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https://www.readbyqxmd.com/read/28821632/transcriptomic-and-epigenetic-regulation-of-disuse-atrophy-and-the-return-to-activity-in-skeletal-muscle
#1
Andrew G Fisher, Robert A Seaborne, Thomas M Hughes, Alex Gutteridge, Claire Stewart, Judy M Coulson, Adam P Sharples, Jonathan C Jarvis
Physical inactivity and disuse are major contributors to age-related muscle loss. Denervation of skeletal muscle has been previously used as a model with which to investigate muscle atrophy following disuse. Although gene regulatory networks that control skeletal muscle atrophy after denervation have been established, the transcriptome in response to the recovery of muscle after disuse and the associated epigenetic mechanisms that may function to modulate gene expression during skeletal muscle atrophy or recovery have yet to be investigated...
August 17, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28819455/microvesicles-as-potential-biomarkers-for-the-identification-of-senescence-in-human-mesenchymal-stem-cells
#2
Qian Lei, Teng Liu, Fei Gao, Hui Xie, Li Sun, Aiqi Zhao, Wenxiang Ren, Hao Guo, Liming Zhang, Hongxiang Wang, Zhichao Chen, An-Yuan Guo, Qiubai Li
Senescence in human mesenchymal stem cells (MSCs) not only contributes to organism aging and the development of a variety of diseases but also severely impairs their therapeutic properties as a promising cell therapy. Studies searching for efficient biomarkers that represent cellular senescence have attracted much attention; however, no single marker currently provides an accurate cell-free representation of cellular senescence. Here, we studied characteristics of MSC-derived microvesicles (MSC-MVs) that may reflect the senescence in their parental MSCs...
2017: Theranostics
https://www.readbyqxmd.com/read/28819095/non-coding-rnas-participate-in-the-regulatory-network-of-cldn4-via-cerna-mediated-mirna-evasion
#3
Yong-Xi Song, Jing-Xu Sun, Jun-Hua Zhao, Yu-Chong Yang, Jin-Xin Shi, Zhong-Hua Wu, Xiao-Wan Chen, Peng Gao, Zhi-Feng Miao, Zhen-Ning Wang
Thousands of genes have been well demonstrated to play important roles in cancer progression. As genes do not function in isolation, they can be grouped into "networks" based on their interactions. In this study, we discover a network regulating Claudin-4 in gastric cancer. We observe that Claudin-4 is up-regulated in gastric cancer and is associated with poor prognosis. Claudin-4 reinforce proliferation, invasion, and EMT in AGS, HGC-27, and SGC-7901 cells, which could be reversed by miR-596 and miR-3620-3p...
August 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28818840/hcn4-ion-channel-function-is-required-for-early-events-that-regulate-anatomical-left-right-patterning-in-a-nodal-and-lefty-asymmetric-gene-expression-independent-manner
#4
Vaibhav P Pai, Valerie Willocq, Emily J Pitcairn, Joan M Lemire, Jean-François Paré, Nian-Qing Shi, Kelly A McLaughlin, Michael Levin
Laterality is a basic characteristic of all life forms, from single cell organisms to complex plants and animals. For many metazoans, consistent left-right asymmetric patterning is essential for the correct anatomy of internal organs, such as the heart, gut, and brain; disruption of left-right asymmetry patterning leads to an important class of birth defects in human patients. Laterality functions across multiple scales, where early embryonic, subcellular and chiral cytoskeletal events are coupled with asymmetric amplification mechanisms and gene regulatory networks leading to asymmetric physical forces that ultimately result in distinct left and right anatomical organ patterning...
August 17, 2017: Biology Open
https://www.readbyqxmd.com/read/28818668/a-bipolar-role-of-the-transcription-factor-erg-for-cnidarian-germ-layer-formation-and-apical-domain-patterning
#5
Aldine R Amiel, Hereroa Johnston, Taylor Chock, Paul Dahlin, Marta Iglesias, Michael Layden, Eric Röttinger, Mark Q Martindale
Germ layer formation and axial patterning are biological processes that are tightly linked during embryonic development of most metazoans. In addition to canonical WNT, it has been proposed that ERK-MAPK signaling is involved in specifying oral as well as aboral territories in cnidarians. However, the effector and the molecular mechanism underlying latter phenomenon is unknown. By screening for potential effectors of ERK-MAPK signaling in both domains, we identified a member of the ETS family of transcription factors, Nverg that is bi-polarily expressed prior to gastrulation...
August 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28818098/sex-chromosomes-drive-gene-expression-and-regulatory-dimorphisms-in-mouse-embryonic-stem-cells
#6
Rachael J Werner, Bryant M Schultz, Jacklyn M Huhn, Jaroslav Jelinek, Jozef Madzo, Nora Engel
BACKGROUND: Pre-implantation embryos exhibit sexual dimorphisms in both primates and rodents. To determine whether these differences reflected sex-biased expression patterns, we generated transcriptome profiles for six 40,XX, six 40,XY, and two 39,X mouse embryonic stem (ES) cells by RNA sequencing. RESULTS: We found hundreds of coding and non-coding RNAs that were differentially expressed between male and female cells. Surprisingly, the majority of these were autosomal and included RNA encoding transcription and epigenetic and chromatin remodeling factors...
August 17, 2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/28817668/titanium-biomaterials-with-complex-surfaces-induced-aberrant-peripheral-circadian-rhythms-in-bone-marrow-mesenchymal-stromal-cells
#7
Nathaniel Hassan, Kirstin McCarville, Kenzo Morinaga, Cristiane M Mengatto, Peter Langfelder, Akishige Hokugo, Yu Tahara, Christopher S Colwell, Ichiro Nishimura
Circadian rhythms maintain a high level of homeostasis through internal feed-forward and -backward regulation by core molecules. In this study, we report the highly unusual peripheral circadian rhythm of bone marrow mesenchymal stromal cells (BMSCs) induced by titanium-based biomaterials with complex surface modifications (Ti biomaterial) commonly used for dental and orthopedic implants. When cultured on Ti biomaterials, human BMSCs suppressed circadian PER1 expression patterns, while NPAS2 was uniquely upregulated...
2017: PloS One
https://www.readbyqxmd.com/read/28814968/asp-based-method-for-the-enumeration-of-attractors-in-non-deterministic-synchronous-and-asynchronous-multi-valued-networks
#8
Emna Ben Abdallah, Maxime Folschette, Olivier Roux, Morgan Magnin
BACKGROUND: This paper addresses the problem of finding attractors in biological regulatory networks. We focus here on non-deterministic synchronous and asynchronous multi-valued networks, modeled using automata networks (AN). AN is a general and well-suited formalism to study complex interactions between different components (genes, proteins,...). An attractor is a minimal trap domain, that is, a part of the state-transition graph that cannot be escaped. Such structures are terminal components of the dynamics and take the form of steady states (singleton) or complex compositions of cycles (non-singleton)...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28814964/milk-disrupts-p53-and-dnmt1-the-guardians-of-the-genome-implications-for-acne-vulgaris-and-prostate-cancer
#9
Bodo C Melnik
There is accumulating evidence that milk shapes the postnatal metabolic environment of the newborn infant. Based on translational research, this perspective article provides a novel mechanistic link between milk intake and milk miRNA-regulated gene expression of the transcription factor p53 and DNA methyltransferase 1 (DNMT1), two guardians of the human genome, that control transcriptional activity, cell survival, and apoptosis. Major miRNAs of milk, especially miRNA-125b, directly target TP53 and complex p53-dependent gene regulatory networks...
2017: Nutrition & Metabolism
https://www.readbyqxmd.com/read/28814798/genetic-polymorphisms-of-lncrna-p53-regulatory-network-genes-are-associated-with-concurrent-chemoradiotherapy-toxicities-and-efficacy-in-nasopharyngeal-carcinoma-patients
#10
Youhong Wang, Zhen Guo, Yu Zhao, Yi Jin, Liang An, Bin Wu, Zhaoqian Liu, Xiaoping Chen, Xiang Chen, Honghao Zhou, Hui Wang, Wei Zhang
The relevance of the transcription factor p53 in cancer is inarguable, and numerous lncRNAs are involved in the p53 regulatory network as either regulators or effectors, triggering a transcriptional response that causes either cell arrest or apoptosis following DNA damage in a p53-dependent manner. Despite the fact that the therapeutic response is improved in NPC, heterogeneity among people remains with regard to the susceptibility of adverse effects and the efficacy of treatments. Therefore, we analysed eight potentially functional SNPs of five genes in the lncRNA-p53 regulatory network in a discovery cohort of 505 NPC patients...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28813680/antibiotics-disrupt-coordination-between-transcriptional-and-phenotypic-stress-responses-in-pathogenic-bacteria
#11
Paul A Jensen, Zeyu Zhu, Tim van Opijnen
Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28813674/an-integrated-systems-biology-approach-identifies-trim25-as-a-key-determinant-of-breast-cancer-metastasis
#12
Logan A Walsh, Mariano J Alvarez, Erich Y Sabio, Marsha Reyngold, Vladimir Makarov, Suranjit Mukherjee, Ken-Wing Lee, Alexis Desrichard, Şevin Turcan, Martin G Dalin, Vinagolu K Rajasekhar, Shuibing Chen, Linda T Vahdat, Andrea Califano, Timothy A Chan
At the root of most fatal malignancies are aberrantly activated transcriptional networks that drive metastatic dissemination. Although individual metastasis-associated genes have been described, the complex regulatory networks presiding over the initiation and maintenance of metastatic tumors are still poorly understood. There is untapped value in identifying therapeutic targets that broadly govern coordinated transcriptional modules dictating metastatic progression. Here, we reverse engineered and interrogated a breast cancer-specific transcriptional interaction network (interactome) to define transcriptional control structures causally responsible for regulating genetic programs underlying breast cancer metastasis in individual patients...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28812536/edgar-a-database-of-disease-gene-associations-with-annotated-relationships-among-genes
#13
Giulia Babbi, Pier Luigi Martelli, Giuseppe Profiti, Samuele Bovo, Castrense Savojardo, Rita Casadio
BACKGROUND: Genetic investigations, boosted by modern sequencing techniques, allow dissecting the genetic component of different phenotypic traits. These efforts result in the compilation of lists of genes related to diseases and show that an increasing number of diseases is associated with multiple genes. Investigating functional relations among genes associated with the same disease contributes to highlighting molecular mechanisms of the pathogenesis. RESULTS: We present eDGAR, a database collecting and organizing the data on gene/disease associations as derived from OMIM, Humsavar and ClinVar...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28811654/characterization-of-the-mollusc-rig-i-mavs-pathway-reveals-an-archaic-antiviral-signalling-framework-in-invertebrates
#14
Baoyu Huang, Linlin Zhang, Yishuai Du, Fei Xu, Li Li, Guofan Zhang
Despite the mitochondrial antiviral signalling protein (MAVS)-dependent RIG-I-like receptor (RLR) signalling pathway in the cytosol plays an indispensable role in the antiviral immunity of the host, surprising little is known in invertebrates. Here we characterized the major members of RLR pathway and investigated their signal transduction a Molluscs. We show that genes involved in RLR pathway were significantly induced during virus challenge, including CgRIG-I-1, CgMAVS, CgTRAF6 (TNF receptor-associated factor 6), and CgIRFs (interferon regulatory factors...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811563/crosstalk-between-diurnal-rhythm-and-water-stress-reveals-an-altered-primary-carbon-flux-into-soluble-sugars-in-drought-treated-rice-leaves
#15
Seo-Woo Kim, Sang-Kyu Lee, Hee-Jeong Jeong, Gynheung An, Jong-Seong Jeon, Ki-Hong Jung
Plants retain rhythmic physiological responses when adapting to environmental challenges. However, possible integrations between drought conditions and those responses have not received much focus, especially regarding crop plants, and the relationship between abiotic stress and the diurnal cycle is generally not considered. Therefore, we conducted a genome-wide analysis to identify genes showing both diurnal regulation and water-deficiency response in rice (Oryza sativa). Among the 712 drought-responsive genes primary identified, 56...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811509/determining-causal-mirnas-and-their-signaling-cascade-in-diseases-using-an-influence-diffusion-model
#16
Joseph J Nalluri, Pratip Rana, Debmalya Barh, Vasco Azevedo, Thang N Dinh, Vladimir Vladimirov, Preetam Ghosh
In recent studies, miRNAs have been found to be extremely influential in many of the essential biological processes. They exhibit a self-regulatory mechanism through which they act as positive/negative regulators of expression of genes and other miRNAs. This has direct implications in the regulation of various pathophysiological conditions, signaling pathways and different types of cancers. Studying miRNA-disease associations has been an extensive area of research; however deciphering miRNA-miRNA network regulatory patterns in several diseases remains a challenge...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811334/argonaute-8-ago8-mediates-the-elicitation-of-primary-defense-against-herbivory
#17
Maitree Pradhan, Priyanka Pandey, Klaus Gase, Murali Shraff, Ravi K Singh, Avinash Sethi, Ian T Baldwin, Shree P Pandey
In Nicotiana attenuata, specific RNA directed RNA polymerase (RdR1) and the Dicer-like proteins (DCL3 and 4) are recruited during herbivore attack to mediate the regulation of defense responses. However, the identity and role(s) of Argonautes (AGOs) involved in herbivory remains unknown. Of the 11 AGOs in the N. attenuata genome, we silenced the expression of 10. Plants silenced in NaAGO8 expression grew normally but were highly susceptible to herbivore attack. Larvae of the Manduca sexta grew faster when consuming irAGO8 plants, but did not differ from WT when consuming plants silenced in AGO1 (a, b and c), AGO2, AGO4 (a and b), AGO7, or AGO10 expression...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28811313/a-key-role-for-foxq2-in-anterior-head-and-central-brain-patterning-in-insects
#18
Peter Kitzmann, Matthias Weißkopf, Magdalena Ines Schacht, Gregor Bucher
Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the red flour beetle Tribolium castaneum ortholog of foxQ2 (Tc-foxQ2) as a novel upstream component of the aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression...
August 15, 2017: Development
https://www.readbyqxmd.com/read/28811264/protein-coding-genes-as-hosts-for-noncoding-rna-expression
#19
REVIEW
Vincent Boivin, Gabrielle Deschamps-Francoeur, Michelle S Scott
With the emergence of high-throughput sequence characterization methods and the subsequent improvements in gene annotations, it is becoming increasingly clear that a large proportion of eukaryotic protein-coding genes (as many as 50% in human) serve as host genes for non-coding RNA genes. Amongst the most extensively characterized embedded non-coding RNA genes, small nucleolar RNAs and microRNAs represent abundant families. Encoded individually or clustered, in sense or antisense orientation with respect to their host and independently expressed or dependent on host expression, the genomic characteristics of embedded genes determine their biogenesis and the extent of their relationship with their host gene...
August 12, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28810905/omni-polya-a-method-and-tool-for-accurate-recognition-of-poly-a-signals-in-human-genomic-dna
#20
Arturo Magana-Mora, Manal Kalkatawi, Vladimir B Bajic
BACKGROUND: Polyadenylation is a critical stage of RNA processing during the formation of mature mRNA, and is present in most of the known eukaryote protein-coding transcripts and many long non-coding RNAs. The correct identification of poly(A) signals (PAS) not only helps to elucidate the 3'-end genomic boundaries of a transcribed DNA region and gene regulatory mechanisms but also gives insight into the multiple transcript isoforms resulting from alternative PAS. Although progress has been made in the in-silico prediction of genomic signals, the recognition of PAS in DNA genomic sequences remains a challenge...
August 15, 2017: BMC Genomics
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