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Epigenetics & Chromatin

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https://www.readbyqxmd.com/read/29126443/ubiquitin-c-terminal-hydrolase-isozyme-l1-is-associated-with-shelterin-complex-at-interstitial-telomeric-sites
#1
Aleksandar Ilic, Sumin Lu, Vikram Bhatia, Farhana Begum, Thomas Klonisch, Prasoon Agarwal, Wayne Xu, James R Davie
BACKGROUND: Ubiquitin C-terminal hydrolase isozyme L1 (UCHL1) is primarily expressed in neuronal cells and neuroendocrine cells and has been associated with various diseases, including many cancers. It is a multifunctional protein involved in deubiquitination, ubiquitination and ubiquitin homeostasis, but its specific roles are disputed and still generally undetermined. RESULTS: Herein, we demonstrate that UCHL1 is associated with genomic DNA in certain prostate cancer cell lines, including DU 145 cells derived from a brain metastatic site, and in HEK293T embryonic kidney cells with a neuronal lineage...
November 10, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29126440/chromatin-organization-changes-during-the-establishment-and-maintenance-of-the-postmitotic-state
#2
Yiqin Ma, Laura Buttitta
BACKGROUND: Genome organization changes during development as cells differentiate. Chromatin motion becomes increasingly constrained and heterochromatin clusters as cells become restricted in their developmental potential. These changes coincide with slowing of the cell cycle, which can also influence chromatin organization and dynamics. Terminal differentiation is often coupled with permanent exit from the cell cycle, and existing data suggest a close relationship between a repressive chromatin structure and silencing of the cell cycle in postmitotic cells...
November 10, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29115969/correction-to-nua4-histone-acetyltransferase-activity-is-required-for-h4-acetylation-on-a-dosage-compensated-monosomic-chromosome-that-confers-resistance-to-fungal-toxins
#3
Hironao Wakabayashi, Christopher Tucker, Gabor Bethlendy, Anatoliy Kravets, Stephen L Welle, Michael Bulger, Jeffrey J Hayes, Elena Rustchenko
After the publication of this work [1], it was noticed that an initial was missing from the author name: Jeffrey Hayes. His name should be written as: Jeffrey J. Hayes.
November 7, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29084613/h2a-o-glcnacylation-at-serine-40-functions-genomic-protection-in-association-with-acetylated-h2az-or-%C3%AE-h2ax
#4
Koji Hayakawa, Mitsuko Hirosawa, Ruiko Tani, Chikako Yoneda, Satoshi Tanaka, Kunio Shiota
BACKGROUND: We have previously reported a novel O-GlcNAc modification at serine 40 (S40) of H2A (H2AS40Gc). S40-type H2A isoforms susceptible to O-GlcNAcylation are evolutionarily new and restricted to the viviparous animals; however, the biological function of H2AS40Gc is largely unknown. H2A isoforms are consisted of S40 and alanine 40 (A40) type and this residue on H2A is located in the L1 of the globular domain, which is also known as a variable portion that distinguishes between the canonical and non-canonical H2A variants...
October 30, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29061172/nua4-histone-acetyltransferase-activity-is-required-for-h4-acetylation-on-a-dosage-compensated-monosomic-chromosome-that-confers-resistance-to-fungal-toxins
#5
Hironao Wakabayashi, Christopher Tucker, Gabor Bethlendy, Anatoliy Kravets, Stephen L Welle, Michael Bulger, Jeffrey Hayes, Elena Rustchenko
BACKGROUND: The major human fungal pathogen Candida albicans possesses a diploid genome, but responds to growth in challenging environments by employing chromosome aneuploidy as an adaptation mechanism. For example, we have shown that C. albicans adapts to growth on the toxic sugar L-sorbose by transitioning to a state in which one chromosome (chromosome 5, Ch5) becomes monosomic. Moreover, analysis showed that while expression of many genes on the monosomic Ch5 is altered in accordance with the chromosome ploidy, expression of a large fraction of genes is increased to the normal diploid level, presumably compensating for gene dose...
October 23, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29061167/genome-wide-profiling-of-transcribed-enhancers-during-macrophage-activation
#6
Elena Denisenko, Reto Guler, Musa M Mhlanga, Harukazu Suzuki, Frank Brombacher, Sebastian Schmeier
BACKGROUND: Macrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. RESULTS: Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in bone marrow-derived mouse macrophages, their time kinetics, and target protein-coding genes...
October 23, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29047414/histone-isoform-h2a1h-promotes-attainment-of-distinct-physiological-states-by-altering-chromatin-dynamics
#7
Saikat Bhattacharya, Divya Reddy, Vinod Jani, Nikhil Gadewal, Sanket Shah, Raja Reddy, Kakoli Bose, Uddhavesh Sonavane, Rajendra Joshi, Sanjay Gupta
BACKGROUND: The distinct functional effects of the replication-dependent histone H2A isoforms have been demonstrated; however, the mechanistic basis of the non-redundancy remains unclear. Here, we have investigated the specific functional contribution of the histone H2A isoform H2A1H, which differs from another isoform H2A2A3 in the identity of only three amino acids. RESULTS: H2A1H exhibits varied expression levels in different normal tissues and human cancer cell lines (H2A1C in humans)...
October 18, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29037228/neuroepigenetic-mechanisms-in-disease
#8
REVIEW
Michael A Christopher, Stephanie M Kyle, David J Katz
Epigenetics allows for the inheritance of information in cellular lineages during differentiation, independent of changes to the underlying genetic sequence. This raises the question of whether epigenetic mechanisms also function in post-mitotic neurons. During the long life of the neuron, fluctuations in gene expression allow the cell to pass through stages of differentiation, modulate synaptic activity in response to environmental cues, and fortify the cell through age-related neuroprotective pathways. Emerging evidence suggests that epigenetic mechanisms such as DNA methylation and histone modification permit these dynamic changes in gene expression throughout the life of a neuron...
October 16, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28982377/environmental-epigenetics-in-zebrafish
#9
REVIEW
Vincenzo Cavalieri, Giovanni Spinelli
It is widely accepted that the epigenome can act as the link between environmental cues, both external and internal, to the organism and phenotype by converting the environmental stimuli to phenotypic responses through changes in gene transcription outcomes. Environmental stress endured by individual organisms can also enforce epigenetic variations in offspring that had never experienced it directly, which is termed transgenerational inheritance. To date, research in the environmental epigenetics discipline has used a wide range of both model and non-model organisms to elucidate the various epigenetic mechanisms underlying the adaptive response to environmental stimuli...
October 5, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28946896/application-of-dual-reading-domains-as-novel-reagents-in-chromatin-biology-reveals-a-new-h3k9me3-and-h3k36me2-3-bivalent-chromatin-state
#10
Rebekka Mauser, Goran Kungulovski, Corinna Keup, Richard Reinhardt, Albert Jeltsch
BACKGROUND: Histone post-translational modifications (PTMs) play central roles in chromatin-templated processes. Combinations of two or more histone PTMs form unique interfaces for readout and recruitment of chromatin interacting complexes, but the genome-wide mapping of coexisting histone PTMs remains an experimentally difficult task. RESULTS: We introduce here a novel type of affinity reagents consisting of two fused recombinant histone modification interacting domains (HiMIDs) for direct detection of doubly modified chromatin...
September 25, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28931432/hypomethylated-domain-enriched-dna-motifs-prepattern-the-accessible-nucleosome-organization-in-teleosts
#11
Ryohei Nakamura, Ayako Uno, Masahiko Kumagai, Shinichi Morishita, Hiroyuki Takeda
BACKGROUND: Gene promoters in vertebrate genomes show distinct chromatin features such as stably positioned nucleosome array and DNA hypomethylation. The nucleosomes are known to have certain sequence preferences, and the prediction of nucleosome positioning from DNA sequence has been successful in some organisms such as yeast. However, at gene promoters where nucleosomes are much more stably positioned than in other regions, the sequence-based model has failed to work well, and sequence-independent mechanisms have been proposed...
September 20, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28927461/additional-sex-combs-interacts-with-enhancer-of-zeste-and-trithorax-and-modulates-levels-of-trimethylation-on-histone-h3k4-and-h3k27-during-transcription-of-hsp70
#12
Taosui Li, Jacob W Hodgson, Svetlana Petruk, Alexander Mazo, Hugh W Brock
BACKGROUND: Maintenance of cell fate determination requires the Polycomb group for repression; the trithorax group for gene activation; and the enhancer of trithorax and Polycomb (ETP) group for both repression and activation. Additional sex combs (Asx) is a genetically identified ETP for the Hox loci, but the molecular basis of its dual function is unclear. RESULTS: We show that in vitro, Asx binds directly to the SET domains of the histone methyltransferases (HMT) enhancer of zeste [E(z)] (H3K27me3) and Trx (H3K4me3) through a bipartite interaction site separated by 846 amino acid residues...
September 19, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28854962/optimized-reduced-representation-bisulfite-sequencing-reveals-tissue-specific-mchh-islands-in-maize
#13
Fei-Man Hsu, Ming-Ren Yen, Chi-Ting Wang, Chien-Yu Lin, Chung-Ju Rachel Wang, Pao-Yang Chen
BACKGROUND: DNA methylation plays important roles in many regulatory processes in plants. It is economically infeasible to profile genome-wide DNA methylation at a single-base resolution in maize, given its genome size of ~2.5 Gb. As an alternative, we adapted region of interest (ROI)-directed reduced representation bisulfite sequencing (RRBS) to survey genome-wide methylation in maize. RESULTS: We developed a pipeline for selecting restriction enzymes in silico and experimentally showed that, in the maize genome, MseI- and CviQI-digested fragments are precisely enriched in promoters and gene bodies, respectively...
August 30, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28835257/long-noncoding-rnas-coordinate-functions-between-mitochondria-and-the-nucleus
#14
REVIEW
Yaru Dong, Takeshi Yoshitomi, Ji-Fan Hu, Jizhe Cui
In animal cells, mitochondria are the primary powerhouses and metabolic factories. They also contain genomes and can produce mitochondrial-specific nucleic acids and proteins. To maintain homeostasis of the entire cell, an intense cross-talk between mitochondria and the nucleus, mediated by encoded noncoding RNAs (ncRNAs), as well as proteins, is required. Long ncRNAs (lncRNAs) contain characteristic structures, and they are involved in the regulation of almost every stage of gene expression, as well as being implicated in a variety of disease states, such as cancer...
August 23, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28830512/histone-4-lysine-8-acetylation-regulates-proliferation-and-host-pathogen-interaction-in-plasmodium-falciparum
#15
Archana P Gupta, Lei Zhu, Jaishree Tripathi, Michal Kucharski, Alok Patra, Zbynek Bozdech
BACKGROUND: The dynamics of histone modifications in Plasmodium falciparum indicates the existence of unique mechanisms that link epigenetic factors with transcription. Here, we studied the impact of acetylated histone code on transcriptional regulation during the intraerythrocytic developmental cycle (IDC) of P. falciparum. RESULTS: Using a dominant-negative transgenic approach, we showed that acetylations of histone H4 play a direct role in transcription. Specifically, these histone modifications mediate an inverse transcriptional relationship between the factors of cell proliferation and host-parasite interaction...
August 22, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28784182/initial-high-resolution-microscopic-mapping-of-active-and-inactive-regulatory-sequences-proves-non-random-3d-arrangements-in-chromatin-domain-clusters
#16
Marion Cremer, Volker J Schmid, Felix Kraus, Yolanda Markaki, Ines Hellmann, Andreas Maiser, Heinrich Leonhardt, Sam John, John Stamatoyannopoulos, Thomas Cremer
BACKGROUND: The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an 'open' local chromatin configuration has long been known. However, the 3D topography of TREs within the nuclear landscape of individual cells in relation to their active or inactive status has remained elusive. Here, we explored the 3D nuclear topography of active and inactive TREs in the context of a recently proposed model for a functionally defined nuclear architecture, where an active and an inactive nuclear compartment (ANC-INC) form two spatially co-aligned and functionally interacting networks...
August 7, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28750655/non-genomic-transmission-of-longevity-between-generations-potential-mechanisms-and%C3%A2-evidence-across-species
#17
REVIEW
Alexander M Vaiserman, Alexander K Koliada, Randy L Jirtle
Accumulating animal and human data indicate that environmental exposures experienced during sensitive developmental periods may strongly influence risk of adult disease. Moreover, the effects triggered by developmental environmental cues can be transgenerationally transmitted, potentially affecting offspring health outcomes. Increasing evidence suggests a central role of epigenetic mechanisms (heritable alterations in gene expression occurring without changes in underlying DNA sequence) in mediating these effects...
July 27, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28747224/regions-of-common-inter-individual-dna-methylation-differences-in-human-monocytes-genetic-basis-and-potential-function
#18
Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein-Hitpass, Anupam Sinha, Karl-Heinz Jöckel, Stefanie Heilmann-Heimbach, Per Hoffmann, Markus M Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
BACKGROUND: There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. RESULTS: We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before...
July 26, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28693562/activation-of-the-alpha-globin-gene-expression-correlates-with-dramatic-upregulation-of-nearby-non-globin-genes-and-changes-in-local-and-large-scale-chromatin-spatial-structure
#19
Sergey V Ulianov, Aleksandra A Galitsyna, Ilya M Flyamer, Arkadiy K Golov, Ekaterina E Khrameeva, Maxim V Imakaev, Nezar A Abdennur, Mikhail S Gelfand, Alexey A Gavrilov, Sergey V Razin
BACKGROUND: In homeotherms, the alpha-globin gene clusters are located within permanently open genome regions enriched in housekeeping genes. Terminal erythroid differentiation results in dramatic upregulation of alpha-globin genes making their expression comparable to the rRNA transcriptional output. Little is known about the influence of the erythroid-specific alpha-globin gene transcription outburst on adjacent, widely expressed genes and large-scale chromatin organization. Here, we have analyzed the total transcription output, the overall chromatin contact profile, and CTCF binding within the 2...
July 11, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28683815/metabolic-labeling-in-middle-down-proteomics-allows-for-investigation-of-the-dynamics-of-the-histone-code
#20
Simone Sidoli, Congcong Lu, Mariel Coradin, Xiaoshi Wang, Kelly R Karch, Chrystian Ruminowicz, Benjamin A Garcia
BACKGROUND: Middle-down mass spectrometry (MS), i.e., analysis of long (~50-60 aa) polypeptides, has become the method with the highest throughput and accuracy for the characterization of combinatorial histone posttranslational modifications (PTMs). The discovery of histone readers with multiple domains, and overall the cross talk of PTMs that decorate histone proteins, has revealed that histone marks have synergistic roles in modulating enzyme recruitment and subsequent chromatin activities...
July 6, 2017: Epigenetics & Chromatin
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