Gene regulation and systems biology最新文献

{"title":"Overfeeding Dairy Cattle During Late-Pregnancy Alters Hepatic PPARα-Regulated Pathways Including Hepatokines: Impact on Metabolism and Peripheral Insulin Sensitivity.","authors":"M Jawad Khan,&nbsp;Carolina B Jacometo,&nbsp;Daniel E Graugnard,&nbsp;Marcio N Corrêa,&nbsp;Eduardo Schmitt,&nbsp;Felipe Cardoso,&nbsp;Juan J Loor","doi":"10.4137/GRSB.S14116","DOIUrl":"https://doi.org/10.4137/GRSB.S14116","url":null,"abstract":"<p><p>Hepatic metabolic gene networks were studied in dairy cattle fed control (CON, 1.34 Mcal/kg) or higher energy (overfed (OVE), 1.62 Mcal/kg) diets during the last 45 days of pregnancy. A total of 57 target genes encompassing PPARα-targets/co-regulators, hepatokines, growth hormone (GH)/insulin-like growth factor 1 (IGF-1) axis, lipogenesis, and lipoprotein metabolism were evaluated on -14, 7, 14, and 30 days around parturition. OVE versus CON cows were in more negative energy balance (NEB) postpartum and had greater serum non-esterified fatty acids (NEFA), β-hydroxybutyrate (BHBA), and liver triacylglycerol (TAG) concentrations. Milk synthesis rate did not differ. Liver from OVE cows responded to postpartal NEB by up-regulating expression of PPARα-targets in the fatty acid oxidation and ketogenesis pathways, along with gluconeogenic genes. Hepatokines (fibroblast growth factor 21 (FGF21), angiopoietin-like 4 (ANGPTL4)) and apolipoprotein A-V (APOA5) were up-regulated postpartum to a greater extent in OVE than CON. OVE led to greater blood insulin prepartum, lower NEFA:insulin, and greater lipogenic gene expression suggesting insulin sensitivity was not impaired. A lack of change in APOB, MTTP, and PNPLA3 coupled with upregulation of PLIN2 postpartum in cows fed OVE contributed to TAG accumulation. Postpartal responses in NEFA and FGF21 with OVE support a role of this hepatokine in diminishing adipose insulin sensitivity. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"97-111"},"PeriodicalIF":0.0,"publicationDate":"2014-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S14116","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32268505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA conformational transitions induced by supercoiling control transcription in chromatin.","authors":"Andrey N Luchnik","doi":"10.4137/GRSB.S13756","DOIUrl":"https://doi.org/10.4137/GRSB.S13756","url":null,"abstract":"<p><p>Regulation of transcription in eukaryotes is considered in the light of recent findings demonstrating the presence of negative and positive superhelical tension in chromatin. This tension induces conformational transitions in DNA duplex. Particularly, the transition into A-form renders DNA accessible and waylaying for initiation of transcription producing RNA molecules long known to belong to the A-conformation. Competition between conformational transitions in various DNA sequences for the energy of elastic spring opens a possibility for understanding of fine tuning of transcription at a distance. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"89-96"},"PeriodicalIF":0.0,"publicationDate":"2014-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S13756","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32196416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tissue-specific gene expression and regulation in liver and muscle following chronic corticosteroid administration.","authors":"Tung T Nguyen, Richard R Almon, Debra C Dubois, Siddharth Sukumaran, William J Jusko, Ioannis P Androulakis","doi":"10.4137/GRSB.S13134","DOIUrl":"10.4137/GRSB.S13134","url":null,"abstract":"<p><p>Although corticosteroids (CSs) affect gene expression in multiple tissues, the array of genes that are regulated by these catabolic steroids is diverse, highly tissue specific, and depends on their functions in the tissue. Liver has many important functions in performing and regulating diverse metabolic processes. Muscle, in addition to its mechanical role, is critical in maintaining systemic energy homeostasis and accounts for about 80% of insulin-directed glucose disposal. Consequently, a better understanding of CS pharmacogenomic effects in these tissues would provide valuable information regarding the tissue-specificity of transcriptional dynamics, and would provide insights into the underlying molecular mechanisms of action for both beneficial and detrimental effects. We performed an integrated analysis of transcriptional data from liver and muscle in response to methylprednisolone (MPL) infusion, which included clustering and functional annotation of clustered gene groups, promoter extraction and putative transcription factor (TF) identification, and finally, regulatory closeness (RC) identification. This analysis allowed the identification of critical transcriptional responses and CS-responsive functions in liver and muscle during chronic MPL administration, the prediction of putative transcriptional regulators relevant to transcriptional responses of CS-affected genes which are also potential secondary bio-signals altering expression levels of target-genes, and the exploration of the tissue-specificity and biological significance of gene expression patterns, CS-responsive functions, and transcriptional regulation. The analysis provided an integrated description of the genomic and functional effects of chronic MPL infusion in liver and muscle. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"75-87"},"PeriodicalIF":0.0,"publicationDate":"2014-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32196415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tetracycline derivative minocycline inhibits autophagy and inflammation in concanavalin-a-activated human hepatoma cells.","authors":"Michel Desjarlais,&nbsp;Jonathan Pratt,&nbsp;Amine Lounis,&nbsp;Catherine Mounier,&nbsp;Khadidja Haidara,&nbsp;Borhane Annabi","doi":"10.4137/GRSB.S13946","DOIUrl":"https://doi.org/10.4137/GRSB.S13946","url":null,"abstract":"<p><p>Inhibition of soluble matrix metalloproteinase (MMP) activity is among the non-antibiotic cellular effects exerted by the anti-inflammatory tetracycline derivative minocycline. The impact of minocycline on the signal transduction functions of membrane-bound MMPs is however unknown. We assessed minocycline in a concanavalin-A (ConA)-activated human HepG2 hepatoma cell model, a condition known to increase the expression of membrane type-1 MMP (MT-MMP) and to trigger inflammatory and autophagy processes. We found that minocycline inhibited ConA-induced formation of autophagic acidic vacuoles, green fluorescent microtubule-associated protein 1 light chain 3 (GFP-LC3) puncta formation, gene and protein expression of autophagy biomarker BCL2/adenovirus E1B 19 kDa interacting protein 3 (BNIP3), invasion biomarker MT1-MMP, and inflammation biomarker cyclooxygenase (COX)-2. Gene silencing of MT1-MMP abrogated ConA-induced formation of autophagic acidic vacuoles and ConA-induced expressions of BNIP3 and COX-2. Minocycline was also shown to inhibit ConA-induced signal transducer and activator of transcription 3 (STAT3) phosphorylation as well as gene expression of NANOS1, a biomarker believed to colocalize with MT1-MMP and the specific silencing of which further inhibited ConA-induced STAT3 phosphorylation. Collectively, our data demonstrate that part of minocycline's effects on autophagy could be exerted through the inhibition of MT1-MMP signaling functions, which contribute to the autophagy and inflammatory phenotype of ConA-activated HepG2 cells. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"63-73"},"PeriodicalIF":0.0,"publicationDate":"2014-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S13946","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32181752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of Emphysema Relevant Molecular Networks from an A/J Mouse Inhalation Study Using Reverse Engineering and Forward Simulation (REFS™).","authors":"Yang Xiang,&nbsp;Ulrike Kogel,&nbsp;Stephan Gebel,&nbsp;Michael J Peck,&nbsp;Manuel C Peitsch,&nbsp;Viatcheslav R Akmaev,&nbsp;Julia Hoeng","doi":"10.4137/GRSB.S13140","DOIUrl":"https://doi.org/10.4137/GRSB.S13140","url":null,"abstract":"<p><p>Chronic obstructive pulmonary disease (COPD) is a respiratory disorder caused by extended exposure of the airways to noxious stimuli, principally cigarette smoke (CS). The mechanisms through which COPD develops are not fully understood, though it is believed that the disease process includes a genetic component, as not all smokers develop COPD. To investigate the mechanisms that lead to the development of COPD/emphysema, we measured whole genome gene expression and several COPD-relevant biological endpoints in mouse lung tissue after exposure to two CS doses for various lengths of time. A novel and powerful method, Reverse Engineering and Forward Simulation (REFS™), was employed to identify key molecular drivers by integrating the gene expression data and four measured COPD-relevant endpoints (matrix metalloproteinase (MMP) activity, MMP-9 levels, tissue inhibitor of metalloproteinase-1 levels and lung weight). An ensemble of molecular networks was generated using REFS™, and simulations showed that it could successfully recover the measured experimental data for gene expression and COPD-relevant endpoints. The ensemble of networks was then employed to simulate thousands of in silico gene knockdown experiments. Thirty-three molecular key drivers for the above four COPD-relevant endpoints were therefore identified, with the majority shown to be enriched in inflammation and COPD. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":" ","pages":"45-61"},"PeriodicalIF":0.0,"publicationDate":"2014-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S13140","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40284528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq.","authors":"Ngoc Tam L Tran,&nbsp;Chun-Hsi Huang","doi":"10.4137/GRSB.S13612","DOIUrl":"https://doi.org/10.4137/GRSB.S13612","url":null,"abstract":"<p><p>Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we further identified highly expressed genes by H3K4me3 mark or by both H3K4me3 and H3K4me1 marks in mouse liver using ChIP-Seq and RNA-Seq. We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions. We also identified novel genes in RNA-Seq experiments for mouse liver and for mouse embryonic stem cells. These genes are not currently in the Ensemble gene database at NCBI. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"33-43"},"PeriodicalIF":0.0,"publicationDate":"2014-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S13612","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32117669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Central Role of the PPARγ Gene Network in Coordinating Beef Cattle Intramuscular Adipogenesis in Response to Weaning Age and Nutrition.","authors":"Sonia J Moisá,&nbsp;Daniel W Shike,&nbsp;Dan B Faulkner,&nbsp;William T Meteer,&nbsp;Duane Keisler,&nbsp;Juan J Loor","doi":"10.4137/GRSB.S11782","DOIUrl":"https://doi.org/10.4137/GRSB.S11782","url":null,"abstract":"<p><p>Adipogenic/lipogenic transcriptional networks regulating intramuscular fat deposition (IMF) in response to weaning age and dietary starch level were studied. The longissimus muscle (LM) of beef steers on an early weaning (141 days age) plus high-starch diet (EWS) or a normal weaning (NW, 222 days age) plus starch creep-feed diet (CFS) was biopsied at 0 (EW), 25, 50, 96 (NW), 167, and 222 (pre-slaughter) days. Expression patterns of 35 target genes were studied. From NW through slaughter, all steers received the same high-starch diet. In EWS steers the expression of PPARG, other adipogenic (CEBPA, ZFP423) and lipogenic (THRSP, SREBF1, INSIG1) activators, and several enzymes (FASN, SCD, ELOVL6, PCK1, DGAT2) that participate in the process of IMF increased gradually to a peak between 96 and 167 days on treatment. Steers in NW did not achieve similar expression levels even by 222 days on treatment, suggesting a blunted response even when fed a high-starch diet after weaning. High-starch feeding at an early age (EWS) triggers precocious and sustained adipogenesis, resulting in greater marbling. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"17-32"},"PeriodicalIF":0.0,"publicationDate":"2014-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S11782","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32106274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Innate immunity interactome dynamics.","authors":"Asmaa Elzawahry,&nbsp;Ashwini Patil,&nbsp;Yutaro Kumagai,&nbsp;Yutaka Suzuki,&nbsp;Kenta Nakai","doi":"10.4137/GRSB.S12850","DOIUrl":"https://doi.org/10.4137/GRSB.S12850","url":null,"abstract":"<p><p>Innate immune response involves protein-protein interactions, deoxyribonucleic acid (DNA)-protein interactions and signaling cascades. So far, thousands of protein-protein interactions have been curated as a static interaction map. However, protein-protein interactions involved in innate immune response are dynamic. We recorded the dynamics in the interactome during innate immune response by combining gene expression data of lipopolysaccharide (LPS)-stimulated dendritic cells with protein-protein interactions data. We identified the differences in interactome during innate immune response by constructing differential networks and identifying protein modules, which were up-/down-regulated at each stage during the innate immune response. For each protein complex, we identified enriched biological processes and pathways. In addition, we identified core interactions that are conserved throughout the innate immune response and their enriched gene ontology terms and pathways. We defined two novel measures to assess the differences between network maps at different time points. We found that the protein interaction network at 1 hour after LPS stimulation has the highest interactions protein ratio, which indicates a role for proteins with large number of interactions in innate immune response. A pairwise differential matrix allows for the global visualization of the differences between different networks. We investigated the toll-like receptor subnetwork and found that S100A8 is down-regulated in dendritic cells after LPS stimulation. Identified protein complexes have a crucial role not only in innate immunity, but also in circadian rhythms, pathways involved in cancer, and p53 pathways. The study confirmed previous work that reported a strong correlation between cancer and immunity. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2014-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S12850","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32052440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases.","authors":"Jun-Ichi Satoh,&nbsp;Natsuki Kawana,&nbsp;Yoji Yamamoto","doi":"10.4137/GRSB.S13204","DOIUrl":"https://doi.org/10.4137/GRSB.S13204","url":null,"abstract":"<p><p>Nuclear respiratory factor 1 (NRF1) serves as a transcription factor that activates the expression of a wide range of nuclear genes essential for mitochondrial biogenesis and function, including mitochondrial respiratory complex subunits, heme biosynthetic enzymes, and regulatory factors involved in the replication and transcription of mitochondrial DNA. Increasing evidence indicates that mitochondrial function is severely compromised in the brains of aging-related neurodegenerative diseases. To identify the comprehensive set of human NRF1 target genes potentially relevant to the pathogenesis of neurodegenerative diseases, we analyzed the NRF1 chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) dataset retrieved from the Encyclopedia of DNA Elements (ENCODE) project. Overall, we identified 2,470 highly stringent ChIP-Seq peaks on protein-coding genes in SK-N-SH human neuroblastoma cells. They were accumulated in the proximal promoter regions with an existence of the NRF1-binding consensus sequence. The set of ChIP-Seq-based NRF1 target genes included known NRF1 targets such as EIF2S1, EIF2S2, CYCS, FMR1, FXR2, E2F6, CD47, and TOMM34. By pathway analysis, the molecules located in the core pathways related to mitochondrial respiratory function were determined to be highly enriched in NRF1 target genes. Furthermore, we found that NRF1 target genes play a pivotal role in regulation of extra-mitochondrial biological processes, including RNA metabolism, splicing, cell cycle, DNA damage repair, protein translation initiation, and ubiquitin-mediated protein degradation. We identified a panel of neurodegenerative disease-related genes, such as PARK2 (Parkin), PARK6 (Pink1), PARK7 (DJ-1), and PAELR (GPR37) for Parkinson's disease, as well as PSENEN (Pen2) and MAPT (tau) for Alzheimer's disease, as previously unrecognized NRF1 targets. These results suggest a logical hypothesis that aberrant regulation of NRF1 and its targets might contribute to the pathogenesis of human neurodegenerative diseases via perturbation of diverse mitochondrial and extra-mitochondrial functions. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"7 ","pages":"139-52"},"PeriodicalIF":0.0,"publicationDate":"2013-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S13204","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31880743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CEBPG Exhibits Allele-Specific Expression in Human Bronchial Epithelial Cells.","authors":"Thomas M Blomquist,&nbsp;Ronald D Brown,&nbsp;Erin L Crawford,&nbsp;Ivana de la Serna,&nbsp;Kandace Williams,&nbsp;Youngsook Yoon,&nbsp;Dawn-Alita Hernandez,&nbsp;James C Willey","doi":"10.4137/GRSB.S11879","DOIUrl":"https://doi.org/10.4137/GRSB.S11879","url":null,"abstract":"<p><p>Inter-individual variation in CCAAT/enhancer binding protein gamma (CEBPG) transcript expression in normal human bronchial epithelial cells (NBEC) is associated with predisposition to lung cancer. We hypothesize that this inter-individual variation is in part explained by cis-acting genetic variation in CEBPG. To test this hypothesis we measured transcript expression derived from each parental copy of CEBPG (ie, allele-specific expression; ASE). There was a significant 2.9-fold higher cell cycle-specific variation in ASE of CEBPG rs2772 A compared to C allele (P < 0.001). In 20% of NBEC samples, CEBPG rs2772 A allele was expressed on average 2.10 fold greater than rs2772 C allele. These data support the hypothesis that genetic variation in linkage disequilibrium with rs2772 influences regulation of CEBPG transcript expression through a trans-effect downstream of RNA polymerase II transcription and confirm that cis-acting genetic variation contributes to inter-individual variation in CEBPG transcript expression in NBEC, which is associated with variation in lung cancer risk. </p>","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"7 ","pages":"125-38"},"PeriodicalIF":0.0,"publicationDate":"2013-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S11879","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31609163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}