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https://www.readbyqxmd.com/read/29163854/interactions-between-tgf-%C3%AE-1-canonical-wnt-%C3%AE-catenin-pathway-and-ppar-%C3%AE-in-radiation-induced-fibrosis
#1
REVIEW
Alexandre Vallée, Yves Lecarpentier, Rémy Guillevin, Jean-Noël Vallée
Radiation therapy induces DNA damage and inflammation leading to fibrosis. Fibrosis can occur 4 to 12 months after radiation therapy. This process worsens with time and years. Radiation-induced fibrosis is characterized by fibroblasts proliferation, myofibroblast differentiation, and synthesis of collagen, proteoglycans and extracellular matrix. Myofibroblasts are non-muscle cells that can contract and relax. Myofibroblasts evolve towards irreversible retraction during fibrosis process. In this review, we discussed the interplays between transforming growth factor-β1 (TGF-β1), canonical WNT/β-catenin pathway and peroxisome proliferator-activated receptor gamma (PPAR γ) in regulating the molecular mechanisms underlying the radiation-induced fibrosis, and the potential role of PPAR γ agonists...
October 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/29157677/dna-methylation-affects-the-lifespan-of-honey-bee-apis-mellifera-l-workers-evidence-for-a-regulatory-module-that-involves-vitellogenin-expression-but-is-independent-of-juvenile-hormone-function
#2
Carlos A M Cardoso-Júnior, Karina R Guidugli-Lazzarini, Klaus Hartfelder
The canonic regulatory module for lifespan of honey bee (Apis mellifera) workers involves a mutual repressor relationship between juvenile hormone (JH) and vitellogenin (Vg). Compared to vertebrates, however, little is known about a possible role of epigenetic factors. The full genomic repertoire of DNA methyltransferases (DNMTs) makes the honey bee an attractive emergent model for studying the role of epigenetics in the aging process of invertebrates, and especially so in social insects. We first quantified the transcript levels of the four DNMTs encoding genes in the head thorax and abdomens of workers of different age, showing that dnmt1a and dnmt3 expression is up-regulated in abdomens of old workers, whereas dnmt1b and dnmt2 are down-regulated in heads of old workers...
November 17, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29155216/communication-between-genomic-and-non-genomic-signaling-events-coordinate-steroid-hormone-actions
#3
Sandi R Wilkenfeld, Chenchu Lin, Daniel E Frigo
Steroid hormones are lipophilic molecules produced in one cell that can travel great distances within the body to elicit biological effects in another cell. In the canonical pathway, steroid hormone binding to a nuclear receptor (NR), often in the cytoplasm, causes the receptor to undergo a conformational change and translocate to the nucleus, where it interacts with specific sequences of DNA to regulate transcription. In addition to the classical genomic mechanism of action, alternate mechanisms of steroid activity have emerged that involve rapid, non-genomic signaling...
November 16, 2017: Steroids
https://www.readbyqxmd.com/read/29149833/g4-interacting-dna-helicases-and-polymerases-potential-therapeutic-targets
#4
Katrina Estep, Thomas J Butler, Jun Ding, Robert M Brosh
Guanine-rich DNA can fold into highly stable non-canonical four-stranded DNA structures called G-quadruplexes. These structures present obstacles for the DNA replication machinery, and it has been hypothesized that both eukaryotic DNA helicases and polymerases have evolved to resolve G4 DNA in vivo. Since the discovery of G-quadruplex DNA in the early 1960's, a number of studies have emerged reporting G-quadruplex DNA unfolding by helicase enzymes and DNA synthesis past G4 by specialized translesion polymerase enzymes...
November 16, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29141206/role-of-the-pif1-pcna-complex-in-pol-%C3%AE-dependent-strand-displacement-dna-synthesis-and-break-induced-replication
#5
Olga Buzovetsky, Youngho Kwon, Nhung Tuyet Pham, Claire Kim, Grzegorz Ira, Patrick Sung, Yong Xiong
The S. cerevisiae Pif1 helicase functions with DNA polymerase (Pol) δ in DNA synthesis during break-induced replication (BIR), a conserved pathway responsible for replication fork repair and telomere recombination. Pif1 interacts with the DNA polymerase processivity clamp PCNA, but the functional significance of the Pif1-PCNA complex remains to be elucidated. Here, we solve the crystal structure of PCNA in complex with a non-canonical PCNA-interacting motif in Pif1. The structure guides the construction of a Pif1 mutant that is deficient in PCNA interaction...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29138484/non-canonical-activation-of-ompr-drives-acid-and-osmotic-stress-responses-in-single-bacterial-cells
#6
Smarajit Chakraborty, Ricksen S Winardhi, Leslie K Morgan, Jie Yan, Linda J Kenney
Unlike eukaryotes, bacteria undergo large changes in osmolality and cytoplasmic pH. It has been described that during acid stress, bacteria internal pH promptly acidifies, followed by recovery. Here, using pH imaging in single living cells, we show that following acid stress, bacteria maintain an acidic cytoplasm and the osmotic stress transcription factor OmpR is required for acidification. The activation of this response is non-canonical, involving a regulatory mechanism requiring the OmpR cognate kinase EnvZ, but not OmpR phosphorylation...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29124284/ca-2-nuclear-factor-of-activated-t-cells-signaling-is-enriched-in-early-onset-rectal-tumors-devoid-of-canonical-wnt-activation
#7
Raju Kumar, Ratheesh Raman, Viswakalyan Kotapalli, Swarnalata Gowrishankar, Saumyadipta Pyne, Jonathan R Pollack, Murali D Bashyam
Our previous extensive analysis revealed a significant proportion of early-onset colorectal tumors from India to be localized to the rectum in younger individuals and devoid of deregulated Wnt/β-catenin signaling. In the current study, we performed a comprehensive genome-wide analysis of clinically well-annotated microsatellite stable early-onset sporadic rectal cancer (EOSRC) samples. Results revealed extensive DNA copy number alterations in rectal tumors in the absence of deregulated Wnt/β-catenin signaling...
November 9, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/29122981/in-situ-imaging-of-mitochondrial-translation-shows-weak-correlation-with-nucleoid-dna-intensity-and-no-suppression-during-mitosis
#8
Christopher Estell, Emmanouela Stamatidou, Sarah El-Messeiry, Andrew Hamilton
Although mitochondrial translation produces only 13 proteins, we show here how this can be labelled and detected in situ by fluorescence microscopy with a simple, rapid and inexpensive procedure using non-canonical amino acid labelling and click chemistry. This allows visualisation of the translational output in different mitochondria within a cell, their position within that cell and a comparison of mitochondrial translation between cells. Most highly translationally active mitochondria were closest to the nucleus but were also found at the distal end of long cellular projections...
November 9, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/29121981/intrinsic-dna-curvature-in-trypanosomes
#9
Pablo Smircich, Najib M El-Sayed, Beatriz Garat
BACKGROUND: Trypanosoma cruzi and Trypanosoma brucei are protozoan parasites causing Chagas disease and African sleeping sickness, displaying unique features of cellular and molecular biology. Remarkably, no canonical signals for RNA polymerase II promoters, which drive protein coding genes transcription, have been identified so far. The secondary structure of DNA has long been recognized as a signal in biological processes and more recently, its involvement in transcription initiation in Leishmania was proposed...
November 9, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29117225/genomic-comparison-between-staphylococcus-aureus-gn-strains-clinically-isolated-from-a-familial-infection-case-is1272-transposition-through-a-novel-inverted-repeat-replacing-mechanism
#10
Tsai-Wen Wan, Wataru Higuchi, Olga E Khokhlova, Wei-Chun Hung, Yasuhisa Iwao, Masataka Wakayama, Noriyoshi Inomata, Tomomi Takano, Yu-Tzu Lin, Olga V Peryanova, Kenji K Kojima, Alla B Salmina, Lee-Jene Teng, Tatsuo Yamamoto
A bacterial insertion sequence (IS) is a mobile DNA sequence carrying only the transposase gene (tnp) that acts as a mutator to disrupt genes, alter gene expressions, and cause genomic rearrangements. "Canonical" ISs have historically been characterized by their terminal inverted repeats (IRs), which may form a stem-loop structure, and duplications of a short (non-IR) target sequence at both ends, called target site duplications (TSDs). The IS distributions and virulence potentials of Staphylococcus aureus genomes in familial infection cases are unclear...
2017: PloS One
https://www.readbyqxmd.com/read/29114260/crosstalk-between-receptor-and-non-receptor-mediated-chemical-modes-of-action-in-rat-livers-converges-through-a-dysregulated-gene-expression-network-at-tumor-suppressor-tp53
#11
Karen M Funderburk, Scott S Auerbach, Pierre R Bushel
Chemicals, toxicants, and environmental stressors mediate their biologic effect through specific modes of action (MOAs). These encompass key molecular events that lead to changes in the expression of genes within regulatory pathways. Elucidating shared biologic processes and overlapping gene networks will help to better understand the toxicologic effects on biological systems. In this study we used a weighted network analysis of gene expression data from the livers of male Sprague-Dawley rats exposed to chemicals that elicit their effects through receptor-mediated MOAs (aryl hydrocarbon receptor, orphan nuclear hormone receptor, or peroxisome proliferator-activated receptor-α) or non-receptor-mediated MOAs (cytotoxicity or DNA damage)...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29108267/beta-catenin-represses-protein-kinase-d1-gene-expression-by-non-canonical-pathway-through-myc-max-transcription-complex-in-prostate-cancer
#12
Bita Nickkholgh, Sivanandane Sittadjody, Michael B Rothberg, Xiaolan Fang, Kunzhao Li, Jeff W Chou, Gregory A Hawkins, K C Balaji
Down regulation of Protein Kinase D1 (PrKD1), a novel serine threonine kinase, in prostate, gastric, breast and colon cancers in humans leads to disease progression. While the down regulation of PrKD1 by DNA methylation in gastric cancer and by nuclear beta-catenin in colon cancer has been shown, the regulatory mechanisms in other cancers are unknown. Because we had demonstrated that PrKD1 is the only known kinase to phosphorylate threonine 120 (T120) of beta-catenin in prostate cancer resulting in increased nuclear beta-catenin, we explored the role of beta-catenin in gene regulation of PrKD1...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29099315/alternative-mrna-processing-sites-decrease-genetic-variability-while-increasing-functional-diversity
#13
Didier Auboeuf
Recent large-scale RNA sequencing efforts have revealed the extensive diversity of mRNA molecules produced from most eukaryotic coding genes, which arises from the usage of alternative, cryptic or non-canonical splicing and intronic polyadenylation sites. The prevailing view regarding the tremendous diversity of coding gene transcripts is that mRNA processing is a flexible and more-or-less noisy process leading to a diversity of proteins on which natural selection can act depending on protein-mediated cellular functions...
November 3, 2017: Transcription
https://www.readbyqxmd.com/read/29098365/mms1-is-an-assistant-for-regulating-g-quadruplex-dna-structures
#14
REVIEW
Eike Schwindt, Katrin Paeschke
The preservation of genome stability is fundamental for every cell. Genomic integrity is constantly challenged. Among those challenges are also non-canonical nucleic acid structures. In recent years, scientists became aware of the impact of G-quadruplex (G4) structures on genome stability. It has been shown that folded G4-DNA structures cause changes in the cell, such as transcriptional up/down-regulation, replication stalling, or enhanced genome instability. Multiple helicases have been identified to regulate G4 structures and by this preserve genome stability...
November 2, 2017: Current Genetics
https://www.readbyqxmd.com/read/29080785/a-conserved-toll-like-receptor-to-nf-%C3%AE%C2%BAb-signaling-pathway-in-the-endangered-coral-orbicella-faveolata
#15
Leah M Williams, Lauren E Fuess, Joseph J Brennan, Katelyn M Mansfield, Erick Salas-Rodriguez, Julianne Welsh, Jake Awtry, Sarah Banic, Cecilia Chacko, Aarthia Chezian, Donovan Dowers, Felicia Estrada, Yu-Hsuan Hsieh, Jiawen Kang, Wanwen Li, Zoe Malchiodi, John Malinowski, Sean Matuszak, Thomas McTigue, David Mueller, Brian Nguyen, Michelle Nguyen, Phuong Nguyen, Sinead Nguyen, Ndidi Njoku, Khusbu Patel, William Pellegrini, Tessa Pliakas, Deena Qadir, Emma Ryan, Alex Schiffer, Amber Thiel, Sarah A Yunes, Kathryn E Spilios, Jorge H Pinzón C, Laura D Mydlarz, Thomas D Gilmore
Herein, we characterize the Toll-like receptor (TLR)-to-NF-κB innate immune pathway of Orbicella faveolata (Of), which is an ecologically important, disease-susceptible, reef-building coral. As compared to human TLRs, the intracellular TIR domain of Of-TLR is most similar to TLR4, and it can interact in vitro with the human TLR4 adapter MYD88. Treatment of O. faveolata tissue with lipopolysaccharide, a ligand for mammalian TLR4, resulted in gene expression changes consistent with NF-κB pathway mobilization...
October 26, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29075360/turnover-of-histones-and-histone-variants-in-postnatal-rat-brain-effects-of-alcohol-exposure
#16
Nadia Rachdaoui, Ling Li, Belinda Willard, Takhar Kasumov, Stephen Previs, Dipak Sarkar
BACKGROUND: Alcohol consumption during pregnancy is a significant public health problem and can result in a continuum of adverse outcomes to the fetus known as fetal alcohol spectrum disorders (FASD). Subjects with FASD show significant neurological deficits, ranging from microencephaly, neurobehavioral, and mental health problems to poor social adjustment and stress tolerance. Neurons are particularly sensitive to alcohol exposure. The neurotoxic action of alcohol, i.e., through ROS production, induces DNA damage and neuronal cell death by apoptosis...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29064490/fluorescent-nucleobases-as-tools-for-studying-dna-and-rna
#17
REVIEW
Wang Xu, Ke Min Chan, Eric T Kool
Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications...
November 2017: Nature Chemistry
https://www.readbyqxmd.com/read/29058704/nuclear-functions-of-nme-proteins
#18
Gemma S Puts, M Kathryn Leonard, Nidhi V Pamidimukkala, Devin E Snyder, David M Kaetzel
The NME family of proteins is composed of 10 isoforms, designated NME1-10, which are diverse in their enzymatic activities and patterns of subcellular localization. Each contains a conserved domain associated with a nucleoside diphosphate kinase (NDPK) function, although not all are catalytically active. Several of the NME isoforms (NME1, NME5, NME7, and NME8) also exhibit a 3'-5' exonuclease activity, suggesting roles in DNA proofreading and repair. NME1 and NME2 have been shown to translocate to the nucleus, although they lack a canonical nuclear localization signal...
October 23, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29036662/parp2-controls-double-strand-break-repair-pathway-choice-by-limiting-53bp1-accumulation-at-dna-damage-sites-and-promoting-end-resection
#19
Alexis Fouquin, Josée Guirouilh-Barbat, Bernard Lopez, Janet Hall, Mounira Amor-Guéret, Vincent Pennaneach
Double strand breaks (DSBs) are one of the most toxic lesions to cells. DSB repair by the canonical non-homologous end-joining (C-EJ) pathway involves minor, if any, processing of the broken DNA-ends, whereas the initiation of DNA resection channels the broken-ends toward DNA repair pathways using various lengths of homology. Mechanisms that control the resection initiation are thus central to the regulation to the choice of DSB repair pathway. Therefore, understanding the mechanisms which regulate the initiation of DNA end-resection is of prime importance...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29021563/non-canonical-reader-modules-of-baz1a-promote-recovery-from-dna-damage
#20
Mariano Oppikofer, Meredith Sagolla, Benjamin Haley, Hui-Min Zhang, Sarah K Kummerfeld, Jawahar Sudhamsu, E Megan Flynn, Tianyi Bai, Jennifer Zhang, Claudio Ciferri, Andrea G Cochran
Members of the ISWI family of chromatin remodelers mobilize nucleosomes to control DNA accessibility and, in some cases, are required for recovery from DNA damage. However, it remains poorly understood how the non-catalytic ISWI subunits BAZ1A and BAZ1B might contact chromatin to direct the ATPase SMARCA5. Here, we find that the plant homeodomain of BAZ1A, but not that of BAZ1B, has the unusual function of binding DNA. Furthermore, the BAZ1A bromodomain has a non-canonical gatekeeper residue and binds relatively weakly to acetylated histone peptides...
October 11, 2017: Nature Communications
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