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Expression genomic integration

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https://www.readbyqxmd.com/read/29144405/genomic-analysis-of-the-asmt-gene-family-in-solanum-lycopersicum
#1
Weicheng Liu, Dake Zhao, Chunfang Zheng, Chen Chen, Xin Peng, Yuan Cheng, Hongjian Wan
Acetylserotonin methyltransferase (ASMT) is the last enzyme of melatonin biosynthesis and may play a rate-limiting role in the melatonin production of plants. In this study, systematic analysis of the ASMT gene family in tomato (Solanum lycopersicum Mill) has been presented by the integration of the structural features, phylogenetic relationships, exon/intron configuration, and expression profile during growth and development, as well as biotic stresses. The results revealed that the tomato genome encoded a minimum of 14 members, containing three probable encoded pseudogenes...
November 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29143556/datalbase-a-database-for-genomic-and-transcriptomic-data-related-to-tal-effectors
#2
Alvaro L Pérez-Quintero, Léo Lamy, Carlos A Zarate, Sébastien Cunnac, Erin L Doyle, Adam J Bogdanove, Boris Szurek, Alexis Derepeer
Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility S genes, triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs' amino acid sequence. New candidate susceptibility genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements (EBEs)...
November 16, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29143332/accurate-prediction-and-elucidation-of-drug-resistance-based-on-the-robust-and-reproducible-chemoresponse-communities
#3
Enyu Dai, Jing Wang, Feng Yang, Xu Zhou, Qian Song, Shuyuan Wang, Xuexin Yu, Dianming Liu, Qian Yang, Hong Dai, Wei Jiang, Hong Ling
Selecting the available treatment for each cancer patient from genomic context is a core goal of precision medicine, but innovative approaches with mechanism interpretation and improved performance are still highly needed. Through utilizing in vitro chemotherapy response data coupled with gene and miRNA expression profiles, we applied a network-based approach that identified markers not as individual molecules but as functional groups extracted from the integrated transcription factor and miRNA regulatory network...
November 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29143239/improving-cellulase-production-in-submerged-fermentation-by-the-expression-of-a-vitreoscilla-hemoglobin-in-trichoderma-reesei
#4
Jie Lin, Xiamei Zhang, Bingran Song, Wei Xue, Xiaoyun Su, Xiuzhen Chen, Zhiyang Dong
Trichoderma reesei is well known as an industrial workhorse fungus in cellulase production. The low dissolved oxygen supply in the highly viscous medium of T. reesei remains a major bottleneck that hampers growth and cellulase production in submerged fermentation. Vitreoscilla hemoglobin (VHb) has been demonstrated to improve metabolism and protein production in different heterologous hosts under hypoxic conditions, but the use of VHb in T. reesei remains uninvestigated. This study examines the effect of VHb in improving T...
November 15, 2017: AMB Express
https://www.readbyqxmd.com/read/29141961/chromatin-accessibility-dynamics-reveal-novel-functional-enhancers-in-c-elegans
#5
Aaron C Daugherty, Robin W Yeo, Jason D Buenrostro, William J Greenleaf, Anshul Kundaje, Anne Brunet
Chromatin accessibility, a crucial component of genome regulation, has primarily been studied in homogeneous and simple systems, such as isolated cell populations or early-development models. Whether chromatin accessibility can be assessed in complex, dynamic systems in vivo with high sensitivity remains largely unexplored. In this study, we use ATAC-seq to identify chromatin accessibility changes in a whole animal, the model organism Caenorhabditis elegans, from embryogenesis to adulthood. Chromatin accessibility changes between developmental stages are highly reproducible, recapitulate histone modification changes, and reveal key regulatory aspects of the epigenomic landscape throughout organismal development...
November 15, 2017: Genome Research
https://www.readbyqxmd.com/read/29141959/an-integrative-strategy-to-identify-the-entire-protein-coding-potential-of-prokaryotic-genomes-by-proteogenomics
#6
Ulrich Omasits, Adithi R Varadarajan, Michael Schmid, Sandra Goetze, Damianos Melidis, Marc Bourqui, Olga Nikolayeva, Maxime Québatte, Andrea Patrignani, Christoph Dehio, Juerg E Frey, Mark D Robinson, Bernd Wollscheid, Christian H Ahrens
Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome...
November 15, 2017: Genome Research
https://www.readbyqxmd.com/read/29139059/evolution-of-rubisco-activase-gene-in-plants
#7
Ragupathi Nagarajan, Kulvinder S Gill
Rubisco activase of plants evolved in a stepwise manner without losing its function to adapt to the major evolutionary events including endosymbiosis and land colonization. Rubisco activase is an essential enzyme for photosynthesis, which removes inhibitory sugar phosphates from the active sites of Rubisco, a process necessary for Rubisco activation and carbon fixation. The gene probably evolved in cyanobacteria as different species differ for its presence. However, the gene is present in all other plant species...
November 14, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29138855/integrated-bioinformatics-analysis-of-the-osteoarthritis%C3%A2-associated-microrna-expression-signature
#8
Xi Wang, Yujie Ning, Bing Zhou, Lei Yang, Yingting Wang, Xiong Guo
Numerous studies have focused on osteoarthritis (OA) cartilage injuries, with observations of abnormalities in microRNA (miRNA) expression levels. The aim of the present study was to consolidate and assess the results of these studies to identify potential miRNA biomarkers of OA. A comprehensive meta‑analysis of eight independent miRNA expression studies in OA was performed using the robust rank aggregation method (RRA), which contained a total of 82 OA and 39 normal cartilage samples. The targets of meta‑signature miRNA were predicted using TargetScan v6...
November 14, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29138277/coupling-shrna-screens-with-single-cell-rna-seq-identifies-a-dual-role-for-mtor-in-reprogramming-induced-senescence
#9
Marieke Aarts, Athena Georgilis, Meryam Beniazza, Patrizia Beolchi, Ana Banito, Thomas Carroll, Marizela Kulisic, Daniel F Kaemena, Gopuraja Dharmalingam, Nadine Martin, Wolf Reik, Johannes Zuber, Keisuke Kaji, Tamir Chandra, Jesús Gil
Expression of the transcription factors OCT4, SOX2, KLF4, and cMYC (OSKM) reprograms somatic cells into induced pluripotent stem cells (iPSCs). Reprogramming is a slow and inefficient process, suggesting the presence of safeguarding mechanisms that counteract cell fate conversion. One such mechanism is senescence. To identify modulators of reprogramming-induced senescence, we performed a genome-wide shRNA screen in primary human fibroblasts expressing OSKM. In the screen, we identified novel mediators of OSKM-induced senescence and validated previously implicated genes such as CDKN1A We developed an innovative approach that integrates single-cell RNA sequencing (scRNA-seq) with the shRNA screen to investigate the mechanism of action of the identified candidates...
November 14, 2017: Genes & Development
https://www.readbyqxmd.com/read/29133912/the-multiple-antibiotic-resistance-operon-of-enteric-bacteria-controls-dna-repair-and-outer-membrane-integrity
#10
Prateek Sharma, James R J Haycocks, Alistair D Middlemiss, Rachel A Kettles, Laura E Sellars, Vito Ricci, Laura J V Piddock, David C Grainger
The multiple antibiotic resistance (mar) operon of Escherichia coli is a paradigm for chromosomally encoded antibiotic resistance in enteric bacteria. The locus is recognised for its ability to modulate efflux pump and porin expression via two encoded transcription factors, MarR and MarA. Here we map binding of these regulators across the E. coli genome and identify an extensive mar regulon. Most notably, MarA activates expression of genes required for DNA repair and lipid trafficking. Consequently, the mar locus reduces quinolone-induced DNA damage and the ability of tetracyclines to traverse the outer membrane...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133827/blastocyst-formation-rate-and-transgene-expression-are-associated-with-gene-insertion-into-safe-and-non-safe-harbors-in-the-cattle-genome
#11
Milad Khorramian Ghahfarokhi, Kianoush Dormiani, Ali Mohammadi, Farnoosh Jafarpour, Mohammad Hossein Nasr-Esfahani
Integration target site is the most important factor in successful production of transgenic animals. However, stable expression of transgene without disturbing the function of the host genome depends on promoter methylation, transgene copy number and transcriptional activity in integration regions. Recently, new genome-editing tools have made much progress, however little attention has been paid to the identification of genomic safe harbors. The aim of the present study was to evaluate the effect of insertion site, promoter and copy number of transgene on the production of embryos from cattle fibroblast cells following somatic cell nuclear transfer (SCNT)...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133300/the-importance-of-satellite-sequence-repression-for-genome-stability
#12
Peter Zeller, Susan M Gasser
Up to two-thirds of eukaryotic genomes consist of repetitive sequences, which include both transposable elements and tandemly arranged simple or satellite repeats. Whereas extensive progress has been made toward understanding the danger of and control over transposon expression, only recently has it been recognized that DNA damage can arise from satellite sequence transcription. Although the structural role of satellite repeats in kinetochore function and end protection has long been appreciated, it has now become clear that it is not only these functions that are compromised by elevated levels of transcription...
November 13, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29132331/adaptation-of-the-goldenbraid-modular-cloning-system-and-creation-of-a-toolkit-for-the-expression-of-heterologous-proteins-in-yeast-mitochondria
#13
Ana Pérez-González, Ryan Kniewel, Marcel Veldhuizen, Hemant K Verma, Mónica Navarro-Rodríguez, Luis M Rubio, Elena Caro
BACKGROUND: There is a need for the development of synthetic biology methods and tools to facilitate rapid and efficient engineering of yeast that accommodates the needs of specific biotechnology projects. In particular, the manipulation of the mitochondrial proteome has interesting potential applications due to its compartmentalized nature. One of these advantages resides in the fact that metalation occurs after protein import into mitochondria, which contains pools of iron, zinc, copper and manganese ions that can be utilized in recombinant metalloprotein metalation reactions...
November 13, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/29130343/defining-baseline-epigenetic-landscapes-in-the-rat-liver
#14
John P Thomson, Raffaele Ottaviano, Roland Buesen, Jonathan G Moggs, Michael Schwarz, Richard R Meehan
Characterization of the hepatic epigenome following exposure to chemicals and therapeutic drugs provides novel insights into toxicological and pharmacological mechanisms, however appreciation of genome-wide inter- and intra-strain baseline epigenetic variation, particularly in under-characterized species such as the rat is limited. Material & methods: To enhance the utility of epigenomic endpoints safety assessment, we map both DNA modifications (5-methyl-cytosine and 5-hydroxymethyl-cytosine) and enhancer related chromatin marks (H3K4me1 and H3K27ac) across multiple male and female rat livers for two important outbred laboratory rat strains (Sprague-Dawley and Wistar)...
November 13, 2017: Epigenomics
https://www.readbyqxmd.com/read/29129922/statistical-and-integrative-system-level-analysis-of-dna-methylation-data
#15
REVIEW
Andrew E Teschendorff, Caroline L Relton
Epigenetics plays a key role in cellular development and function. Alterations to the epigenome are thought to capture and mediate the effects of genetic and environmental risk factors on complex disease. Currently, DNA methylation is the only epigenetic mark that can be measured reliably and genome-wide in large numbers of samples. This Review discusses some of the key statistical challenges and algorithms associated with drawing inferences from DNA methylation data, including cell-type heterogeneity, feature selection, reverse causation and system-level analyses that require integration with other data types such as gene expression, genotype, transcription factor binding and other epigenetic information...
November 13, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29127397/spagm-inferring-subpathway-activity-by-integrating-gene-and-mirna-expression-robust-functional-signature-identification-for-melanoma-prognoses
#16
Chun-Long Zhang, Yan-Jun Xu, Hai-Xiu Yang, Ying-Qi Xu, De-Si Shang, Tan Wu, Yun-Peng Zhang, Xia Li
MicroRNAs (miRNAs) regulate biological pathways by inhibiting gene expression. However, most current analytical methods fail to consider miRNAs, when inferring functional or pathway activities. In this study, we developed a model called sPAGM to infer subpathway activities by integrating gene and miRNA expressions. In this model, we reconstructed subpathway graphs by embedding miRNA components, and characterized subpathway activity (sPA) scores by simultaneously considering the expression levels of miRNAs and genes...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29127022/genetic-and-immune-profiles-of-solid-predominant-lung-adenocarcinoma-reveal-potential-immunotherapeutic-strategies
#17
Zhong-Yi Dong, Chao Zhang, Yu-Fa Li, Jian Su, Zhi Xie, Si-Yang Liu, Li-Xu Yan, Zhi-Hong Chen, Xue-Ning Yang, Jun-Tao Lin, Hai-Yan Tu, Jin-Ji Yang, Qing Zhou, Yue-Li Sun, Wen-Zhao Zhong, Yi-Long Wu
BACKGROUND: Subtype classification of lung adenocarcinoma (LUAD) divides different survivals and therapeutic vulnerabilities, while the underlying molecular mechanism is little to be known. This study sought to determine the genetic and immune profiles of histologic subtypes and identify the evidence for adjuvant immunotherapy. PATIENTS AND METHODS: We performed an integrated analysis on multidimensional data from a discovery set including cohorts of The Cancer Genome Atlas (TCGA) and the Broad set from the LUAD public database, and a validation set from the Guangdong Lung Cancer Institute (GLCI)...
November 7, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/29126833/brca1-and-brca2-expression-patterns-and-prognostic-significance-in-digestive-system-cancers
#18
Gui-Hua Wang, Chun-Mei Zhao, Ying Huang, Wei Wang, Shu Zhang, Xudong Wang
The role of BRCA1 and BRCA2 genes is mainly to maintain genome integrity in response to DNA damage through different mechanisms. Deregulation of BRCA1 and BRCA2 is associated with the development of tumor and altered sensitivity to chemotherapeutic agents. In this study, we determined protein expression of BRCA1 and BRCA2 in four digestive system cancers (gastric cancer, colorectal cancer, hepatocellular carcinoma, and pancreatic cancer) by immunohistochemistry (IHC) on tissue microarrays. A total of 1546 samples of four types of cancer tissues, their matched adjacent non-tumor tissues, and corresponding benign tissues were studied respectively...
November 7, 2017: Human Pathology
https://www.readbyqxmd.com/read/29124898/impaired-competence-in-flagellar-mutants-of-bacillus-subtilis-is-connected-to-the-regulatory-network-governed-by-degu
#19
Theresa Hölscher, Tina Schiklang, Anna Dragoš, Anne-Kathrin Dietel, Christian Kost, Ákos T Kovács
The competent state is a developmentally distinct phase, in which bacteria are able to take up and integrate exogenous DNA into their genome. Bacillus subtilis is one of the naturally competent bacterial species and the domesticated laboratory strain 168 is easily transformable. In this study, we report a reduced transformation frequency of B. subtilis mutants lacking functional and structural flagellar components. This includes hag, the gene encoding the flagellin protein forming the filament of the flagellum...
November 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29123978/deep-sequencing-and-comprehensive-expression-analysis-identifies-several-molecules-potentially-related-to-human-poorly-differentiated-hepatocellular-carcinoma
#20
Ping Shao, Deguang Sun, Liming Wang, Rong Fan, Zhenming Gao
Hepatocellular carcinoma (HCC) that is graded histologically as poorly differentiated has a high recurrence, metastasis and poor prognosis. We sought to determine the regulatory mechanisms of HCC tumorigenesis and to identify molecules closely related to poorly differentiated HCC. High-throughput sequencing was used to construct microRNA (miRNA) and mRNA expression profiles for poorly differentiated HCC tissues and adjacent tissues. Network analysis was carried out to study miRNA-target interactions. Integrating the miRNA and mRNA data of HCC with four tumor grades from The Cancer Genome Atlas (TCGA) portal enabled the identification of potential closely related molecules for early diagnosis of poorly differentiated HCC...
November 2017: FEBS Open Bio
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