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https://www.readbyqxmd.com/read/29028263/epigenomic-annotation-based-interpretation-of-genomic-data-from-enrichment-analysis-to-machine-learning
#1
Mikhail G Dozmorov
Motivation: One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The interpretation of these genome-wide ROIs represents a challenge as the majority of them lie outside of functionally well-defined protein coding regions. Recent efforts by the members of the International Human Epigenome Consortium have generated volumes of functional/regulatory data (reference epigenomic datasets), effectively annotating the genome with epigenomic properties...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29024646/the-epstein-barr-virus-regulome-in-lymphoblastoid-cells
#2
Sizun Jiang, Hufeng Zhou, Jun Liang, Catherine Gerdt, Chong Wang, Liangru Ke, Stefanie C S Schmidt, Yohei Narita, Yijie Ma, Shuangqi Wang, Tyler Colson, Benjamin Gewurz, Guoliang Li, Elliott Kieff, Bo Zhao
Epstein-Barr virus (EBV) transforms B cells to continuously proliferating lymphoblastoid cell lines (LCLs), which represent an experimental model for EBV-associated cancers. EBV nuclear antigens (EBNAs) and LMP1 are EBV transcriptional regulators that are essential for LCL establishment, proliferation, and survival. Starting with the 3D genome organization map of LCL, we constructed a comprehensive EBV regulome encompassing 1,992 viral/cellular genes and enhancers. Approximately 30% of genes essential for LCL growth were linked to EBV enhancers...
October 11, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28991264/architectural-alterations-of-the-fission-yeast-genome-during-the-cell-cycle
#3
Hideki Tanizawa, Kyoung-Dong Kim, Osamu Iwasaki, Ken-Ichi Noma
Eukaryotic genomes are highly ordered through various mechanisms, including topologically associating domain (TAD) organization. We employed an in situ Hi-C approach to follow the 3D organization of the fission yeast genome during the cell cycle. We demonstrate that during mitosis, large domains of 300 kb-1 Mb are formed by condensin. This mitotic domain organization does not suddenly dissolve, but gradually diminishes until the next mitosis. By contrast, small domains of 30-40 kb that are formed by cohesin are relatively stable across the cell cycle...
October 9, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28989052/in-silico-analysis-of-cytochrome-p450-monooxygenases-in-chronic-granulomatous-infectious-fungus-sporothrix-schenckii-special-focus-on-cyp51
#4
Retshedisitswe Godfrey Matowane, Lukasz Wieteska, Hans Denis Bamal, Ipeleng Kopano Rosinah Kgosiemang, Mari Van Wyk, Nessie Agnes Manume, Sara Mohamed Hasaan Abdalla, Samson Sitheni Mashele, Dominik Gront, Khajamohiddin Syed
Sporotrichosis is an emerging chronic, granulomatous, subcutaneous, mycotic infection caused by Sporothrix species. Sporotrichosis is treated with the azole drug itraconazole as ketoconazole is ineffective. It is a well-known fact that azole drugs act by inhibiting cytochrome P450 monooxygenases (P450s), heme-thiolate proteins. To date, nothing is known about P450s in Sporothrix schenckii and the molecular basis of its resistance to ketoconazole. Here we present genome-wide identification, annotation, phylogenetic analysis and comprehensive P450 family-level comparative analysis of S...
October 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28988229/studying-kidney-disease-using-tissue-and-genome-engineering-in-human-pluripotent-stem-cells
#5
Elena Garreta, Federico González, Núria Montserrat
Kidney morphogenesis and patterning have been extensively studied in animal models such as the mouse and zebrafish. These seminal studies have been key to define the molecular mechanisms underlying this complex multistep process. Based on this knowledge, the last 3 years have witnessed the development of a cohort of protocols allowing efficient differentiation of human pluripotent stem cells (hPSCs) towards defined kidney progenitor populations using two-dimensional (2D) culture systems or through generating organoids...
October 7, 2017: Nephron
https://www.readbyqxmd.com/read/28984194/the-international-conference-on-intelligent-biology-and-medicine-icibm-2016-putting-systems-biology-to-work
#6
EDITORIAL
W Jim Zheng, Jianhua Ruan, Hua Xu, Zhongming Zhao, Zhangdong Liu
Between December 8-10, 2016, the International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held in Houston, Texas, USA. The conference included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics in 3D genome structure analysis and visualization, next generation sequencing analysis, computational drug discovery, medical informatics, cancer genomics and systems biology. Systems biology has been a main theme in ICIBM 2016, with exciting advances were presented in many areas of systems biology...
October 3, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28984189/the-international-conference-on-intelligent-biology-and-medicine-icibm-2016-from-big-data-to-big-analytical-tools
#7
EDITORIAL
Zhandong Liu, W Jim Zheng, Genevera I Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao
The 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held on December 8-10, 2016 in Houston, Texas, USA. ICIBM included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics on 3D genomics structural analysis, next generation sequencing (NGS) analysis, computational drug discovery, medical informatics, cancer genomics, and systems biology. Here, we present a summary of the nine research articles selected from ICIBM 2016 program for publishing in BMC Bioinformatics...
October 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28980447/rjsplot-interactive-graphs-with-r
#8
David Barrios, Carlos Prieto
Data visualization techniques provide new methods for the generation of interactive graphs. These graphs allow a better exploration and interpretation of data but their creation requires advanced knowledge of graphical libraries. Recent packages have enabled the integration of interactive graphs in R. However, R provides limited graphical packages that allow the generation of interactive graphs for computational biology applications. The present project has joined the analytical power of R with the interactive graphical features of JavaScript in a new R package (RJSplot)...
October 5, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28978030/genetic-profile-and-biological-implication-of-pin2-trf1-interacting-telomerase-inhibitor-1-pinx1-in-human-cancers-an-analysis-using-the-cancer-genome-atlas
#9
Wei-Juan Huang, Mei Li, Xiao-Han Jin, Xiao-Jia Huang, Wei Zhao, Xiao-Peng Tian
Pin2/TRF1-interacting telomere inhibitor 1 (PinX1) was originally identified as a telomerase inhibitor, involved in maintaining telomerase activity, telomere length, and chromosomal stability. However, research has shown that PinX1 can have opposing molecular status in its expression patterns in several other tumor types. We thus investigated the genetic profile and biological implication of PinX1 in several human cancers using the cBioportal database. Our results showed that PinX1 deletion accounted for the most alterations, with the frequency of its deletion regularly occurring in pathological types of carcinosarcoma and adenocarcinoma...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28977854/clinically-relevant-morphological-structures-in-breast-cancer-represent-transcriptionally-distinct-tumor-cell-populations-with-varied-degrees-of-epithelial-mesenchymal-transition-and-cd44-cd24-stemness
#10
Evgeny V Denisov, Nikolay A Skryabin, Tatiana S Gerashchenko, Lubov A Tashireva, Jochen Wilhelm, Mikhail A Buldakov, Aleksei A Sleptcov, Igor N Lebedev, Sergey V Vtorushin, Marina V Zavyalova, Nadezhda V Cherdyntseva, Vladimir M Perelmuter
Intratumor morphological heterogeneity in breast cancer is represented by different morphological structures (tubular, alveolar, solid, trabecular, and discrete) and contributes to poor prognosis; however, the mechanisms involved remain unclear. In this study, we performed 3D imaging, laser microdissection-assisted array comparative genomic hybridization and gene expression microarray analysis of different morphological structures and examined their association with the standard immunohistochemistry scorings and CD44(+)CD24(-) cancer stem cells...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28977568/computational-characterization-of-chromatin-domain-boundary-associated-genomic-elements
#11
Seungpyo Hong, Dongsup Kim
Topologically associated domains (TADs) are 3D genomic structures with high internal interactions that play important roles in genome compaction and gene regulation. Their genomic locations and their association with CCCTC-binding factor (CTCF)-binding sites and transcription start sites (TSSs) were recently reported. However, the relationship between TADs and other genomic elements has not been systematically evaluated. This was addressed in the present study, with a focus on the enrichment of these genomic elements and their ability to predict the TAD boundary region...
August 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28977418/developmentally-regulated-higher-order-chromatin-interactions-orchestrate-b-cell-fate-commitment
#12
Ravi Boya, Anurupa Devi Yadavalli, Sameena Nikhat, Sreenivasulu Kurukuti, Dasaradhi Palakodeti, Jagan M R Pongubala
Genome organization in 3D nuclear-space is important for regulation of gene expression. However, the alterations of chromatin architecture that impinge on the B cell-fate choice of multi-potent progenitors are still unclear. By integrating in situ Hi-C analyses with epigenetic landscapes and genome-wide expression profiles, we tracked the changes in genome architecture as the cells transit from a progenitor to a committed state. We identified the genomic loci that undergo developmental switch between A and B compartments during B-cell fate determination...
August 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28976964/chromosome-biology-how-to-build-a-cohesive-genome-in-3d
#13
Rachel Patton McCord
No abstract text is available yet for this article.
October 4, 2017: Nature
https://www.readbyqxmd.com/read/28974055/a-comparative-genomic-and-transcriptomic-survey-provides-novel-insights-into-n-acetylserotonin-methyltransferase-asmt-in-fish
#14
Kai Zhang, Zhiqiang Ruan, Jia Li, Chao Bian, Xinxin You, Steven L Coon, Qiong Shi
Melatonin is a multifunctional bioactive molecule that plays comprehensive physiological roles in all living organisms. N-acetylserotonin methyltransferase (ASMT, also known as hydroxyindole O-methyltransferase or HIOMT) is the final enzyme for biosynthesis of melatonin. Here, we performed a comparative genomic and transcriptomic survey to explore the ASMT family in fish. Two ASMT isotypes (ASMT1 and ASMT2) and a new ASMT-like (ASMTL) are all extracted from teleost genomes on the basis of phylogenetic and synteny analyses...
October 2, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28973992/3d-spatially-resolved-models-of-the-intracellular-dynamics-of-the-hepatitis-c-genome-replication-cycle
#15
Markus M Knodel, Sebastian Reiter, Paul Targett-Adams, Alfio Grillo, Eva Herrmann, Gabriel Wittum
Mathematical models of virus dynamics have not previously acknowledged spatial resolution at the intracellular level despite substantial arguments that favor the consideration of intracellular spatial dependence. The replication of the hepatitis C virus (HCV) viral RNA (vRNA) occurs within special replication complexes formed from membranes derived from endoplasmatic reticulum (ER). These regions, termed membranous webs, are generated primarily through specific interactions between nonstructural virus-encoded proteins (NSPs) and host cellular factors...
September 30, 2017: Viruses
https://www.readbyqxmd.com/read/28970326/heat-shock-protein-genes-undergo-dynamic-alteration-in-their-3d-structure-and-genomic-organization-in-response-to-thermal-stress
#16
Surabhi Chowdhary, Amoldeep S Kainth, David S Gross
Three-dimensional chromatin organization is important for proper gene regulation, yet how the genome is remodeled in response to stress is largely unknown. Here we use a highly sensitive version of chromosome conformation capture (3C) in combination with fluorescence microscopy to investigate Heat Shock Protein (HSP) gene conformation and 3D nuclear organization in budding yeast. In response to acute thermal stress, HSP genes undergo intense intragenic folding interactions that go well beyond 5' -3' gene looping previously described for Pol II genes...
October 2, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28967693/huma-a-platform-for-the-analysis-of-genetic-variation-in-humans
#17
David K Brown, Özlem Tastan Bishop
The completion of the human genome project at the beginning of the 21(st) century, along with the rapid advancement of sequencing technologies thereafter, has resulted in exponential growth of biological data. In genetics, this has given rise to numerous variation databases, created to store and annotate the ever-expanding dataset of known mutations. Usually, these databases focus on variation at the sequence level. Few databases focus on the analysis of variation at the 3D level i.e. mapping, visualizing, and determining the effects of variation in protein structures...
October 2, 2017: Human Mutation
https://www.readbyqxmd.com/read/28964856/complete-genome-sequences-and-phylogenetic-analysis-of-encephalomyocarditis-virus-strains-isolated-from-pigs-and-rats-origin
#18
Huimin Liu, Yongtao Li, Guozhi Zhang, Siyao Sang, Chuanqing Wang, Hongtao Chang
In order to evaluate the genetic variability of encephalomyocarditis virus (EMCV), the whole genomes of six EMCV field isolates originating from pigs and rats origin in different regions of central China, were phylogenetically and comparatively analyzed. Phylogenetic analysis of whole genome sequences, open reading frame (ORF), capsid coding region (CCR) and VP3/VP1 using neighbor-joining analysis revealed that these isolates belonged to lineage 1. Nucleotide sequences of six isolates showed more than 99% pairwise identity rates, and the sequences of isolates from pig and boar in the same region were completely identical with each other, without any genetic deletion or insertion...
September 28, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28964259/three-dimensional-genome-architecture-and-emerging-technologies-looping-in-disease
#19
REVIEW
Arpit Mishra, R David Hawkins
Genome compaction is a universal feature of cells and has emerged as a global regulator of gene expression. Compaction is maintained by a multitude of architectural proteins, long non-coding RNAs (lncRNAs), and regulatory DNA. Each component comprises interlinked regulatory circuits that organize the genome in three-dimensional (3D) space to manage gene expression. In this review, we update the current state of 3D genome catalogues and focus on how recent technological advances in 3D genomics are leading to an enhanced understanding of disease mechanisms...
September 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28955645/in-silico-analysis-molecular-cloning-expression-and-characterization-of-l-asparaginase-gene-from-lactobacillus-reuteri-dsm-20016
#20
Suresh Susan Aishwarya, Sellamuthu Iyappan, Kamepali Vijaya Lakshmi, Kandathil Narayanan Rajnish
l-Asparaginase is employed in leukaemic treatment and in processing starchy foods. The in silico analysis of Lactobacillus reuteri DSM 20016 reveals the presence of an l-asparaginase gene with theoretical pI value of 4.99. 3D structure prediction was carried out and one model was selected based on the validation scores of 86.293 for ERRAT, 92.10% for VERIFY 3D and Ramachandran plot. Multiple sequence alignment of the protein sequences of l-asparaginases I and II of Escherichia coli, Erwinia chrysanthemum and Homo sapiens shows their sequence similarity...
October 2017: 3 Biotech
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