Gene regulation and systems biology最新文献_第4页

Epigenetic Regulation of Tissue-Type Plasminogen Activator in Human Brain Tissue and Brain-Derived Cells 组织型纤溶酶原激活剂在人脑组织和脑源性细胞中的表观遗传调控

Gene regulation and systems biology Pub Date : 2016-01-24 DOI: 10.4137/GRSB.S30241

M. Olsson, K. Hultman, S. Dunoyer-Geindre, M. Curtis, R. Faull, E. Kruithof, C. Jern

{"title":"Epigenetic Regulation of Tissue-Type Plasminogen Activator in Human Brain Tissue and Brain-Derived Cells","authors":"M. Olsson, K. Hultman, S. Dunoyer-Geindre, M. Curtis, R. Faull, E. Kruithof, C. Jern","doi":"10.4137/GRSB.S30241","DOIUrl":"https://doi.org/10.4137/GRSB.S30241","url":null,"abstract":"The serine protease tissue-type plasminogen activator (t-PA) is involved in both vital physiological brain processes, such as synaptic plasticity, and pathophysiological conditions, such as neurodegeneration and ischemic stroke. Recent data suggest that epigenetic mechanisms play an important role in the regulation of t-PA in human endothelial cells. However, there are limited data on epigenetic regulation of t-PA in human brain-derived cells. We demonstrate that treatment of cultured human neurons and human astrocytes with the histone deacetylase inhibitors trichostatin A (TSA) and MS-275 resulted in a two- to threefold increase in t-PA mRNA and protein expression levels. Next, we performed a chromatin immunoprecipitation assay on treated astrocytes with antibodies directed against acetylated histones H3 and H4 (both markers of gene activation). Treatment with MS-275 and TSA for 24 hours resulted in a significant increase in H3 acetylation, which could explain the observed increase in t-PA gene activity after the inhibition of histone deacety-lation. Furthermore, DNA methylation analysis of cultured human neurons and astrocytes, as well as human postmortem brain tissue, revealed a stretch of unmethylated CpG dinucleotides in the proximal t-PA promoter, whereas more upstream CpGs were highly methylated. Taken together, these results implicate involvement of epigenetic mechanisms in the regulation of t-PA expression in the human brain.","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"10 1","pages":"9 - 13"},"PeriodicalIF":0.0,"publicationDate":"2016-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S30241","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70703081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Transcriptomic Sequencing Reveals a Set of Unique Genes Activated by Butyrate-Induced Histone Modification 转录组测序揭示了一组由丁酸盐诱导的组蛋白修饰激活的独特基因

Gene regulation and systems biology Pub Date : 2016-01-21 DOI: 10.4137/GRSB.S35607

Congjun Li, Robert W. Li, R. Baldwin, L. Blomberg, Sitao Wu, Weizhong Li

引用次数: 20

Biochemical Analysis of Genome Functions Using Locus-Specific Chromatin Immunoprecipitation Technologies 利用基因座特异性染色质免疫沉淀技术对基因组功能进行生化分析

Gene regulation and systems biology Pub Date : 2016-01-18 DOI: 10.4137/GRSB.S32520

T. Fujita, H. Fujii

引用次数: 12

tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins. trna衍生的短非编码RNA作为Argonaute蛋白的相互作用伙伴。

Gene regulation and systems biology Pub Date : 2015-09-10 eCollection Date: 2015-01-01 DOI: 10.4137/GRSB.S29411

Megumi Shigematsu, Yohei Kirino

引用次数: 75

Effects of High Fat Feeding on Adipose Tissue Gene Expression in Diabetic Goto-Kakizaki Rats. 高脂喂养对糖尿病后崎大鼠脂肪组织基因表达的影响。

Gene regulation and systems biology Pub Date : 2015-08-10 eCollection Date: 2015-01-01 DOI: 10.4137/GRSB.S25172

Bai Xue, Jing Nie, Xi Wang, Debra C DuBois, William J Jusko, Richard R Almon

{"title":"Effects of High Fat Feeding on Adipose Tissue Gene Expression in Diabetic Goto-Kakizaki Rats.","authors":"Bai Xue, Jing Nie, Xi Wang, Debra C DuBois, William J Jusko, Richard R Almon","doi":"10.4137/GRSB.S25172","DOIUrl":"https://doi.org/10.4137/GRSB.S25172","url":null,"abstract":"Development and progression of type 2 diabetes is a complex interaction between genetics and environmental influences. High dietary fat is one environmental factor that is conducive to the development of insulin-resistant diabetes. In the present report, we compare the responses of lean poly-genic, diabetic Goto-Kakizaki (GK) rats to those of control Wistar-Kyoto (WKY) rats fed a high fat diet from weaning to 20 weeks of age. This comparison included a wide array of physiological measurements along with gene expression profiling of abdominal adipose tissue using Affymetrix gene array chips. Animals of both strains fed a high fat diet or a normal diet were sacrificed at 4, 8, 12, 16, and 20 weeks for this comparison. The microarray analysis revealed that the two strains developed different adaptations to increased dietary fat. WKY rats decrease fatty acid synthesis and lipogenic processes whereas GK rats increase lipid elimination. However, on both diets the major differences between the two strains remained essentially the same. Specifically relative to the WKY strain, the GK strain showed lipoatrophy, chronic inflammation, and insulin resistance. ","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"9 ","pages":"15-26"},"PeriodicalIF":0.0,"publicationDate":"2015-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S25172","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34019993","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}

引用次数: 14

p53 Contributes to Differentiating Gene Expression Following Exposure to Acetaminophen and Its Less Hepatotoxic Regioisomer Both In Vitro and In Vivo. p53对暴露于对乙酰氨基酚及其肝毒性较低的区域异构体后基因表达的差异有贡献。

Gene regulation and systems biology Pub Date : 2015-06-01 eCollection Date: 2015-01-01 DOI: 10.4137/GRSB.S25388

Brendan D Stamper, Michael L Garcia, Duy Q Nguyen, Richard P Beyer, Theo K Bammler, Frederico M Farin, Terrance J Kavanagh, Sidney D Nelson

{"title":"p53 Contributes to Differentiating Gene Expression Following Exposure to Acetaminophen and Its Less Hepatotoxic Regioisomer Both In Vitro and In Vivo.","authors":"Brendan D Stamper, Michael L Garcia, Duy Q Nguyen, Richard P Beyer, Theo K Bammler, Frederico M Farin, Terrance J Kavanagh, Sidney D Nelson","doi":"10.4137/GRSB.S25388","DOIUrl":"https://doi.org/10.4137/GRSB.S25388","url":null,"abstract":"The goal of the present study was to compare hepatic toxicogenomic signatures across in vitro and in vivo mouse models following exposure to acetaminophen (APAP) or its relatively nontoxic regioisomer 3'-hydroxyacetanilide (AMAP). Two different Affymetrix microarray platforms and one Agilent Oligonucleotide microarray were utilized. APAP and AMAP treatments resulted in significant and large changes in gene expression that were quite disparate, and likely related to their different toxicologic profiles. Ten transcripts, all of which have been implicated in p53 signaling, were identified as differentially regulated at all time-points following APAP and AMAP treatments across multiple microarray platforms. Protein-level quantification of p53 activity aligned with results from the transcriptomic analysis, thus supporting the implicated mechanism of APAP-induced toxicity. Therefore, the results of this study provide good evidence that APAP-induced p53 phosphorylation and an altered p53-driven transcriptional response are fundamental steps in APAP-induced toxicity. ","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"9 ","pages":"1-14"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S25388","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33373385","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}

引用次数: 9

A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity. 一个假想的异卵单胞菌alde1蛋白(amad1_06475)被预测为具有RNA伴侣活性的冷休克蛋白。

Gene regulation and systems biology Pub Date : 2014-12-18 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S20802

Arafat Rahman Oany, Shah Adil Ishtiyaq Ahmad, Km Kaderi Kibria, Mohammad Uzzal Hossain, Tahmina Pervin Jyoti

{"title":"A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity.","authors":"Arafat Rahman Oany, Shah Adil Ishtiyaq Ahmad, Km Kaderi Kibria, Mohammad Uzzal Hossain, Tahmina Pervin Jyoti","doi":"10.4137/GRSB.S20802","DOIUrl":"https://doi.org/10.4137/GRSB.S20802","url":null,"abstract":"Alteromonas macleodii AltDE1 is a deep sea protobacteria that is distinct from the surface isolates of the same species. This study was designed to elucidate the biological function of amad1_06475, a hypothetical protein of A. macleodii AltDE1. The 70 residues protein sequence showed considerable homology with cold-shock proteins (CSPs) and RNA chaperones from different organisms. Multiple sequence alignment further supported the presence of conserved csp domain on the protein sequence. The three-dimensional structure of the protein was also determined, and verified by PROCHECK, Verify3D, and QMEAN programs. The predicted structure contained five anti-parallel β-strands and RNA-binding motifs, which are characteristic features of prokaryotic CSPs. Finally, the binding of a thymidine-rich oligonucleotide and a single uracil molecule in the active site of the protein further strengthens our prediction about the function of amad1_06475 as a CSP and thereby acting as a RNA chaperone. The binding was performed by molecular docking tools and was compared with similar binding of 3PF5 (PDB) and 2HAX (PDB), major CSPs of Bacillus subtilis and Bacillus caldolyticus, respectively. ","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"141-7"},"PeriodicalIF":0.0,"publicationDate":"2014-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S20802","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32962752","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}

引用次数: 3

A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia. 基于chip - seq的小胶质细胞PU.1/Spi1靶基因的综合分析

Gene regulation and systems biology Pub Date : 2014-12-08 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S19711

Jun-Ichi Satoh, Naohiro Asahina, Shouta Kitano, Yoshihiro Kino

{"title":"A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia.","authors":"Jun-Ichi Satoh, Naohiro Asahina, Shouta Kitano, Yoshihiro Kino","doi":"10.4137/GRSB.S19711","DOIUrl":"https://doi.org/10.4137/GRSB.S19711","url":null,"abstract":"Microglia are resident mononuclear phagocytes that play a principal role in the maintenance of normal tissue homeostasis in the central nervous system (CNS). Microglia, rapidly activated in response to proinflammatory stimuli, are accumulated in brain lesions of neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. The E26 transformation-specific (ETS) family transcription factor PU.1/Spi1 acts as a master regulator of myeloid and lymphoid development. PU.1-deficient mice show a complete loss of microglia, indicating that PU.1 plays a pivotal role in microgliogenesis. However, the comprehensive profile of PU.1/Spi1 target genes in microglia remains unknown. By analyzing a chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) dataset numbered SRP036026 with the Strand NGS program, we identified 5,264 Spi1 target protein-coding genes in BV2 mouse microglial cells. They included Spi1, Irf8, Runx1, Csf1r, Csf1, Il34, Aif1 (Iba1), Cx3cr1, Trem2, and Tyrobp. By motif analysis, we found that the PU-box consensus sequences were accumulated in the genomic regions surrounding ChIP-Seq peaks. By using pathway analysis tools of bioinformatics, we found that ChIP-Seq-based Spi1 target genes show a significant relationship with diverse pathways essential for normal function of monocytes/macrophages, such as endocytosis, Fc receptor-mediated phagocytosis, and lysosomal degradation. These results suggest that PU.1/Spi1 plays a crucial role in regulation of the genes relevant to specialized functions of microglia. Therefore, aberrant regulation of PU.1 target genes might contribute to the development of neurodegenerative diseases with accumulation of activated microglia. ","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"127-39"},"PeriodicalIF":0.0,"publicationDate":"2014-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S19711","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32962751","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}

引用次数: 63

Endothelin-1 but not Endothelial Nitric Oxide Synthase Gene Polymorphism is Associated with Sickle Cell Disease in Africa. 非洲人的镰状细胞病与内皮素-1而非内皮型一氧化氮合酶基因多态性相关

Gene regulation and systems biology Pub Date : 2014-05-25 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S14836

Tanya J Thakur, Aldiouma Guindo, Londyn R Cullifer, Yi Li, Ikhide G Imumorin, Dapa A Diallo, Bolaji N Thomas

{"title":"Endothelin-1 but not Endothelial Nitric Oxide Synthase Gene Polymorphism is Associated with Sickle Cell Disease in Africa.","authors":"Tanya J Thakur, Aldiouma Guindo, Londyn R Cullifer, Yi Li, Ikhide G Imumorin, Dapa A Diallo, Bolaji N Thomas","doi":"10.4137/GRSB.S14836","DOIUrl":"https://doi.org/10.4137/GRSB.S14836","url":null,"abstract":"Sickle cell disease shows marked variability in severity and pathophysiology among individuals, probably linked to differential expression of various adhesion molecules. In this study, we investigated the differential distribution, genomic diversity and haplotype frequency of endothelial nitric oxide synthase (eNOS) and endothelin-1 (ET-1) polymorphisms, recently implicated as important in modification of disease severity. One hundred and forty five sickle cell disease patients (HbSS) and 244 adult and pediatric controls, without sickle cell disease (HbAA), were recruited from Mali. Genotypic analysis of the functionally significant eNOS variants (T786C, G894T and intron 4) and endothelin-1 (G5665T) was carried out with a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. Our results show that the wild type alleles are the most frequent for all eNOS variants between cases and controls. Allelic and genotypic frequencies of eNOS polymorphic groups are not significantly different between cases and controls (P > 0.05). In addition, there is no association between eNOS variants and sickle cell disease, contrary to published reports. On the other hand, we report that endothelin-1 (G5665T) mutant variant had the lowest allelic frequency, and is significantly associated with sickle cell disease in Africa (P < 0.05). Similarly, haplotype frequencies were the same between cases and controls, except for the haplotype combining all mutant variants (T, C, 4a; P = 0.01). eNOS polymorphic variants are less frequent, with no significance with sickle cell disease in Africa. On the other hand, endothelin-1 is associated with sickle cell disease, and has the capacity to redefine pathophysiology and possibly serve as modulator of disease phenotype. ","PeriodicalId":73138,"journal":{"name":"Gene regulation and systems biology","volume":"8 ","pages":"119-26"},"PeriodicalIF":0.0,"publicationDate":"2014-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4137/GRSB.S14836","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32425481","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}

引用次数: 25

Species-Specific Regulation of t-PA and PAI-1 Gene Expression in Human and Rat Astrocytes. 人和大鼠星形胶质细胞中t-PA和PAI-1基因表达的物种特异性调控。

Gene regulation and systems biology Pub Date : 2014-05-08 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S13387

Anna Tjärnlund-Wolf, Karin Hultman, Fredrik Blomstrand, Michael Nilsson, Robert L Medcalf, Christina Jern

引用次数: 6