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Overfeeding Dairy Cattle During Late-Pregnancy Alters Hepatic PPARα-Regulated Pathways Including Hepatokines: Impact on Metabolism and Peripheral Insulin Sensitivity. 妊娠后期过量喂养奶牛改变肝脏ppar α调控通路,包括肝因子:对代谢和外周胰岛素敏感性的影响
Pub Date : 2014-04-03 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S14116
M Jawad Khan, Carolina B Jacometo, Daniel E Graugnard, Marcio N Corrêa, Eduardo Schmitt, Felipe Cardoso, Juan J Loor

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.

研究了妊娠最后45 d饲喂控制饲粮(CON, 1.34 Mcal/kg)和高能量饲粮(OVE, 1.62 Mcal/kg)的奶牛肝脏代谢基因网络。共57个靶基因,包括ppar α-靶点/共调节因子、肝因子、生长激素(GH)/胰岛素样生长因子1 (IGF-1)轴、脂肪生成和脂蛋白代谢,在分娩前后-14、7、14和30天进行评估。OVE奶牛与CON奶牛相比,产后负能量平衡(NEB)更严重,血清非酯化脂肪酸(NEFA)、β-羟基丁酸(BHBA)和肝脏甘油三酯(TAG)浓度更高。乳汁合成速率无显著差异。OVE奶牛的肝脏通过上调脂肪酸氧化和生酮途径中ppar α-靶点以及糖异生基因的表达来响应产后NEB。产后肝因子(成纤维细胞生长因子21 (FGF21),血管生成素样4 (ANGPTL4))和载脂蛋白a - v (APOA5)在OVE组的上调幅度大于con组。OVE导致更高的血胰岛素准备,更低的NEFA:胰岛素,更高的脂肪生成基因表达,表明胰岛素敏感性未受损。在饲喂OVE的奶牛中,APOB、MTTP和PNPLA3缺乏变化,加上产后PLIN2的上调,导致了TAG的积累。NEFA和FGF21伴OVE的产后反应支持该肝因子在降低脂肪胰岛素敏感性中的作用。
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引用次数: 67
DNA conformational transitions induced by supercoiling control transcription in chromatin. 染色质超卷曲控制转录诱导的DNA构象转变。
Pub Date : 2014-03-12 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S13756
Andrey N Luchnik

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.

在真核生物转录的调节被认为是在最近的发现表明存在负和正的超螺旋张力在染色质。这种张力引起DNA双链的构象转变。特别是,转化为a -构象使DNA易于接近,并为转录起始提供了途径,产生长期以来已知属于a -构象的RNA分子。不同DNA序列的构象转换之间对弹性弹簧能量的竞争为理解转录的远程微调提供了可能。
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引用次数: 6
Tissue-specific gene expression and regulation in liver and muscle following chronic corticosteroid administration. 长期服用皮质类固醇后肝脏和肌肉中组织特异性基因的表达和调节。
Pub Date : 2014-03-10 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S13134
Tung T Nguyen, Richard R Almon, Debra C Dubois, Siddharth Sukumaran, William J Jusko, Ioannis P Androulakis

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.

尽管皮质类固醇(CSs)会影响多种组织中的基因表达,但受这些分解代谢类固醇调控的基因却多种多样,具有高度的组织特异性,并取决于它们在组织中的功能。肝脏在执行和调节各种代谢过程中具有许多重要功能。肌肉除了具有机械作用外,在维持全身能量平衡方面也至关重要,约占胰岛素引导的葡萄糖处置的 80%。因此,更好地了解 CS 药物基因组在这些组织中的作用将为转录动态的组织特异性提供有价值的信息,并有助于深入了解有益和有害作用的潜在分子机制。我们对输注甲基强的松龙(MPL)后肝脏和肌肉的转录数据进行了综合分析,其中包括聚类基因组的聚类和功能注释、启动子提取和推定转录因子(TF)鉴定,以及最后的调控亲和性(RC)鉴定。通过这项分析,确定了慢性 MPL 给药期间肝脏和肌肉中的关键转录反应和 CS 响应功能,预测了与受 CS 影响基因的转录反应相关的假定转录调节因子(它们也是改变靶基因表达水平的潜在次级生物信号),并探索了基因表达模式、CS 响应功能和转录调节的组织特异性和生物学意义。该分析综合描述了长期输注 MPL 对肝脏和肌肉基因组和功能的影响。
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引用次数: 0
Tetracycline derivative minocycline inhibits autophagy and inflammation in concanavalin-a-activated human hepatoma cells. 四环素衍生物二甲胺四环素抑制刀豆蛋白a激活的人肝癌细胞的自噬和炎症。
Pub Date : 2014-03-04 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S13946
Michel Desjarlais, Jonathan Pratt, Amine Lounis, Catherine Mounier, Khadidja Haidara, Borhane Annabi

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.

抑制可溶性基质金属蛋白酶(MMP)活性是抗炎四环素衍生物米诺环素发挥的非抗生素细胞作用之一。米诺环素对膜结合MMPs信号转导功能的影响尚不清楚。我们在ConA激活的人HepG2肝癌细胞模型中评估了二甲胺四环素,这种情况已知会增加膜1型MMP (MT-MMP)的表达,并引发炎症和自噬过程。我们发现二甲胺四环素抑制cona诱导的自噬酸性液泡的形成、绿色荧光微管相关蛋白1轻链3 (GFP-LC3)斑点的形成、自噬生物标志物BCL2/腺病毒E1B 19kda相互作用蛋白3 (BNIP3)、入侵生物标志物MT1-MMP和炎症生物标志物环氧化酶(COX)-2的基因和蛋白表达。MT1-MMP的基因沉默消除了cona诱导的自噬酸性液泡的形成和cona诱导的BNIP3和COX-2的表达。米诺环素还被证明可以抑制cona诱导的STAT3磷酸化以及NANOS1的基因表达,NANOS1是一种生物标志物,被认为与MT1-MMP共定位,其特异性沉默进一步抑制了cona诱导的STAT3磷酸化。总之,我们的数据表明,米诺环素对自噬的部分影响可能是通过抑制MT1-MMP信号功能来发挥的,这有助于cona激活的HepG2细胞的自噬和炎症表型。
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引用次数: 15
Discovery of Emphysema Relevant Molecular Networks from an A/J Mouse Inhalation Study Using Reverse Engineering and Forward Simulation (REFS™). 利用逆向工程和正向模拟(REFS™)从A/J小鼠吸入研究中发现肺气肿相关分子网络。
Pub Date : 2014-02-19 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S13140
Yang Xiang, Ulrike Kogel, Stephan Gebel, Michael J Peck, Manuel C Peitsch, Viatcheslav R Akmaev, Julia Hoeng

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.

慢性阻塞性肺疾病(COPD)是由于呼吸道长期暴露于有害刺激(主要是香烟烟雾)而引起的一种呼吸系统疾病。COPD发展的机制尚不完全清楚,尽管人们认为该疾病过程包括遗传成分,因为并非所有吸烟者都会患上COPD。为了研究导致COPD/肺气肿发展的机制,我们测量了暴露于两种CS剂量不同时间后小鼠肺组织的全基因组基因表达和几种COPD相关生物学终点。通过整合基因表达数据和四个copd相关终点(基质金属蛋白酶(MMP)活性、MMP-9水平、金属蛋白酶-1组织抑制剂水平和肺重量),采用一种新颖而强大的方法——逆向工程和正向模拟(REFS™)来识别关键的分子驱动因素。使用REFS™生成了一个分子网络集合,模拟结果表明,它可以成功地恢复基因表达和copd相关终点的测量实验数据。然后利用网络集合来模拟数千个硅基因敲除实验。因此,确定了上述四个COPD相关终点的33个分子关键驱动因素,其中大多数显示在炎症和COPD中富集。
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引用次数: 5
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. H3K4me3和H3K4me1在小鼠肝脏和小鼠胚胎干细胞中的基因表达及基因本体富集分析
Pub Date : 2014-01-20 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S13612
Ngoc Tam L Tran, Chun-Hsi Huang

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.

最近的研究已经确定了小鼠基因组中的顺式调控元件及其基因组定位。最近的发现表明,H3赖氨酸4三甲基化(H3K4me3)结合作为活性启动子的富集,以及H3赖氨酸4单甲基化(H3K4me1)在启动子区域外的存在作为增强子的标志。在本研究中,我们利用ChIP-Seq和RNA-Seq进一步鉴定了小鼠肝脏中H3K4me3标记或H3K4me3和H3K4me1标记的高表达基因。我们发现,在小鼠中,肝脏具有胚胎干细胞相关功能,而胚胎干细胞也具有肝脏相关功能。我们还在小鼠肝脏和小鼠胚胎干细胞的RNA-Seq实验中发现了新的基因。这些基因目前不在NCBI的Ensemble基因数据库中。
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引用次数: 3
Central Role of the PPARγ Gene Network in Coordinating Beef Cattle Intramuscular Adipogenesis in Response to Weaning Age and Nutrition. PPARγ基因网络在协调肉牛对断奶日龄和营养的肌内脂肪形成中的核心作用
Pub Date : 2014-01-08 eCollection Date: 2014-01-01 DOI: 10.4137/GRSB.S11782
Sonia J Moisá, Daniel W Shike, Dan B Faulkner, William T Meteer, Duane Keisler, Juan J Loor

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.

研究了断奶日龄和饲粮淀粉水平对肌内脂肪沉积(IMF)调控的成脂/成脂转录网络。分别在0 (EW)、25、50、96 (NW)、167和222(屠宰前)天对早期断奶(141日龄)加高淀粉饲粮(EWS)或正常断奶(NW, 222日龄)加淀粉匍匐饲粮(CFS)的肉牛最长肌(LM)进行活组织检查。研究了35个靶基因的表达模式。从西北至屠宰,所有阉牛均饲喂相同的高淀粉日粮。在EWS小鼠中,参与IMF过程的PPARG、其他致脂因子(CEBPA、ZFP423)和致脂因子(THRSP、SREBF1、INSIG1)以及几种酶(FASN、SCD、ELOVL6、PCK1、DGAT2)的表达在治疗后96 ~ 167天逐渐增加,达到峰值。西北地区的阉牛即使在治疗222天后也没有达到类似的表达水平,这表明即使在断奶后喂食高淀粉饮食,它们的反应也会变迟钝。早期高淀粉喂养(EWS)会引发早熟和持续的脂肪生成,导致更大的大理石纹。
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引用次数: 50
Innate immunity interactome dynamics. 先天免疫相互作用动力学。
Pub Date : 2014-01-06 DOI: 10.4137/GRSB.S12850
Asmaa Elzawahry, Ashwini Patil, Yutaro Kumagai, Yutaka Suzuki, Kenta Nakai

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.

先天免疫反应包括蛋白质-蛋白质相互作用、脱氧核糖核酸(DNA)-蛋白质相互作用和信号级联反应。到目前为止,数千种蛋白质与蛋白质之间的相互作用已经被整理成一张静态相互作用图。然而,先天免疫反应中涉及的蛋白质-蛋白质相互作用是动态的。我们将脂多糖(LPS)刺激的树突状细胞的基因表达数据与蛋白质-蛋白质相互作用数据相结合,记录了先天免疫应答过程中相互作用组的动态。我们通过构建差异网络和鉴定在先天免疫应答的每个阶段上调/下调的蛋白模块,确定了先天免疫应答过程中相互作用组的差异。对于每种蛋白质复合物,我们确定了富集的生物过程和途径。此外,我们确定了在整个先天免疫反应中保守的核心相互作用及其丰富的基因本体术语和途径。我们定义了两种新的测量方法来评估不同时间点网络地图之间的差异。我们发现,LPS刺激后1小时的蛋白相互作用网络中相互作用蛋白比例最高,这表明大量相互作用的蛋白在先天免疫应答中起作用。两两差分矩阵允许对不同网络之间的差异进行全局可视化。我们研究了toll样受体亚网络,发现S100A8在LPS刺激后在树突状细胞中下调。已确定的蛋白质复合物不仅在先天免疫中起着至关重要的作用,而且在昼夜节律、癌症通路和p53通路中也起着至关重要的作用。这项研究证实了之前的研究,即癌症和免疫力之间存在很强的相关性。
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引用次数: 3
Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. 基于chip - seq的NRF1靶基因通路分析提出了其参与神经退行性疾病发病机制的逻辑假设。
Pub Date : 2013-11-04 eCollection Date: 2013-01-01 DOI: 10.4137/GRSB.S13204
Jun-Ichi Satoh, Natsuki Kawana, Yoji Yamamoto

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.

核呼吸因子1 (NRF1)是一种转录因子,可激活线粒体生物发生和功能所必需的多种核基因的表达,包括线粒体呼吸复合体亚基、血红素生物合成酶和参与线粒体DNA复制和转录的调节因子。越来越多的证据表明,线粒体功能在与衰老相关的神经退行性疾病的大脑中严重受损。为了鉴定可能与神经退行性疾病发病机制相关的人类NRF1靶基因,我们分析了从DNA元件百科全书(ENCODE)项目中检索的NRF1染色质免疫沉淀和深度测序(ChIP-Seq)数据集。总的来说,我们在SK-N-SH人神经母细胞瘤细胞中鉴定了2470个高度严格的蛋白质编码基因ChIP-Seq峰。它们聚集在近端启动子区域,存在nrf1结合的一致序列。这组基于chip - seq的NRF1靶基因包括已知的NRF1靶基因,如EIF2S1、EIF2S2、CYCS、FMR1、FXR2、E2F6、CD47和TOMM34。通过通路分析,确定了位于与线粒体呼吸功能相关的核心通路中的分子在NRF1靶基因中高度富集。此外,我们发现NRF1靶基因在线粒体外生物过程的调控中发挥关键作用,包括RNA代谢、剪接、细胞周期、DNA损伤修复、蛋白质翻译起始和泛素介导的蛋白质降解。我们确定了一组神经退行性疾病相关基因,如帕金森病的PARK2 (Parkin)、PARK6 (Pink1)、PARK7 (DJ-1)和PAELR (GPR37),以及阿尔茨海默病的PSENEN (Pen2)和MAPT (tau),作为以前未被识别的NRF1靶点。这些结果提出了一个合乎逻辑的假设,即NRF1及其靶点的异常调节可能通过干扰多种线粒体和线粒体外功能而参与人类神经退行性疾病的发病机制。
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引用次数: 116
CEBPG Exhibits Allele-Specific Expression in Human Bronchial Epithelial Cells. CEBPG在人支气管上皮细胞中表现出等位基因特异性表达。
Pub Date : 2013-07-04 Print Date: 2013-01-01 DOI: 10.4137/GRSB.S11879
Thomas M Blomquist, Ronald D Brown, Erin L Crawford, Ivana de la Serna, Kandace Williams, Youngsook Yoon, Dawn-Alita Hernandez, James C Willey

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.

正常人支气管上皮细胞(NBEC) CCAAT/增强子结合蛋白γ (CEBPG)转录物表达的个体间变异与肺癌易感性相关。我们假设CEBPG的顺式作用遗传变异部分解释了这种个体间变异。为了验证这一假设,我们测量了来自每个CEBPG亲本拷贝的转录本表达(即等位基因特异性表达;日月光半导体)。CEBPG rs2772a基因的ASE细胞周期特异性变异比C基因高2.9倍(P < 0.001)。在20%的NBEC样本中,CEBPG rs2772 A等位基因的平均表达量是rs2772 C等位基因的2.10倍。这些数据支持了与rs2772连锁不平衡的遗传变异通过RNA聚合酶II转录下游的反式效应影响CEBPG转录物表达调控的假设,并证实了顺式作用的遗传变异导致了NBEC中CEBPG转录物表达的个体间差异,而这种差异与肺癌风险的变化有关。
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引用次数: 11
期刊
Gene regulation and systems biology
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