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Tissue specific gene network

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https://www.readbyqxmd.com/read/28918159/identification-of-circular-rna-in-the-bombyx-mori-silk-gland
#1
Huaiyan Gan, Tieshan Feng, Yuqian Wu, Chun Liu, Qingyou Xia, Tingcai Cheng
Bombyx mori is an economically important holometabolous lepidopteran insect. In B. mori endogenous noncoding RNAs such as microRNAs (miRNAs) and Piwi-interacting RNAs play crucial biological functions in metamorphosis and sex determination. In addition, circular RNAs (circRNAs) have been recently identified as noncoding RNAs in most common model organisms and show potential as gene regulators. However, to date, there have been few studies on the circRNAs present in the B. mori genome conducted to date. Here, we identified 3916 circRNAs by deep circular transcriptome sequencing using the silk gland of B...
September 13, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28915785/seed-maturation-associated-transcriptional-programs-and-regulatory-networks-underlying-genotypic-difference-in-seed-dormancy-and-size-weight-in-wheat-triticum-aestivum-l
#2
Yuji Yamasaki, Feng Gao, Mark C Jordan, Belay T Ayele
BACKGROUND: Maturation forms one of the critical seed developmental phases and it is characterized mainly by programmed cell death, dormancy and desiccation, however, the transcriptional programs and regulatory networks underlying acquisition of dormancy and deposition of storage reserves during the maturation phase of seed development are poorly understood in wheat. The present study performed comparative spatiotemporal transcriptomic analysis of seed maturation in two wheat genotypes with contrasting seed weight/size and dormancy phenotype...
September 16, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28915634/dna-methylation-signature-of-long-noncoding-rna-genes-during-human-pre-implantation-embryonic-development
#3
Jingyu Li, Wei Han, Xiaoli Shen, Shubiao Han, Hong Ye, Guoning Huang
DNA methylation have crucial roles in regulating the expression of developmental genes during mammalian pre-implantation embryonic development (PED). However, the DNA methylation dynamic pattern of long noncoding RNA (lncRNA) genes, one type of epigenetic regulators, in human PED have not yet been demonstrated. Here, we performed a comprehensive analysis of lncRNA genes in human PED based on public reduced representation bisulphite sequencing (RRBS) data. We observed that both lncRNA and protein-coding genes complete the major demethylation wave at the 2-cell stage, whereas the promoters of lncRNA genes show higher methylation level than protein-coding genes during PED...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915238/a-high-resolution-atlas-of-gene-expression-in-the-domestic-sheep-ovis-aries
#4
Emily L Clark, Stephen J Bush, Mary E B McCulloch, Iseabail L Farquhar, Rachel Young, Lucas Lefevre, Clare Pridans, Hiu Tsang, Chunlei Wu, Cyrus Afrasiabi, Mick Watson, C Bruce Whitelaw, Tom C Freeman, Kim M Summers, Alan L Archibald, David A Hume
Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset...
September 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28914394/bioinformatics-based-identification-of-methylated-differentially-expressed-genes-and-related-pathways-in-gastric-cancer
#5
Hao Li, Jing-Wei Liu, Shuang Liu, Yuan Yuan, Li-Ping Sun
BACKGROUND AND AIMS: The aim of the study was to identify methylated-differentially expressed genes (MDEGs) in gastric cancer and investigate their potential pathways. METHODS: Expression profiling (GSE13911 and GSE29272) and methylation profiling (GSE25869 and GSE30601) data were obtained from GEO DataSets. Differentially expressed genes and differentially methylated genes were identified using GEO2R. Gene ontology and pathway enrichment analyses were performed for the MDEGs...
September 15, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28913343/exacerbating-and-reversing-lysosomal-storage-diseases-from-yeast-to-humans
#6
REVIEW
Tamayanthi Rajakumar, Andrew B Munkacsi, Stephen L Sturley
Lysosomal storage diseases (LSDs) arise from monogenic deficiencies in lysosomal proteins and pathways and are characterized by a tissue-wide accumulation of a vast variety of macromolecules, normally specific to each genetic lesion. Strategies for treatment of LSDs commonly depend on reduction of the offending metabolite(s) by substrate depletion or enzyme replacement. However, at least 44 of the ~50 LSDs are currently recalcitrant to intervention. Murine models have provided significant insights into our understanding of many LSD mechanisms; however, these systems do not readily permit phenotypic screening of compound libraries, or the establishment of genetic or gene-environment interaction networks...
August 25, 2017: Microbial Cell
https://www.readbyqxmd.com/read/28903493/editor-s-highlight-formulation-and-toxicology-evaluation-of-the-intrathecal-ayx1-dna-decoy-in-sprague-dawley-rats
#7
Julien Mamet, David C Yeomans, Tony L Yaksh, Donald C Manning, Scott Harris
The longevity of pain after surgery is debilitating and limits the recovery of patients. AYX1 is a double-stranded, unprotected, 23 base-pair oligonucleotide designed to reduce acute post-surgical pain and prevent its chronification with a single intrathecal perioperative dose. AYX1 mimics the DNA sequence normally bound by EGR1 on chromosomes, a transcription factor transiently induced in the dorsal root ganglia-spinal cord network following a noxious input. AYX1 binds to EGR1 and prevents it from launching waves of gene regulation that are necessary to maintain pain over time...
September 1, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28901494/molecular-mechanisms-of-pathogenesis-in-hepatocellular-carcinoma-revealed-by-rna%C3%A2-sequencing
#8
Yao Liu, Zhe Yang, Feng Du, Qiao Yang, Jie Hou, Xiaohong Yan, Yi Geng, Yaning Zhao, Hua Wang
The present study aimed to explore the underlying molecular mechanisms of hepatocellular carcinoma (HCC). RNA‑sequencing profiles GSM629264 and GSM629265, from the GSE25599 data set, were downloaded from the Gene Expression Omnibus database and processed by quality evaluation. GSM629264 and GSM629265 were from HCC and adjacent non‑cancerous tissues, respectively. TopHat software was used for alignment analysis, followed by the detection of novel splicing sites. In addition, the Cufflinks software package was used to analyze gene expressions, and the Cuffdiff program was used to screen for differently expressed genes (DEGs) and differentially expressed splicing variants...
September 11, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28901463/microrna-expression-profiles-and-networks-in-placentas-complicated-with-selective-intrauterine-growth-restriction
#9
Hong Wen, Lu Chen, Jing He, Jun Lin
The microRNA (miRNA) profiles of placentas complicated with selective intrauterine growth restriction (sIUGR) are unknown. In the present study, the sIUGR‑associated placental miRNA expression was investigated using microarray and confirmatory reverse transcriptase‑quantitative polymerase chain reaction studies. Placenta samples around the individual insertion region for each umbilical cord were collected from monochorionic twins complicated with (n=17) or without sIUGR (control, n=16). miRNA profile analysis was performed on two sIUGR cases and one control using an Affymetrix microRNA 4...
September 11, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28899360/biological-networks-in-parkinson-s-disease-an-insight-into-the-epigenetic-mechanisms-associated-with-this-disease
#10
Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya, Sanghamitra Bandyopadhyay
BACKGROUND: Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. RESULT: We have studied gene co-expression network obtained from a PD-specific microarray data. The co-expression network identified 11 hub genes, of which eight genes are not previously known to be associated with PD...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28899340/regulatory-network-changes-between-cell-lines-and-their-tissues-of-origin
#11
Camila M Lopes-Ramos, Joseph N Paulson, Cho-Yi Chen, Marieke L Kuijjer, Maud Fagny, John Platig, Abhijeet R Sonawane, Dawn L DeMeo, John Quackenbush, Kimberly Glass
BACKGROUND: Cell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tissues, a systematic overview of the differences between the regulatory processes of a cell line and those of its tissue of origin has not been conducted. The RNA-Seq data generated by the GTEx project is the first available data resource in which it is possible to perform a large-scale transcriptional and regulatory network analysis comparing cell lines with their tissues of origin...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28892639/genetic-networks-in-plant-vascular-development
#12
Raili Ruonala, Donghwi Ko, Ykä Helariutta
Understanding the development of vascular tissues in plants is crucial because the evolution of vasculature enabled plants to thrive on land. Various systems and approaches have been used to advance our knowledge about the genetic regulation of vasculature development, from the scale of single genes to networks. In this review, we provide a perspective on the major approaches used in studying plant vascular development, and we cover the mechanisms and genetic networks underlying vascular tissue specification, patterning, and differentiation...
September 11, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28888423/transposons-as-tools-for-functional-genomics-in-vertebrate-models
#13
REVIEW
Koichi Kawakami, David A Largaespada, Zoltán Ivics
Genetic tools and mutagenesis strategies based on transposable elements are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of their inherent capacity to insert into DNA, transposons can be developed into powerful tools for chromosomal manipulations. Transposon-based forward mutagenesis screens have numerous advantages including high throughput, easy identification of mutated alleles, and providing insight into genetic networks and pathways based on phenotypes...
September 6, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28888422/exome-sequencing-landscape-analysis-in-ovarian-clear-cell-carcinoma-shed-light-on-key-chromosomal-regions-and-mutation-gene-networks
#14
Ryusuke Murakami, Noriomi Matsumura, J B Brown, Koichiro Higasa, Takanobu Tsutsumi, Mayumi Kamada, Hisham Abou-Taleb, Yuko Hosoe, Sachiko Kitamura, Ken Yamaguchi, Kaoru Abiko, Junzo Hamanishi, Tsukasa Baba, Masafumi Koshiyama, Yasushi Okuno, Ryo Yamada, Fumihiko Matsuda, Ikuo Konishi, Masaki Mandai
Previous studies have reported genome-wide mutation profile analyses in ovarian clear cell carcinomas (OCCCs). This study aims to identify specific novel molecular alterations by combined analyses of somatic mutation and copy number variation. We performed whole exome sequencing of 39 OCCC samples with 16 matching blood tissue samples. Four hundred twenty-six genes had recurrent somatic mutations. Among the 39 samples, ARID1A (62%) and PIK3CA (51%) were frequently mutated, as were genes such as KRAS (10%), PPP2R1A (10%), and PTEN (5%), that have been reported in previous OCCC studies...
October 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28881752/integrated-expression-profiles-analysis-reveals-novel-predictive-biomarker-in-pancreatic-ductal-adenocarcinoma
#15
Hongzhe Li, Xinjing Wang, Yuan Fang, Zhen Huo, Xiongxiong Lu, Xi Zhan, Xiaxin Deng, Chenghong Peng, Baiyong Shen
Pancreatic ductal adenocarcinoma (PDAC) is the most lethal human malignant tumor, with a dismal 5-year survival rate of less than 5%. The lack of specific symptoms at early tumor stages and the paucity of biomarkers contribute to the poor diagnosis of pancreatic ductal adenocarcinoma. To improve prognosis, a screening biomarker for early diagnosis of pancreatic cancer is in urgent need. We searched the databases of expression profiling by array on GEO, aiming at comparing gene expression profile of matched pairs of pancreatic tumor and adjacent non-tumor tissues, and we screen out 4 suitable series of gene expression microarray data ("GSE15471", "GSE18670", "GSE28735" and "GSE58561")...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28872670/tcr-pmhc-encounter-differentially-regulates-transcriptomes-of-tissue-resident-cd8-t-cells
#16
Akihiro Yoshikawa, Kevin Bi, Derin B Keskin, Guanglang Zhang, Bruce Reinhold, Ellis L Reinherz
To investigate the role of TCR-pMHC interaction in regulating lung CD8 tissue-resident T cell (TR ) differentiation, polyclonal responses were compared against NP366-374 /D(b) and PA224-233 /D(b) , two immunodominant epitopes that arise during influenza A infection in mice. Memory niches distinct from iBALTs develop within the lamina propria, supporting CD103+ and CD103- CD8 TR generation and intraepithelial translocation. Gene set enrichment analysis (GSEA) and weighted gene co-expression network analysis (WGCNA) identify dominant TCR, adherence junction, RIG-I-like and NOD-like pattern recognition receptor as well as TGFβ signaling pathways and memory signatures among PA224-233 /D(b) T cells consistent with T resident memory (TRM ) status...
September 5, 2017: European Journal of Immunology
https://www.readbyqxmd.com/read/28869592/reconstruction-of-enhancer-target-networks-in-935-samples-of-human-primary-cells-tissues-and-cell-lines
#17
Qin Cao, Christine Anyansi, Xihao Hu, Liangliang Xu, Lei Xiong, Wenshu Tang, Myth T S Mok, Chao Cheng, Xiaodan Fan, Mark Gerstein, Alfred S L Cheng, Kevin Y Yip
We propose a new method for determining the target genes of transcriptional enhancers in specific cells and tissues. It combines global trends across many samples and sample-specific information, and considers the joint effect of multiple enhancers. Our method outperforms existing methods when predicting the target genes of enhancers in unseen samples, as evaluated by independent experimental data. Requiring few types of input data, we are able to apply our method to reconstruct the enhancer-target networks in 935 samples of human primary cells, tissues and cell lines, which constitute by far the largest set of enhancer-target networks...
September 4, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28859407/systems-biology-of-phenotypic-robustness-and-plasticity
#18
H Frederik Nijhout, Farrah Sadre-Marandi, Janet Best, Michael C Reed
Gene regulatory networks, cellular biochemistry, tissue function, and whole body physiology are imbued with myriad overlapping and interacting homeostatic mechanisms that ensure that many phenotypes are robust to genetic and environmental variation. Animals also often have plastic responses to environmental variables, which means that many different phenotypes can correspond to a single genotype. Since natural selection acts on phenotypes, this raises the question of how selection can act on the genome if genotypes are decoupled from phenotypes by robustness and plasticity mechanisms...
August 1, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/28855394/an-in-vivo-genetic-screen-in-drosophila-identifies-the-orthologue-of-human-cancer-testis-gene-spo11-among-a-network-of-targets-to-inhibit-lethal-3-malignant-brain-tumour-growth
#19
Fabrizio Rossi, Cristina Molnar, Kazuya Hashiyama, Jan P Heinen, Judit Pampalona, Salud Llamazares, José Reina, Tomomi Hashiyama, Madhulika Rai, Giulia Pollarolo, Ismael Fernández-Hernández, Cayetano Gonzalez
Using transgenic RNAi technology, we have screened over 4000 genes to identify targets to inhibit malignant growth caused by the loss of function of lethal(3)malignant brain tumour in Drosophila in vivo We have identified 131 targets, which belong to a wide range of gene ontologies. Most of these target genes are not significantly overexpressed in mbt tumours hence showing that, rather counterintuitively, tumour-linked overexpression is not a good predictor of functional requirement. Moreover, we have found that most of the genes upregulated in mbt tumours remain overexpressed in tumour-suppressed double-mutant conditions, hence revealing that most of the tumour transcriptome signature is not necessarily correlated with malignant growth...
August 2017: Open Biology
https://www.readbyqxmd.com/read/28851834/exploring-regulation-in-tissues-with-eqtl-networks
#20
Maud Fagny, Joseph N Paulson, Marieke L Kuijjer, Abhijeet R Sonawane, Cho-Yi Chen, Camila M Lopes-Ramos, Kimberly Glass, John Quackenbush, John Platig
Characterizing the collective regulatory impact of genetic variants on complex phenotypes is a major challenge in developing a genotype to phenotype map. Using expression quantitative trait locus (eQTL) analyses, we constructed bipartite networks in which edges represent significant associations between genetic variants and gene expression levels and found that the network structure informs regulatory function. We show, in 13 tissues, that these eQTL networks are organized into dense, highly modular communities grouping genes often involved in coherent biological processes...
August 29, 2017: Proceedings of the National Academy of Sciences of the United States of America
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