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https://www.readbyqxmd.com/read/28240205/-how-genomic-approaches-help-the-understanding-of-the-initiation-of-dna-replication
#1
Benoit Miotto
Eukaryotic DNA replication starts at multiple sites distributed throughout the genome called origins of replication. The identification of the position of these origins in the genome, as well as the description of their sequence features and chromatin structure, have been the center of many studies over the last years. A handful of sophisticated methods has been developed to capture replication initiation events, to detect replication factors binding sites onto the chromatin and to computationally analyze these data at the genome scale...
February 2017: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/28239446/mechanism-of-transcription-coupled-dna-modification-recognition
#2
REVIEW
Ji Hyun Shin, Liang Xu, Dong Wang
As a key enzyme for gene expression, RNA polymerase II (pol II) reads along the DNA template and catalyzes accurate mRNA synthesis during transcription. On the other hand, genomic DNA is under constant attack by endogenous and environmental stresses. These attack cause many DNA lesions. Pol II functions as a specific sensor that is able to recognize changes in DNA sequences and structures and induces different outcomes. A critical question in the field is how Pol II recognizes and senses these DNA modifications or lesions...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/28226235/plant-mitochondrial-genomes-dynamics-and-mechanisms-of-mutation
#3
José M Gualberto, Kathleen J Newton
The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified...
February 9, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28225881/zinc-and-metalloproteinases-2-and-9-what-is-their-relation-with-breast-cancer
#4
Aldenora Oliveira do Nascimento Holanda, Ana Raquel Soares de Oliveira, Kyria Jayanne Clímaco Cruz, Juliana Soares Severo, Jennifer Beatriz Silva Morais, Benedito Borges da Silva, Dilina do Nascimento Marreiro
Zinc is the catalytic component of proteins that regulate responses to DNA damage, intracellular signaling enzymes, and matrix metalloproteinases, which are important proteins in carcinogenesis. The objective of this review is to bring current information on the participation of zinc and matrix metalloproteinases types 2 and 9 in mechanisms involved in the pathogenesis of breast cancer. We conducted a literature review, in consultation with the PubMed, Lilacs, and Scielo databases. The zinc and cysteine residues are structural elements shared by all members of the family of matrix metalloproteinases, and these proteins appear to be involved in the propagation of various types of neoplasms, including breast cancer...
January 1, 2017: Revista da Associação Médica Brasileira
https://www.readbyqxmd.com/read/28220209/s-phase-checkpoint-regulations-that-preserve-replication-and-chromosome-integrity-upon-dntp-depletion
#5
REVIEW
Michele Giannattasio, Dana Branzei
DNA replication stress, an important source of genomic instability, arises upon different types of DNA replication perturbations, including those that stall replication fork progression. Inhibitors of the cellular pool of deoxynucleotide triphosphates (dNTPs) slow down DNA synthesis throughout the genome. Following depletion of dNTPs, the highly conserved replication checkpoint kinase pathway, also known as the S-phase checkpoint, preserves the functionality and structure of stalled DNA replication forks and prevents chromosome fragmentation...
February 20, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28220120/neutrophil-extracellular-traps-and-its-implications-in-inflammation-an-overview
#6
REVIEW
Vidal Delgado-Rizo, Marco A Martínez-Guzmán, Liliana Iñiguez-Gutierrez, Alejandra García-Orozco, Anabell Alvarado-Navarro, Mary Fafutis-Morris
In addition to physical barriers, neutrophils are considered a part of the first line of immune defense. They can be found in the bloodstream, with a lifespan of 6-8 h, and in tissue, where they can last up to 7 days. The mechanisms that neutrophils utilize for host defense are phagocytosis, degranulation, cytokine production, and, the most recently described, neutrophil extracellular trap (NET) production. NETs are DNA structures released due to chromatin decondensation and spreading, and they thus occupy three to five times the volume of condensed chromatin...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28218725/treating-cancer-by-targeting-telomeres-and-telomerase
#7
REVIEW
Marko Ivancich, Zachary Schrank, Luke Wojdyla, Brandon Leviskas, Adijan Kuckovic, Ankita Sanjali, Neelu Puri
Telomerase is expressed in more than 85% of cancer cells. Tumor cells with metastatic potential may have a high telomerase activity, allowing cells to escape from the inhibition of cell proliferation due to shortened telomeres. Human telomerase primarily consists of two main components: hTERT, a catalytic subunit, and hTR, an RNA template whose sequence is complimentary to the telomeric 5'-dTTAGGG-3' repeat. In humans, telomerase activity is typically restricted to renewing tissues, such as germ cells and stem cells, and is generally absent in normal cells...
February 19, 2017: Antioxidants (Basel, Switzerland)
https://www.readbyqxmd.com/read/28216634/detecting-rna-modifications-in-the-epitranscriptome-predict-and-validate
#8
REVIEW
Mark Helm, Yuri Motorin
RNA modifications are emerging players in the field of post-transcriptional regulation of gene expression, and are attracting a comparable degree of research interest to DNA and histone modifications in the field of epigenetics. We now know of more than 150 RNA modifications and the true potential of a few of these is currently emerging as the consequence of a leap in detection technology, principally associated with high-throughput sequencing. This Review outlines the major developments in this field through a structured discussion of detection principles, lays out advantages and drawbacks of new high-throughput methods and presents conventional biophysical identification of modifications as meaningful ways for validation...
February 20, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28215500/environmental-epigenomics-current-approaches-to-assess-epigenetic-effects-of-endocrine-disrupting-compounds-edc-s-on-human-health
#9
REVIEW
Natalia Tapia-Orozco, Gerardo Santiago-Toledo, Valeria Barrón, Ana María Espinosa-García, José Antonio García-García, Roeb García-Arrazola
Environmental Epigenomics is a developing field to study the epigenetic effect on human health from exposure to environmental factors. Endocrine disrupting chemicals have been detected primarily in pharmaceutical drugs, personal care products, food additives, and food containers. Exposure to endocrine-disrupting chemicals (EDCs) has been associated with a high incidence and prevalence of many endocrine-related disorders in humans. Nevertheless, further evidence is needed to establish a correlation between exposure to EDC and human disorders...
February 10, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28214670/metal-mediated-dna-assembly-with-ligand-based-nucleosides
#10
REVIEW
Soham Mandal, Jens Müller
Nucleic acids such as DNA are increasingly being applied in nanotechnology, as a result of their capability to self-assemble reversibly. The formal replacement of canonical base pairs by metal-mediated ones enables a site-specific introduction of metal-based functionality into these biomolecules, leading to the formation of predesigned metal arrays. This article offers an overview of structural aspects of metal-mediated base pairs, reviews recent advances in the field of metal-mediated base pairing and presents potential applications of the resulting metal-modified nucleic acids...
February 16, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28213686/the-iswi-remodeler-in-plants-protein-complexes-biochemical-functions-and-developmental-roles
#11
REVIEW
Dongjie Li, Jie Liu, Wu Liu, Guang Li, Zhongnan Yang, Peng Qin, Lin Xu
Imitation Switch (ISWI) is a member of the ATP-dependent chromatin remodeling factor family, whose members move or restructure nucleosomes using energy derived from ATP hydrolysis. ISWI proteins are conserved in eukaryotes and usually form complexes with DDT (DNA-binding homeobox and different transcription factors)-domain proteins. Here, we review recent research on ISWI in the model plant Arabidopsis thaliana (AtISWI). AtISWI forms complexes with AtDDT-domain proteins, many of which have domain structures that differ from those of DDT-domain proteins in yeast and animals...
February 17, 2017: Chromosoma
https://www.readbyqxmd.com/read/28208770/splicing-and-polyadenylation-of-human-papillomavirus-type-16-mrnas
#12
REVIEW
Chengjun Wu, Naoko Kajitani, Stefan Schwartz
The human papillomavirus type 16 (HPV16) life cycle can be divided into an early stage in which the HPV16 genomic DNA is replicated, and a late stage in which the HPV16 structural proteins are synthesized and virions are produced. A strong coupling between the viral life cycle and the differentiation state of the infected cell is highly characteristic of all HPVs. The switch from the HPV16 early gene expression program to the late requires a promoter switch, a polyadenylation signal switch and a shift in alternative splicing...
February 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28208701/excitotoxins-mitochondrial-and-redox-disturbances-in-multiple-sclerosis
#13
REVIEW
Cecilia Rajda, Dániel Pukoli, Zsuzsanna Bende, Zsófia Majláth, László Vécsei
Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS). There is increasing evidence that MS is not only characterized by immune mediated inflammatory reactions, but also by neurodegenerative processes. There is cumulating evidence that neurodegenerative processes, for example mitochondrial dysfunction, oxidative stress, and glutamate (Glu) excitotoxicity, seem to play an important role in the pathogenesis of MS. The alteration of mitochondrial homeostasis leads to the formation of excitotoxins and redox disturbances...
February 8, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28208646/recognition-of-local-dna-structures-by-p53-protein
#14
Václav Brázda, Jan Coufal
p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53...
February 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28199368/secondary-structure-prediction-revisited-theoretical-%C3%AE-sheet-propensity-and-coil-propensity-represent-structures-of-amyloids-and-aid-in-elucidating-phenomena-involved-in-interspecies-transmission-of-prions
#15
Yuzuru Taguchi, Noriyuki Nishida
Prions are unique infectious agents, consisting solely of abnormally-folded prion protein (PrPSc). However, they possess virus-like features, including strain diversity, the ability to adapt to new hosts and to be altered evolutionarily. Because prions lack genetic material (DNA and RNA), these biological phenomena have been attributed to the structural properties of PrPSc. Therefore, many structural models of the structure of PrPSc have been proposed based on the limited structural information available, regardless of the incompatibility with high-resolution structural analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28199214/base-excision-repair-of-oxidative-dna-damage-from-mechanism-to-disease
#16
Amy M Whitaker, Matthew A Schaich, Mallory S Smith, Tony S Flynn, Bret D Freudenthal
Reactive oxygen species continuously assault the structure of DNA resulting in oxidation and fragmentation of the nucleobases. Both oxidative DNA damage itself and its repair mediate the progression of many prevalent human maladies. The major pathway tasked with removal of oxidative DNA damage, and hence maintaining genomic integrity, is base excision repair (BER). The aphorism that structure often dictates function has proven true, as numerous recent structural biology studies have aided in clarifying the molecular mechanisms used by key BER enzymes during the repair of damaged DNA...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28196731/natural-history-of-conversion-of-leber-s-hereditary-optic-neuropathy-a-prospective-case-series
#17
Tiffany Jean Hwang, Rustum Karanjia, Milton Nunes Moraes-Filho, Jesse Gale, Jeffrey Show Tran, Edward R Chu, Solange R Salomao, Adriana Berezovsky, Rubens Belfort, Milton Nunes Moraes, Federico Sadun, Anna Maria DeNegri, Chiara La Morgia, Piero Barboni, Carolina do V F Ramos, Carlos Filipe Chicani, Peter A Quiros, Valerio Carelli, Alfredo A Sadun
PURPOSE: To illustrate the natural history of Leber's hereditary optic neuropathy (LHON). DESIGN: Prospective observational case series. PARTICIPANTS: The Soave-Brazil pedigree of m.11778G>A/ND4 mitochondrial DNA LHON mutation. METHODS: A prospectively acquired database of the Soave-Brazil pedigree was reviewed. Data from 285 individuals were included in the database over a 15-year period. The pedigree was reviewed for unaffected mutation carriers who converted to affected status, 6 patients with LHON were identified...
February 10, 2017: Ophthalmology
https://www.readbyqxmd.com/read/28196338/telomerase-and-telomere-biology-in-hematological-diseases-a-new-therapeutic-target
#18
REVIEW
Alessandro Allegra, Vanessa Innao, Giuseppa Penna, Demetrio Gerace, Andrea G Allegra, Caterina Musolino
Telomeres are structures confined at the ends of eukaryotic chromosomes. With each cell division, telomeric repeats are lost because DNA polymerases are incapable to fully duplicate the very ends of linear chromosomes. Loss of repeats causes cell senescence, and apoptosis. Telomerase neutralizes loss of telomeric sequences by adding telomere repeats at the 3' telomeric overhang. Telomere biology is frequently associated with human cancer and dysfunctional telomeres have been proved to participate to genetic instability...
February 7, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28183261/lactate-dehydrogenase-inhibition-biochemical-relevance-and-therapeutical-potential
#19
Giuseppina Laganà, Davide Barreca, Antonella Calderaro, Ersilia Bellocco
Lactate dehydrogenase (LHD) is a key enzyme of anaerobic metabolism in almost all living organisms and it is also a functional checkpoint for glucose restoration during gluconeogenesis and single-stranded DNA metabolism. This enzyme has a well preserved structure during evolution and among the species, with little, but sometimes very useful, changes in the amino acid sequence, which makes it an attractive target for the design and construction of functional molecules able to modulate its catalytic potential and expression...
February 8, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28181049/condensin-master-organizer-of-the-genome
#20
REVIEW
Paul Kalitsis, Tao Zhang, Kathryn M Marshall, Christian F Nielsen, Damien F Hudson
A fundamental requirement in nature is for a cell to correctly package and divide its replicated genome. Condensin is a mechanical multisubunit complex critical to this process. Condensin uses ATP to power conformational changes in DNA to enable to correct DNA compaction, organization, and segregation of DNA from the simplest bacteria to humans. The highly conserved nature of the condensin complex and the structural similarities it shares with the related cohesin complex have provided important clues as to how it functions in cells...
February 9, 2017: Chromosome Research
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