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Ji-Long Liu, Miao Zhao
Endometriosis affects 5-10% of women in reproductive age, leading to dysmenorrhea, pelvic pain and infertility; however, our understanding on the pathogenesis of this disease remains incomplete. In the present study, we performed a systematic analysis of endometriosis-related genes using text mining. Taking text mining results as input, we subsequently generated a filtered gene set by computing the likelihood of finding more than expected occurrences for every gene across the disease-centered subset of the PubMed database...
October 13, 2016: Genomics
Jeffrey R Row, Michael E Donaldson, Jessica N Longhi, Barry J Saville, Dennis L Murray
A potential cause of amphibian population declines are the impacts of environmental degradation on tadpole development. We conducted RNA sequencing on developing northern leopard frog tadpoles and through de novo transcriptome assembly we annotated a large number of open reading frames comparable in number and extent to genes identified in Xenopus. Using our transcriptome, we found transcript level changes between early (Gosner 26-31) and late (Gosner 36-41) stage tadpoles were the greatest in the tail, which is reabsorbed throughout development...
October 11, 2016: Genomics
Miho M Suzuki, Tomoko Mori, Noriyuki Satoh
The initiation of embryonic gene expression in ascidian embryos appears to be tightly regulated by the number of DNA replication cycles. DNA methylation is thought to contribute to the clock mechanism that counts the rounds of DNA replication. We used mass spectrometry and whole genome bisulfite sequencing to characterize DNA methylation changes that occur in early developmental stages of the ascidian, Ciona intestinalis. We found that global DNA methylation in early Ciona development was static, and a base-wise comparison between the genomes of consecutive developmental stages found no DNA demethylation that was related to zygotic gene activation...
October 5, 2016: Genomics
Christopher G Bell
Epigenomic analysis gives a molecular insight into cell-specific genomic activity. It provides a detailed functional plan to dissect an organism, tissue by tissue. Therefore comparative epigenomics may increase understanding of human-acquired traits, by revealing regulatory changes in systems such as the neurological, musculoskeletal, and immunological. Enhancer loci evolve fast by hijacking elements from other tissues or rewiring and amplifying existing units for human-specific function. Promoters by contrast often require a CpG dense genetic infrastructure...
October 1, 2016: Genomics
Shannon Hateley, Ravikumar Hosamani, Shilpa R Bhardwaj, Lior Pachter, Sharmila Bhattacharya
Altered gravity can perturb normal development and induce corresponding changes in gene expression. Understanding this relationship between the physical environment and a biological response is important for NASA's space travel goals. We use RNA-Seq and qRT-PCR techniques to profile changes in early Drosophila melanogaster pupae exposed to chronic hypergravity (3g, or three times Earth's gravity). During the pupal stage, D. melanogaster rely upon gravitational cues for proper development. Assessing gene expression changes in the pupae under altered gravity conditions helps highlight gravity-dependent genetic pathways...
September 10, 2016: Genomics
Lei Yang, Shiyuan Wang, Meng Zhou, Xiaowen Chen, Yongchun Zuo, Yingli Lv
Essential genes are those that are indispensable for the survival and propagation of an organism. TATA-containing genes are associated with responses to various stresses and are highly regulated. Although both essential genes and TATA genes are very important in the function of biological systems, their relationship remains unclear because they have typically been researched independently. In this study, to investigate the relationship between essential genes and TATA genes, S. cerevisiae genes were classified as: essential TATA-containing, non-essential TATA-containing, essential non-TATA, and non-essential non-TATA genes...
September 6, 2016: Genomics
Shahid Ali, Bibi Amina, Saneela Anwar, Rashid Minhas, Nazia Parveen, Uzma Nawaz, Syed Sikandar Azam, Amir Ali Abbasi
To elucidate important cellular and molecular interactions that regulate patterning and skeletal development, vertebrate limbs served as a model organ. A growing body of evidence from detailed studies on a subset of limb regulators like the HOXD cluster or SHH, reveals the importance of enhancers in limb related developmental and disease processes. Exploiting the recent genome-wide availability of functionally confirmed enhancer dataset, this study establishes regulatory interactions for dozens of human limb developmental genes...
August 28, 2016: Genomics
Tung Hoang, Changchuan Yin, Stephen S-T Yau
Numerical encoding plays an important role in DNA sequence analysis via computational methods, in which numerical values are associated with corresponding symbolic characters. After numerical representation, digital signal processing methods can be exploited to analyze DNA sequences. To reflect the biological properties of the original sequence, it is vital that the representation is one-to-one. Chaos Game Representation (CGR) is an iterative mapping technique that assigns each nucleotide in a DNA sequence to a respective position on the plane that allows the depiction of the DNA sequence in the form of image...
August 15, 2016: Genomics
Ashley J Vargas, John Quackenbush, Kimberly Glass
BACKGROUND: Weight loss may decrease risk of colorectal cancer in obese individuals, yet its effect in the colorectum is not well understood. We used integrative network modeling, Passing Attributes between Networks for Data Assimilation, to estimate transcriptional regulatory network models from mRNA expression levels from rectal mucosa biopsies measured pre- and post-weight loss in 10 obese, pre-menopausal women. RESULTS: We identified significantly greater regulatory targeting of glucose transport pathways in the post-weight loss regulatory network, including "regulation of glucose transport" (FDR=0...
August 11, 2016: Genomics
Qiang Zhang, Hong Li, Xiao-Qing Zhao, Hui Xue, Yan Zheng, Hu Meng, Yun Jia, Su-Ling Bo
Within two years of their discovery in 1977, introns were found to have a positive effect on gene expression. Our result shows that introns can achieve gene expression and regulation through interaction with corresponding mRNA sequences. On the base of Smith-Waterman method, local comparing helps us get the optimal matched segments between intron sequences and mRNA sequences. Studying the distribution regulation of the optimal matching region on intron sequences of ribosomal protein genes about 27 species, we find that the intron length evolution processes beginning from 5' end to 3' end and increasing one by one structural unit, which comes up with a possible mechanism for the intron length evolution...
August 2016: Genomics
Heeyoun Bunch, Brian P Lawney, Adam Burkholder, Duanduan Ma, Xiaofeng Zheng, Shmulik Motola, David C Fargo, Stuart S Levine, Yaoyu E Wang, Guang Hu
Mammalian genomes encode a large number of non-coding RNAs (ncRNAs) that greatly exceed mRNA genes. While the physiological and pathological roles of ncRNAs have been increasingly understood, the mechanisms of regulation of ncRNA expression are less clear. Here, our genomic study has shown that a significant number of long non-coding RNAs (lncRNAs, >1000 nucleotides) harbor RNA polymerase II (Pol II) engaged with the transcriptional start site. A pausing and transcriptional elongation factor for protein-coding genes, tripartite motif-containing 28 (TRIM28) regulates the transcription of a subset of lncRNAs in mammalian cells...
August 2016: Genomics
Sally Yepes, Rocío López, Rafael E Andrade, Paula A Rodriguez-Urrego, Liliana López-Kleine, Maria Mercedes Torres
Co-expression networks may provide insights into the patterns of molecular interactions that underlie cellular processes. To obtain a better understanding of miRNA expression patterns in gastric adenocarcinoma and to provide markers that can be associated with histopathological findings, we performed weighted gene correlation network analysis (WGCNA) and compare it with a supervised analysis. Integrative analysis of target predictions and miRNA expression profiles in gastric cancer samples was also performed...
August 2016: Genomics
Bong-Seok Jo, In-Uk Koh, Jae-Bum Bae, Ho-Yeong Yu, Eun-Seok Jeon, Hae-Young Lee, Jae-Joong Kim, Murim Choi, Sun Shim Choi
Dilated cardiomyopathy (DCM) is one of the main causes of heart failure (called cardiomyopathies) in adults. Alterations in epigenetic regulation (i.e., DNA methylation) have been implicated in the development of DCM. Here, we identified a total of 1828 differentially methylated probes (DMPs) using the Infinium 450K HumanMethylation Bead chip by comparing the methylomes between 18 left ventricles and 9 right ventricles. Alterations in DNA methylation levels were observed mainly in lowly methylated regions corresponding to promoter-proximal regions, which become hypermethylated in severely affected left ventricles...
August 2016: Genomics
Vinayak Bhandari, Paul C Boutros
Treatment of cancer is becoming increasingly personalized and biomarkers continue to be developed to refine treatment decisions. Tumour mRNA abundance data is commonly used to develop such biomarkers, often to predict patient survival. However, survival analyses present unique challenges and it is unknown whether analysing mRNA abundance information in a discrete or continuous manner yields different results. To address this, we analysed 1988 primary breast tumour transcriptomes. When compared univariately, approximately 60% of all genes showed differences between the discrete and continuous Cox proportional hazards models with q-value differences spanning four orders of magnitude for some genes...
August 2016: Genomics
Tomohito Taminato, Daisuke Yokota, Soh Araki, Hiroki Ovara, Kyo Yamasu, Akinori Kawamura
Chromatin immunoprecipitation (ChIP) against enhancer-associated marks with massive sequencing is a powerful approach to identify genome-wide distributions of putative enhancers. However, functional in vivo analysis is required to elucidate the activities of predicted enhancers. Using zebrafish embryos, we established a ChIP-Injection method that enables identification of functional enhancers based on their enhancer activities in embryos. Each reporter gene possessing the enhancer-associated genomic region enriched by ChIP was injected into zebrafish embryos to analyze the activity of putative enhancers...
August 2016: Genomics
Monica J Piatek, Victoria Henderson, Hany S Zynad, Andreas Werner
Natural antisense transcripts (NATs) can interfere with the expression of complementary sense transcripts with exquisite specificity. We have previously cloned NATs of Slc34a loci (encoding Na-phosphate transporters) from fish and mouse. Here we report the cloning of a human SLC34A1-related NAT that represents an alternatively spliced PFN3 transcript (Profilin3). The transcript is predominantly expressed in testis. Phylogenetic comparison suggests two distinct mechanisms producing Slc34a-related NATs: Alternative splicing of a transcript from a protein coding downstream gene (Pfn3, human/mouse) and transcription from the bi-directional promoter (Rbpja, zebrafish)...
August 2016: Genomics
Jianhua Ruan, Md Jamiul Jahid, Fei Gu, Chengwei Lei, Yi-Wen Huang, Ya-Ting Hsu, David G Mutch, Chun-Liang Chen, Nameer B Kirma, Tim H-M Huang
To develop accurate prognostic models is one of the biggest challenges in "omics"-based cancer research. Here, we propose a novel computational method for identifying dysregulated gene subnetworks as biomarkers to predict cancer recurrence. Applying our method to the DNA methylome of endometrial cancer patients, we identified a subnetwork consisting of differentially methylated (DM) genes, and non-differentially methylated genes, termed Epigenetic Connectors (EC), that are topologically important for connecting the DM genes in a protein-protein interaction network...
July 21, 2016: Genomics
Tony L Brown, Theresa M Meloche
The journey related to genomic information access and utilization by researchers and clinicians has barely begun to be travelled. There remains a broad horizon in the research and clinical arenas for fulfillment of that journey. Exciting is the potential depth and breadth of research, clinical applications, and more personalized medicine, that remain on the horizon. Exome sequencing has clarified the responsibilities of over 130 genes, greatly expanding the medical genetics database and enabling the development of orphan disease-based pharmaceuticals...
July 4, 2016: Genomics
Shi Huang
No abstract text is available yet for this article.
July 2016: Genomics
Kakali Biswas, Sandip Chakraborty, Soumita Podder, Tapash Chandra Ghosh
In mammals, it has long been suggested that brain-specific genes (BSGs) and widely expressed genes (WEGs) have seemingly lower dN/dS ratio than any other gene sets. However, to what extent these genes differ in their dN/dS ratio has still remained controversial. Here, we have revealed lower dN/dS ratio of BSGs than WEGs in human-mouse, human-orangutan, human-chimpanzee and mouse-rat orthologous pair. The significance level of dN/dS ratio difference indicates a trend of decreasing difference as complexity of compared pairs increases...
July 2016: Genomics
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