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https://www.readbyqxmd.com/read/29054929/mitogen-and-stress-activated-protein-kinase-1-is-required-for-gonadotropin-releasing-hormone-mediated-activation-of-gonadotropin-%C3%AE-subunit-expression
#1
Majd Haj, Andrea Wijeweera, Sergei Rudnizky, Jack Taunton, Lilach Pnueli, Philippa Melamed
Pituitary gonadotropin hormones are regulated by gonadotropin-releasing hormone (GnRH) via MAPK signaling pathways which stimulate gene transcription of the common α-subunit (Cga) and the hormone-specific β-subunits of gonadotropin. We have reported previously that GnRH-induced activities at these genes include various histone modifications, but we did not examine histone phosphorylation. This modification adds a negative charge to residues of the histone tails that interact with the negatively charged DNA, is associated with closed chromatin during mitosis, but is increased at certain genes for transcriptional activation...
October 20, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29053953/histone-h3-dual-ubiquitylation-mediates-maintenance-dna-methylation
#2
Kendra R Vann, Tatiana G Kutateladze
Epigenetic marks, including DNA methylation and posttranslational modifications (PTMs) in histones, are important factors in determining the fate of replicating cells. In this issue of Molecular Cell, Ishiyama et al. (2017) reveal yet another layer in a remarkably complex mechanism of maintenance DNA methylation.
October 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29052202/identification-of-parent-of-origin-dependent-qtls-using-bulk-segregant-sequencing-bulk-seq
#3
Nuno D Pires, Ueli Grossniklaus
Parent-of-origin effects play important roles in plant reproduction and are often mediated by epigenetic modifications at the histone or DNA level. However, the genetic basis underlying these modifications can be challenging to identify. Here, we describe an approach (Bulk-Seq) that can be used to map loci mediating parent-of-origin-dependent effects using whole-genome sequencing of pools of DNA.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052201/in-vitro-assays-to-measure-histone-methyltransferase-activity-using-different-chromatin-substrates
#4
Yannick Jacob, Philipp Voigt
In vitro histone modification (HM) assays are used to characterize the activity of chromatin-modifying enzymes. These assays provide information regarding the modification sites on histones, the product specificity, and the impact of other histone or nucleotide modifications on enzyme activity. In particular, histone methyltransferase (HMT) assays have been instrumental in elucidating the activity and site specificity of many plant HMT enzymes. In this chapter, we describe a general protocol that can be used to perform HMT assays using different chromatin substrates, detection methods, and enzymes directly purified from plant material or heterologous sources...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052197/profiling-histone-modifications-in-synchronized-floral-tissues-for-quantitative-resolution-of-chromatin-and-transcriptome-dynamics
#5
Julia Engelhorn, Frank Wellmer, Cristel C Carles
Covalent histone modifications and their effects on chromatin state and accessibility play a key role in the regulation of gene expression in eukaryotes. To gain insights into their functions during plant growth and development, the distribution of histone modifications can be analyzed at a genome-wide scale through chromatin immunoprecipitation assays followed by sequencing of the isolated genomic DNA. Here, we present a protocol for systematic analysis of the distribution and dynamic changes of selected histone modifications, during flower development in the model plant Arabidopsis thaliana...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052194/unraveling-the-complex-epigenetic-mechanisms-that-regulate-gene-activity
#6
Marian Bemer
Our understanding of the epigenetic mechanisms that regulate gene expression has been largely increased in recent years by the development and refinement of different techniques. This has revealed that gene transcription is highly influenced by epigenetic mechanisms, i.e., those that do not involve changes in the genome sequence, but rather in nuclear architecture, chromosome conformation and histone and DNA modifications. Our understanding of how these different levels of epigenetic regulation interact with each other and with classical transcription-factor based gene regulation to influence gene transcription has just started to emerge...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052191/histone-h1-purification-and-post-translational-modification-profiling-by-high-resolution-mass-spectrometry
#7
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/29052190/mapping-of-histone-modifications-in-plants-by-tandem-mass-spectrometry
#8
Walid Mahrez, Lars Hennig
To get an insight into the mechanisms of gene expression regulation in eukaryotic organisms, it is necessary to decipher the connection between the different chemical modifications occurring on the chromatin, at both the DNA and the associated histone proteins. Histones are basic proteins, which pack the DNA into nucleosomes, and are hot spots for several posttranslational modifications. Elucidating combinatorial histone modifications co-occurring on the same histone protein will greatly contribute to our understanding of the mechanisms involved in the development of eukaryotes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052189/cell-type-specific-profiling-of-chromatin-modifications-and-associated-proteins
#9
Ana Karina Morao, Erwann Caillieux, Vincent Colot, François Roudier
Progression of a cell along a differentiation path is characterized by changes in gene expression profiles. Alterations of these transcriptional programs result from cell type-specific transcription factors that act in a dynamic chromatin environment. Understanding the precise contribution of these molecular factors during the differentiation process requires accessing specific cell types within a developing organ. This chapter describes a streamlined and alternative version of INTACT, a method enabling the isolation of specific cell populations by affinity-purification of tagged nuclei and the subsequent analysis of gene expression, transcription factor binding profiles, as well as chromatin state at a genome-wide scale...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052187/sequential-chip-protocol-for-profiling-bivalent-epigenetic-modifications-rechip
#10
Bénédicte Desvoyes, Joana Sequeira-Mendes, Zaida Vergara, Sofia Madeira, Crisanto Gutierrez
Identification of chromatin modifications, e.g., histone acetylation and methylation, among others, is widely carried out by using a chromatin immunoprecipitation (ChIP) strategy. The information obtained with these procedures is useful to gain an overall picture of modifications present in all cells of the population under study. It also serves as a basis to figure out the mechanisms of chromatin organization and gene regulation at the population level. However, the ultimate goal is to understand gene regulation at the level of single chromatin fibers...
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
#11
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/29050335/evidence-for-the-association-of-chromatin-and-microrna-regulation-in-the-human-genome
#12
Bang-Bao Tao, Xi-Qiang Liu, Wenhao Zhang, Shu Li, Dong Dong, Mang Xiao, Jun Zhong
Both microRNAs (miRNAs) and chromatin regulation play important roles in cellular processes and they function at different regulatory levels of transcription. Although efforts have been devoted to the investigation of miRNA and chromatin regulation, there's still no comprehensive work to illustrate their relationships due tothe lack of whole-genome wide datasets in different human cellular contexts. Based on the recently published large-scale epigenetic data, we examined the association between miRNA and epigenetic machinery...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29048620/dna-methylation-and-histone-modifications-as-epigenetic-regulation-in-prostate-cancer-review
#13
Maria Nowacka-Zawisza, Ewelina Wiśnik
Prostate cancer is the second most commonly diagnosed cancer in men in Poland after lung cancer and the third leading cause of cancer-related mortality after lung and colon cancer. The etiology of most cases of prostate cancer are not fully known, and therefore it is essential to search for the molecular basis of prostate cancer and markers for the early diagnosis of this type of cancer. Epigenetics deals with changes in gene expression that are not determined by changes in the DNA sequence. Epigenetic changes refer to changes in the structure of DNA, which are the result of DNA modification after replication and/or post-translational modification of proteins associated with DNA...
September 20, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29046054/porphyromonas-gingivalis-lipopolysaccharide-stimulation-in-human-periodontal-ligament-stem-cells-role-of-epigenetic-modifications-to-the-inflammation
#14
Francesca Diomede, Soundara Rajan Thangavelu, Ilaria Merciaro, Monica D'Orazio, Placido Bramanti, Emanuela Mazzon, Oriana Trubiani
Periodontitis is a chronic oral inflammatory disease produced by bacteria. Gingival retraction and bone and connective tissues resorption are the hallmarks of this disease. Chronic periodontitis may contribute to the risk of onset or progression of neuroinflammatory pathological conditions, such as Alzheimer's disease. The main goal of the present study was to investigate if the role of epigenetic modulations is involved in periodontitis using human periodontal ligament stem cells (hPDLSCs) as an in vitro model system...
August 25, 2017: European Journal of Histochemistry: EJH
https://www.readbyqxmd.com/read/29045501/scaffold-dependent-histone-deacetylase-hdac-inhibitor-induced-re-equilibration-of-the-subcellular-localization-and-post-translational-modification-state-of-class-i-hdacs
#15
Thomas W Hanigan, Taha Y Taha, Shaimaa M Aboukhatwa, Jonna Frasor, Pavel A Petukhov
The mechanism of action of histone deacetylase inhibitors (HDACi) is mainly attributed to the inhibition of the deacetylase catalytic activity for their histone substrates. In this study, we analyzed the abundance of class I HDACs in the cytosolic, nuclear soluble and chromatin bound cellular fractions in breast cancer cells after HDACi treatment. We found that potent N-hydroxy propenamide-based HDACi induced a concentration dependent decrease in the HDAC1 associated with chromatin and a lasting concomitant increase in cytoplasmic HDAC1 while maintaining total protein expression...
2017: PloS One
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
#16
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/29043652/statistical-analysis-and-quality-assessment-of-chip-seq-data-with-drompa
#17
Ryuichiro Nakato, Katsuhiko Shirahige
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. As there are various factors during sample preparation that affect the obtained results, multilateral quality assessments are essential. Here, we describe a step-by-step protocol using DROMPA, a program for user-friendly ChIP-seq pipelining. DROMPA can be used for quality assessment, data normalization, visualization, peak calling, and multiple statistical analyses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043603/epigenetic-modifications-of-gene-expression-by-lifestyle-and-environment
#18
REVIEW
Qudeer Ahmed Abdul, Byung Pal Yu, Hae Young Chung, Hyun Ah Jung, Jae Sue Choi
Epigenetics oftenly described as the heritable changes in gene expression independent of changes in DNA sequence. Various environmental factors such as nutrition-dietary components, lifestyle, exercise, physical activity, toxins, and other contributing factors remodel the genome either in a constructive or detrimental way. Since epigenetic changes are reversible and nutrition is one of the many epigenetic regulators that modify gene expression without changing the DNA sequence, dietary nutrients and bioactive food components contribute to epigenetic phenomena either by directly suppressing DNA methylation or histone catalyzing enzymes or by changing the availability of substrates required for enzymatic reactions...
October 17, 2017: Archives of Pharmacal Research
https://www.readbyqxmd.com/read/29042275/basil-polysaccharide-attenuates-hepatocellular-carcinoma-metastasis-in-rat-by-suppressing-h3k9me2-histone-methylation-under-hepatic-artery-ligation-induced-hypoxia
#19
Bing Feng, Ying Zhu, Zuqing Su, Lipeng Tang, Chaoyue Sun, Caiyun Li, Guangjuan Zheng
Hepatocellular carcinoma (HCC) is one of the most common and fatal cancers in the world. Tumor metastasis is an important factor of poor prognosis in patients with HCC. Tumor hypoxia can promote tumor cell metastasis in HCC. Epigenetic modification is closely related to tumor hypoxia and metastasis. In our previous research, we found that basil polysaccharide suppressed migration and invasion of HCC cell by inhibiting hypoxia induced histone methylation in vitro. In the present study, we investigated the effect of basil polysaccharide on the walker 256 carcinoma cell metastasis in rat...
October 14, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29040973/sulforaphane-and-epigallocatechin-gallate-restore-estrogen-receptor-expression-by-modulating-epigenetic-events-in-the-breast-cancer-cell-line-mda-mb-231-a-systematic-review-and-meta-analysis
#20
Vincenza Gianfredi, Samuele Vannini, Massimo Moretti, Milena Villarini, Nicola Luigi Bragazzi, Alberto Izzotti, Daniele Nucci
BACKGROUND/AIMS: Epigenetics refers to modifications in gene activity and expression without alteration at the DNA sequence. Environment and diet could influence gene expression. Diet modifications may be meaningful in preventing and treating chronic diseases, cancer included. Dietary bioactive compounds, such as polyphenols (e.g., curcumin, resveratrol, or epigallocatechin gallate [EGCG]) or isothiocyanate (e.g., sulforaphane [SFN]), can regulate histone acetylation. The aim of this systematic review and meta-analysis was to evaluate the effect of SFN and EGCG on breast cancer (BC) cells cultured in vitro...
October 18, 2017: Journal of Nutrigenetics and Nutrigenomics
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