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https://www.readbyqxmd.com/read/30336329/capturing-auxin-response-factors-syntax-using-dna-binding-models
#1
Arnaud Stigliani, Raquel Martin-Arevalillo, Jérémy Lucas, Adrien Bessy, Thomas Vinos-Poyo, Victoria Mironova, Teva Vernoux, Renaud Dumas, François Parcy
Auxin is a key hormone performing a wealth of functions throughout the plant life cycle. It acts largely by regulating genes at the transcriptional level through a family of transcription factors (TF) called auxin response factors (ARF). Even if all ARF monomers analysed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here we use position weight matrices (PWM) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data...
October 15, 2018: Molecular Plant
https://www.readbyqxmd.com/read/30336173/proteomic-profiling-of-the-white-shrimp-litopenaeus-vannamei-boone-1931-hemocytes-infected-with-white-spot-syndrome-virus-reveals-the-induction-of-allergy-related-proteins
#2
Ariadne Hernández-Pérez, Jesús Alejandro Zamora-Briseño, Eliel Ruiz-May, Alejandro Pereira-Santana, José Miguel Elizalde-Contreras, Sirenia Pozos-González, Edgar Torres-Irineo, Jorge Hernández-López, Martha Gabriela Gaxiola-Cortés, Rossanna Rodríguez-Canul
To elucidate the proteomic responses of shrimp hemocytes to white spot syndrome virus (WSSV) infection at the proteome level, a quantitative shotgun proteomic analysis was performed to detect differentially synthesized proteins in infected hemocytes of white shrimp (Litopenaeus vannamei). We identified 1528 proteins associated to 203 gene ontology (GO) categories. The most representative GO categories were regulation of cellular processes, organic substance metabolic processes and nitrogen compound metabolic processes...
October 15, 2018: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/30336114/fact-complex-gene-duplicates-exhibit-redundant-and-non-redundant-functions-in-c-elegans
#3
Brittany Z Suggs, Aislinn L Latham, Adriana T Dawes, Helen M Chamberlin
FACT (facilitates chromatin transcription) is a histone chaperone complex important in genomic processes including transcription, DNA replication, and DNA repair. FACT is composed of two proteins, SSRP1 and SPT16, which are highly conserved across eukaryotes. While the mechanisms for FACT in nucleosome reorganization and its relationship to DNA processes is well established, how these roles impact coordination in multicellular animal development are less well understood. Here we characterize the genes encoding FACT complex proteins in the nematode C...
October 15, 2018: Developmental Biology
https://www.readbyqxmd.com/read/30336027/new-insights-into-quinine-dna-binding-using-raman-spectroscopy-and-molecular-dynamics-simulations
#4
David Punihaole, Riley J Workman, Shiv Upadhyay, Craig Van Bruggen, Andrew J Schmitz, Theresa M Reineke, Renee R Frontiera
Quinine's ability to bind DNA and potentially inhibit transcription and translation has been examined as a mode of action for its antimalarial activity. UV absorption and fluorescence-based studies have lacked the chemical specificity to develop an unambiguous molecular-level picture of the binding interaction. To address this, we use Raman spectroscopy and molecular dynamics (MD) to investigate quinine-DNA interactions. We demonstrate that quinine's strongest Raman band in the fingerprint region, which derives from a symmetric stretching mode of the quinoline ring, is highly sensitive to the local chemical environment and pH...
October 17, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30335176/nucmap-a-database-of-genome-wide-nucleosome-positioning-map-across-species
#5
Yongbing Zhao, Jinyue Wang, Fang Liang, Yanxia Liu, Qi Wang, Hao Zhang, Meiye Jiang, Zhewen Zhang, Wenming Zhao, Yiming Bao, Zhang Zhang, Jiayan Wu, Yan W Asmann, Rujiao Li, Jingfa Xiao
Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species...
October 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30335167/homodimerization-regulates-an-endothelial-specific-signature-of-the-sox18-transcription-factor
#6
Mehdi Moustaqil, Frank Fontaine, Jeroen Overman, Alex McCann, Timothy L Bailey, Paulina Rudolffi Soto, Akshay Bhumkar, Nichole Giles, Dominic J B Hunter, Yann Gambin, Mathias Francois, Emma Sierecki
During embryogenesis, vascular development relies on a handful of transcription factors that instruct cell fate in a distinct sub-population of the endothelium (1). The SOXF proteins that comprise SOX7, 17 and 18, are molecular switches modulating arterio-venous and lymphatic endothelial differentiation (2,3). Here, we show that, in the SOX-F family, only SOX18 has the ability to switch between a monomeric and a dimeric form. We characterized the SOX18 dimer in binding assays in vitro, and using a split-GFP reporter assay in a zebrafish model system in vivo...
October 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30335163/long-non-coding-rna-chro1-facilitates-atrx-daxx-dependent-h3-3-deposition-for-transcription-associated-heterochromatin-reorganization
#7
Jinyoung Park, Hongmin Lee, Namshik Han, Sojung Kwak, Han-Teo Lee, Jae-Hwan Kim, Keonjin Kang, Byoung Ha Youn, Jae-Hyun Yang, Hyeon-Ju Jeong, Jong-Sun Kang, Seon-Young Kim, Jeung-Whan Han, Hong-Duk Youn, Eun-Jung Cho
Constitutive heterochromatin undergoes a dynamic clustering and spatial reorganization during myogenic differentiation. However the detailed mechanisms and its role in cell differentiation remain largely elusive. Here, we report the identification of a muscle-specific long non-coding RNA, ChRO1, involved in constitutive heterochromatin reorganization. ChRO1 is induced during terminal differentiation of myoblasts, and is specifically localized to the chromocenters in myotubes. ChRO1 is required for efficient cell differentiation, with global impacts on gene expression...
October 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30335157/regulation-of-hltf-mediated-pcna-polyubiquitination-by-rfc-and-pcna-monoubiquitination-levels-determines-choice-of-damage-tolerance-pathway
#8
Yuji Masuda, Satoshi Mitsuyuki, Rie Kanao, Asami Hishiki, Hiroshi Hashimoto, Chikahide Masutani
DNA-damage tolerance protects cells via at least two sub-pathways regulated by proliferating cell nuclear antigen (PCNA) ubiquitination in eukaryotes: translesion DNA synthesis (TLS) and template switching (TS), which are stimulated by mono- and polyubiquitination, respectively. However, how cells choose between the two pathways remains unclear. The regulation of ubiquitin ligases catalyzing polyubiquitination, such as helicase-like transcription factor (HLTF), could play a role in the choice of pathway. Here, we demonstrate that the ligase activity of HLTF is stimulated by double-stranded DNA via HIRAN domain-dependent recruitment to stalled primer ends...
October 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30335076/-relationships-of-rs7341475-polymorphism-and-dna-methylation-in-the-reelin-gene-with-schizophrenia-symptoms
#9
M V Alfimova, N V Kondratyev, A K Golov, S A Golubev, D Yu Galaktionova, T V Nasedkina, V E Golimbet
AIM: To study the role of polymorphism rs7341475 and methylation of the reelin gene in symptoms of schizophrenia and semantic verbal fluency. MATERIAL AND METHODS: Genotypes at the locus rs7341475 were identified in 556 patients with schizophrenic disorders. PANSS scores were obtained for 549 patients and 221 patients performed a test for semantic verbal fluency. The association of the reelin promoter methylation with the PANSS and verbal fluency measures was evaluated in 35 patients...
2018: Zhurnal Nevrologii i Psikhiatrii Imeni S.S. Korsakova
https://www.readbyqxmd.com/read/30334737/a-new-experimental-platform-facilitates-assessment-of-the-transcriptional-and-chromatin-landscapes-of-aging-yeast
#10
David G Hendrickson, Ilya Soifer, Bernd J Wranik, Griffin Kim, Michael Robles, Patrick A Gibney, R Scott McIsaac
Replicative aging of Saccharomyces cerevisiae is an established model system for eukaryotic cellular aging. A limitation in yeast lifespan studies has been the difficulty of separating old cells from young cells in large quantities. We engineered a new platform, the Miniature-chemostat Aging Device (MAD), that enables purification of aged cells at sufficient quantities for genomic and biochemical characterization of aging yeast populations. Using MAD, we measured DNA accessibility and gene expression changes in aging cells...
October 18, 2018: ELife
https://www.readbyqxmd.com/read/30334070/mrna-as-novel-technology-for-passive-immunotherapy
#11
REVIEW
Thomas Schlake, Andreas Thess, Moritz Thran, Ingo Jordan
While active immunization elicits a lasting immune response by the body, passive immunotherapy transiently equips the body with exogenously generated immunological effectors in the form of either target-specific antibodies or lymphocytes functionalized with target-specific receptors. In either case, administration or expression of recombinant proteins plays a fundamental role. mRNA prepared by in vitro transcription (IVT) is increasingly appreciated as a drug substance for delivery of recombinant proteins. With its biological role as transient carrier of genetic information translated into protein in the cytoplasm, therapeutic application of mRNA combines several advantages...
October 17, 2018: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/30333958/the-ethnic-specific-spectrum-of-germline-nucleotide-variants-in-dna-damage-response-and-repair-genes-in-hereditary-breast-and-ovarian-cancer-patients-of-tatar-descent
#12
Olga I Brovkina, Leila Shigapova, Daria A Chudakova, Marat G Gordiev, Rafael F Enikeev, Maxim O Druzhkov, Dmitriy S Khodyrev, Elena I Shagimardanova, Alexey G Nikitin, Oleg A Gusev
The Russian population consists of more than 100 ethnic groups, presenting a unique opportunity for the identification of hereditary pathogenic mutations. To gain insight into the landscape of heredity pathogenic variants, we employed targeted next-generation sequencing to analyze the germline mutation load in the DNA damage response and repair genes of hereditary breast and ovary cancer syndrome (HBOCS) patients of Tatar ethnicity, which represents ~4% of the total Russian population. Several pathogenic mutations were identified in DNA double-strand break repair genes, and the spectrum of these markers in Tatar patients varied from that previously reported for patients of Slavic ancestry...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/30333755/a-novel-dnmt3a1-transcript-inhibits-adipogenesis
#13
Bahareldin A Abdalla, Zhenhui Li, Hongjia Ouyang, Endashaw Jebessa, Tianhao Sun, Jia-Ao Yu, Bolin Cai, Biao Chen, Qinghua Nie, Xiquan Zhang
DNA (cytosine-5)-methyltransferase 3a ( Dnmt3a ) is an enzyme that catalyzes the transfer of methyl groups to specific CpG forms in DNA. In mammals, two variant transcripts of Dnmt3a have been successfully identified. To the best of our knowledge, no Dnmt3a transcripts in an avian have been successfully identified. This study was performed to detect different transcripts of Dnmt3a in chickens and to examine whether a novel Dnmt3a transcript named Dnmt3a1 may regulate adipogenesis. In addition to cloning, sequencing, transcript detection, and expression studies, a novel Dnmt3a1 transcript overexpression and knockdown were conducted to explore the potential role of Dnmt3a1 in preadipocyte proliferation and the early stage of adipocyte differentiation...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/30333188/transcription-initiation-defines-kinetoplast-rna-boundaries
#14
François M Sement, Takuma Suematsu, Liye Zhang, Tian Yu, Lan Huang, Inna Aphasizheva, Ruslan Aphasizhev
Mitochondrial genomes are often transcribed into polycistronic RNAs punctuated by tRNAs whose excision defines mature RNA boundaries. Although kinetoplast DNA lacks tRNA genes, it is commonly held that in Trypanosoma brucei the monophosphorylated 5' ends of functional molecules typify precursor partitioning by an unknown endonuclease. On the contrary, we demonstrate that individual mRNAs and rRNAs are independently synthesized as 3'-extended precursors. The transcription-defined 5' terminus is converted into a monophosphorylated state by the pyrophosphohydrolase complex, termed the "PPsome...
October 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30333187/ribonuclease-activity-of-marf1-controls-oocyte-rna-homeostasis-and-genome-integrity-in-mice
#15
Qingqing Yao, Guangyi Cao, Mingzhe Li, Baixing Wu, Xiaoyun Zhang, Teng Zhang, Jing Guo, Hong Yin, Lanying Shi, Jiayi Chen, Xiang Yu, Lina Zheng, Jinbiao Ma, You-Qiang Su
Producing normal eggs for fertilization and species propagation requires completion of meiosis and protection of the genome from the ravages of retrotransposons. Mutation of Marf1 (meiosis regulator and mRNA stability factor 1) results in defects in both these key processes in mouse oocytes and thus in infertility. MARF1 was predicted to have ribonuclease activity, but the structural basis for the function of MARF1 and the contribution of its putative ribonuclease domain to the mutant oocyte phenotype was unknown...
October 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30333146/an-effector-from-the-cyst-nematode-heterodera-schachtii-derepresses-host-rrna-genes-by-altering-histone-acetylation
#16
Vijayapalani Paramasivan, Tarek Hewezi, Frederic Pontvianne, Thomas J Baum
Cyst nematodes are plant-pathogenic animals that secrete effector proteins into plant root cells to alter host gene expression and reprogram these cells to form specialized feeding sites, known as syncytia. The molecular mechanisms of these effectors are mostly unknown. We determined that the sugar beet cyst nematode (Heterodera schachtii) 32E03 effector protein strongly inhibits the activities of Arabidopsis thaliana histone deacetylases including the HDT1 enzyme, which has a known function in the regulation of rRNA gene expression through chromatin modifications...
October 17, 2018: Plant Cell
https://www.readbyqxmd.com/read/30332964/the-multifunctional-protein-p62-and-its-mechanistic-roles-in-cancers
#17
Shunbin Ning, Ling Wang
The multifunctional signaling hub p62 is well recognized as ubiquitin sensor and selective autophagy adaptor under myriad stress conditions including cancer. As a ubiquitin sensor, p62 promotes NFκB activation by facilitating TRAF6 ubiquitination and aggregation. As a selective autophagy receptor, p62 links ubiquitinated substrates including p62 itself for lysosome-mediated degradation. p62 plays crucial roles in myriad cellular processes including DNA damage response, aging/senescence, infection and immunity, chronic inflammation, and cancerogenesis, dependent on or independent of autophagy...
October 16, 2018: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/30332797/the-viral-tegument-protein-pp65-impairs-transcriptional-upregulation-of-il-1%C3%AE-by-human-cytomegalovirus-through-inhibition-of-nf-kb-activity
#18
Matteo Biolatti, Valentina Dell'Oste, Sara Scutera, Francesca Gugliesi, Gloria Griffante, Marco De Andrea, Tiziana Musso, Santo Landolfo
Interleukin-1β (IL-1β) is a key effector of the inflammasome complex in response to pathogens and danger signals. Although it is well known that assembly of the inflammasome triggers proteolytic cleavage of the biologically inactive precursor pro-IL-1β into its mature secreted form, the mechanism by which human cytomegalovirus (HCMV) regulates IL-1β production via the inflammasome is still poorly understood. Here, we show that the infection of human foreskin fibroblasts (HFFs) with a mutant HCMV lacking the tegument protein pp65 (v65Stop) results in higher expression levels of mature IL-1β compared to its wild-type counterpart, suggesting that pp65 mediates HCMV immune evasion through downmodulation of IL-1β...
October 16, 2018: Viruses
https://www.readbyqxmd.com/read/30332629/the-nuclear-receptor-ppar%C3%AE-controls-progressive-macrophage-polarization-as-a-ligand-insensitive-epigenomic-ratchet-of-transcriptional-memory
#19
Bence Daniel, Gergely Nagy, Zsolt Czimmerer, Attila Horvath, David W Hammers, Ixchelt Cuaranta-Monroy, Szilard Poliska, Petros Tzerpos, Zsuzsanna Kolostyak, Tristan T Hays, Andreas Patsalos, René Houtman, Sascha Sauer, Jean Francois-Deleuze, Fraydoon Rastinejad, Balint L Balint, H Lee Sweeney, Laszlo Nagy
Macrophages polarize into distinct phenotypes in response to complex environmental cues. We found that the nuclear receptor PPARγ drove robust phenotypic changes in macrophages upon repeated stimulation with interleukin (IL)-4. The functions of PPARγ on macrophage polarization in this setting were independent of ligand binding. Ligand-insensitive PPARγ bound DNA and recruited the coactivator P300 and the architectural protein RAD21. This established a permissive chromatin environment that conferred transcriptional memory by facilitating the binding of the transcriptional regulator STAT6 and RNA polymerase II, leading to robust production of enhancer and mRNAs upon IL-4 re-stimulation...
October 16, 2018: Immunity
https://www.readbyqxmd.com/read/30332327/genetic-and-epigenetic-determinants-establish-a-continuum-of-hsf1-occupancy-and-activity-across-the-yeast-genome
#20
David Pincus, Jayamani Anandhakumar, Prathapan Thiru, Michael J Guertin, Alexander M Erkine, David S Gross
Heat Shock Factor 1 is the master transcriptional regulator of molecular chaperones and binds to the same cis-acting Heat Shock Element (HSE) across the eukaryotic lineage. In budding yeast, Hsf1 drives the transcription of ∼20 genes essential to maintain proteostasis under basal conditions, yet its specific targets and extent of inducible binding during heat shock remain unclear. Here, we combine Hsf1 ChIP-seq, nascent RNA-seq and Hsf1 nuclear depletion to quantify Hsf1 binding and transcription across the yeast genome...
October 17, 2018: Molecular Biology of the Cell
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