can be a very time-consuming task. Moreover, a SNP selected in this way may not be easily visualized in its genomic context by a standard user hoping to correlate it with other valuable information. Here we propose a web form built on top of Circos that can assist SNP-centred screening, based on their location in the genome and the regulatory modules they can disrupt. Its use may allow researchers to prioritize SNPs in genotyping and disease studies...
September 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28959888/multi-protease-strategy-identifies-three-pe2-missing-proteins-in-human-testis-tissue
#19
Yihao Wang, Yang Chen, Yao Zhang, Wei Wei, Yanchang Li, Tao Zhang, Fuchu He, Yue Gao, Ping Xu
Although 5 years of the missing proteins (MPs) study have been completed, searching for MPs remains one of the core missions of the Chromosome-Centric Human Proteome Project (C-HPP). Following the next-50-MPs challenge of the C-HPP, we have focused on the testis-enriched MPs by various strategies since 2015. On the basis of the theoretical analysis of MPs (2017-01, neXtProt) using multiprotease digestion, we found that nonconventional proteases (e.g. LysargiNase, GluC) could improve the peptide diversity and sequence coverage compared with Trypsin...
October 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28955993/lsd1-kdm1-isoform-lsd1-8a-contributes-to-neural-differentiation-in-small-cell-lung-cancer
#20
Takanobu Jotatsu, Shigehiro Yagishita, Ken Tajima, Fumiyuki Takahashi, Kaoru Mogushi, Moulid Hidayat, Aditya Wirawan, Ryo Ko, Ryota Kanemaru, Naoko Shimada, Keiko Mitani, Tsuyoshi Saito, Kazuya Takamochi, Kenji Suzuki, Shinji Kohsaka, Shinya Kojima, Hiroshi Mukae, Kazuhiro Yatera, Kazuhisa Takahashi
Small cell lung cancer (SCLC) is an aggressive neuroendocrine tumor characterized by rapid progression. The mechanisms that lead to a shift from initial therapeutic sensitivity to ultimate therapeutic resistance are poorly understood. Although the SCLC genomic landscape led to the discovery of promising agents targeting genetic alterations that were already under investigation, results have been disappointing. Achievements in targeted therapeutics have not been observed for over 30 years. Therefore, the underlying disease biology and novel targets urgently require a better understanding...
March 2017: Biochemistry and Biophysics Reports
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