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https://www.readbyqxmd.com/read/28728396/characterization-and-functional-inferences-of-a-genome-wide-dna-methylation-profile-in-the-loin-longissimus-dorsi-muscle-of-swine
#1
Woonsu Kim, Hyesun Park, Kang-Seok Seo, Seongwon Seo
Objective: DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. Methods: A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates)...
May 14, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28727982/genome-wide-dna-methylation-profile-of-prepubertal-porcine-testis
#2
Xi Chen, Liu-Hong Shen, Li-Xuan Gui, Fang Yang, Jie Li, Sui-Zhong Cao, Zhi-Cai Zuo, Xiao-Ping Ma, Jun-Liang Deng, Zhi-Hua Ren, Zhong-Xu Chen, Shu-Min Yu
The biological structure and function of the mammalian testis undergo important developmental changes during prepuberty and DNA methylation is dynamically regulated during testis development. In this study, we generated the first genome-wide DNA methylation profile of prepubertal porcine testis using methyl-DNA immunoprecipitation (MeDIP) combined with high-throughput sequencing (MeDIP-seq). Over 190 million high-quality reads were generated, containing 43642 CpG islands. There was an overall downtrend of methylation during development, which was clear in promoter regions but less so in gene-body regions...
July 21, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28726847/mapping-genome-wide-transcription-factor-binding-sites-using-dap-seq
#3
Anna Bartlett, Ronan C O'Malley, Shao-Shan Carol Huang, Mary Galli, Joseph R Nery, Andrea Gallavotti, Joseph R Ecker
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX)...
August 2017: Nature Protocols
https://www.readbyqxmd.com/read/28726800/role-of-nicotinamide-n-methyltransferase-in-dorsal-striatum-in-cocaine-place-preference
#4
Li Luo, Fei-Fei Shang, Hailei Long, Linhong Jiang, Ruiming Zhu, Qian Zhao, Hui Gu, Jueying Kong, Wei Xu, Yinglan Zhao, Xiaobo Cen
Nicotinamide N-methyltransferase (NNMT) transfers the methyl from S-adenosyl-L-methionine (SAM) to nicotinamide (NA) to produce S-adenosyl-L-homocysteine (SAH) and 1-methylnicotinamide (MeN). NNMT has been implicated in a variety of diseases; however, the role of NNMT in drug addiction is largely unknown. Here, we found that the expression of Nnmt was significantly upregulated in the dorsal striatum (DS) of cocaine-conditioned mice. Cocaine significantly decreased SAM/SAH ratio levels in the DS, which was accompanied with the decreased activities of Rac1 and RhoA...
July 20, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28726778/protection-of-mcc950-against-high-glucose-induced-human-retinal-endothelial-cell-dysfunction
#5
Yi Zhang, Xuehua Lv, Zizhong Hu, Xiaojian Ye, Xinhua Zheng, Yuzhi Ding, Ping Xie, Qinghuai Liu
Diabetic retinopathy (DR) is a well-known microvascular complication related to inflammation. Mcc950 is a potent and specific inhibitor of the NLRP3 inflammasome but its influence on DR has not been studied. Thus, we evaluated the anti-inflammatory effects of Mcc950 on high-glucose-induced human retinal endothelial cells (HRECs) and the potential underlying mechanism. In surgical excised proliferative membranes from DR patients, high expression of NLRP3, caspase 1 and IL-1β was observed and co-localization of NLRP3 and IL-1β occurred in CD31+ labeled HRECs...
July 20, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28726294/screening-and-structural-and-functional-investigation-of-a-novel-ferritin-from-phascolosoma-esculenta
#6
Hongwei Ding, Dijun Zhang, Shuangshuang Chu, Jun Zhou, Xiurong Su
Ferritins are primary iron storage proteins and play a crucial role in iron storage and detoxification. Yeast two-hybrid method was employed to screen the cDNA library of Phascolosoma esculenta. Sequence of positive colony FER147 was analyzed. The higher similarity and conserved motifs for ferritin indicated that it belonged to a new member of ferritin family. The interaction between Ferritin and Fer147 was further confirmed through co-immunoprecipitation. The pET-28a-FER147 prokaryotic expression vector was constructed...
July 20, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28725180/endothelial-nitric-oxide-synthase-is-present-in-dendritic-spines-of-neurons-in-primary-cultures
#7
Ariel Caviedes, Manuel Varas-Godoy, Carlos Lafourcade, Soledad Sandoval, Javiera Bravo-Alegria, Thilo Kaehne, Angela Massmann, Jorge P Figueroa, Francisco Nualart, Ursula Wyneken
Nitric oxide exerts important regulatory functions in various brain processes. Its synthesis in neurons has been most commonly ascribed to the neuronal nitric oxide synthase (nNOS) isoform. However, the endothelial isoform (eNOS), which is significantly associated with caveolae in different cell types, has been implicated in synaptic plasticity and is enriched in the dendrites of CA1 hippocampal neurons. Using high resolution microscopy and co-distribution analysis of eNOS with synaptic and raft proteins, we now show for the first time in primary cortical and hippocampal neuronal cultures, virtually devoid of endothelial cells, that eNOS is present in neurons and is localized in dendritic spines...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28724759/cholesterol-25-hydroxylase-inhibits-porcine-reproductive-and-respiratory-syndrome-virus-replication-through-enzyme-activity-dependent-and-independent-mechanisms
#8
Wenting Ke, Liurong Fang, Huiyuan Jing, Ran Tao, Ting Wang, Yang Li, Siwen Long, Dang Wang, Shaobo Xiao
Cholesterol 25-hydroxylase (CH25H) has recently been identified as a host restriction factor that exerts antiviral effects by catalyzing the production of 25-hydroxycholesterol (25HC). CH25H can be rapidly induced upon infection with some viruses. Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus, has ranked among the most important swine pathogens since it was discovered in the late 1980s. In this study, we found that PRRSV infection significantly downregulated the expression of CH25H in cells by a so far unknown mechanism, suggesting that CH25H might exert antiviral activity against PRRSV...
July 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28724612/regulation-of-pdz-domain-containing-1-pdzk1-expression-by-hepatocyte-nuclear-factor-1-alpha-hnf1%C3%AE-in-human-kidney
#9
Katharina Prestin, Janine Hussner, Celio Ferreira, Isabell Seibert, Vivien Breitung, Uwe Zimmermann, Henriette Elisabeth Meyer Zu Schwabedissen
In the renal proximal tubule the secretion and reabsorption of glomerularly filtrated compounds is realized by a functional network of uptake and efflux transporters. The activity and localization of several transporters expressed at the apical tubular membrane is regulated by the membrane associated protein PDZ domain containing 1 (PDZK1). We aimed to characterize the transcriptional regulation of this modulator of renal transport. Coexpression analyses of PDZK1 and putative regulators were performed using human kidney samples...
July 19, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28724430/egfr-modulates-monounsaturated-fatty-acid-synthesis-through-phosphorylation-of-scd1-in-lung-cancer
#10
Jiqin Zhang, Fei Song, Xiaojing Zhao, Hua Jiang, Xiuqi Wu, Biao Wang, Min Zhou, Mi Tian, Bizhi Shi, Huamao Wang, Yuanhui Jia, Hai Wang, Xiaorong Pan, Zonghai Li
BACKGROUND: Epidermal growth factor receptor (EGFR), a well-known oncogenic driver, contributes to the initiation and progression of a wide range of cancer types. Aberrant lipid metabolism including highly produced monounsaturated fatty acids (MUFA) is recognized as a hallmark of cancer. However, how EGFR regulates MUFA synthesis in cancer remains elusive. This is the focus of our study. METHODS: The interaction between EGFR and stearoyl-CoA desaturase-1 (SCD1) was detected byco-immunoprecipitation...
July 19, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28723896/maternal-h3k27me3-controls-dna-methylation-independent-imprinting
#11
Azusa Inoue, Lan Jiang, Falong Lu, Tsukasa Suzuki, Yi Zhang
Mammalian sperm and oocytes have different epigenetic landscapes and are organized in different fashions. After fertilization, the initially distinct parental epigenomes become largely equalized with the exception of certain loci, including imprinting control regions. How parental chromatin becomes equalized and how imprinting control regions escape from this reprogramming is largely unknown. Here we profile parental allele-specific DNase I hypersensitive sites in mouse zygotes and morula embryos, and investigate the epigenetic mechanisms underlying these allelic sites...
July 19, 2017: Nature
https://www.readbyqxmd.com/read/28721853/us10-a-novel-npro-interacting-protein-inhibits-classical-swine-fever-virus-replication
#12
Huifang Lv, Wang Dong, Gui Qian, Jie Wang, Xiaomeng Li, Zhi Cao, Qizhuang Lv, Chengbao Wang, Kangkang Guo, Yanming Zhang
Classical swine fever (CSF) is a severe, febrile and highly contagious disease caused by classical swine fever virus (CSFV) that has resulted in huge economic losses in the pig industry worldwide. CSFV Npro has been actively studied but remains incompletely understood. Few studies have investigated the cellular proteins that interact with Npro and their participation in viral replication. Here, the yeast two-hybrid (Y2H) system was employed to screen Npro-interacting proteins from a porcine alveolar macrophage (PAM) cDNA library, and a blast search of the NCBI database revealed that 15 cellular proteins interact with Npro...
July 18, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28720704/cytosolic-interaction-of-type-iii-human-cd38-with-cib1-modulates-cellular-cyclic-adp-ribose-levels
#13
Jun Liu, Yong Juan Zhao, Wan Hua Li, Yun Nan Hou, Ting Li, Zhi Ying Zhao, Cheng Fang, Song Lu Li, Hon Cheung Lee
CD38 catalyzes the synthesis of the Ca(2+) messenger, cyclic ADP-ribose (cADPR). It is generally considered to be a type II protein with the catalytic domain facing outside. How it can catalyze the synthesis of intracellular cADPR that targets the endoplasmic Ca(2+) stores has not been resolved. We have proposed that CD38 can also exist in an opposite type III orientation with its catalytic domain facing the cytosol. Here, we developed a method using specific nanobodies to immunotarget two different epitopes simultaneously on the catalytic domain of the type III CD38 and firmly established that it is naturally occurring in human multiple myeloma cells...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720061/the-long-non-coding-rna-malat1-promotes-the-migration-and-invasion-of-hepatocellular-carcinoma-by-sponging-mir-204-and-releasing-sirt1
#14
Zhouhua Hou, Xuwen Xu, Ledu Zhou, Xiaoyu Fu, Shuhui Tao, Jiebin Zhou, Deming Tan, Shuiping Liu
Increasing evidence supports the significance of long non-coding RNA in cancer development. Several recent studies suggest the oncogenic activity of long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) in hepatocellular carcinoma. In this study, we explored the molecular mechanisms by which MALAT1 modulates hepatocellular carcinoma biological behaviors. We found that microRNA-204 was significantly downregulated in sh-MALAT1 HepG2 cell and 15 hepatocellular carcinoma tissues by quantitative real-time polymerase chain reaction analysis...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28718849/an-efficient-method-to-transcription-factor-binding-sites-imputation-via-simultaneous-completion-of-multiple-matrices-with-positional-consistency
#15
Wei-Li Guo, De-Shuang Huang
Transcription factors (TFs) are DNA-binding proteins that have a central role in regulating gene expression. Identification of DNA-binding sites of TFs is a key task in understanding transcriptional regulation, cellular processes and disease. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) enables genome-wide identification of in vivo TF binding sites. However, it is still difficult to map every TF in every cell line owing to cost and biological material availability, which poses an enormous obstacle for integrated analysis of gene regulation...
July 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28717224/fibulin-4-deposition-requires-emilin-1-in-the-extracellular-matrix-of-osteoblasts
#16
Alvise Schiavinato, Douglas R Keene, Thomas Imhof, Roberto Doliana, Takako Sasaki, Gerhard Sengle
Tissue microenvironments formed by extracellular matrix networks play an important role in regulating tissue structure and function. Extracellular microfibrillar networks composed of fibrillins and their associated ligands such as LTBPs, fibulins, and EMILINs are of particular interest in this regard since they provide a specialized cellular microenvironment guiding proper morphology and functional behavior of specialized cell types. To understand how cellular microenvironments composed of intricate microfibrillar networks influence cell fate decisions in a contextual manner, more information about the spatiotemporal localization, deposition, and function of their components is required...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716730/interaction-of-small-g-protein-signaling-modulator-3-with-connexin-43-contributes-to-myocardial-infarction-in-rat-hearts
#17
Chang Youn Lee, Jung-Won Choi, Sunhye Shin, Jiyun Lee, Hyang-Hee Seo, Soyeon Lim, Seahyoung Lee, Hyun-Chul Joo, Sang Woo Kim, Ki-Chul Hwang
Connexin 43 (Cx43), a ubiquitous connexin expressed in the heart and skin, is associated with a variety of hereditary conditions. Therefore, the characterization of Cx43-interacting proteins and their dynamics is important to understand not only the molecular mechanisms underlying pathological malfunction of gap junction-mediated intercellular communication but also to identify novel and unanticipated biological functions of Cx43. In the present study, we observed potential targets of Cx43 to determine new molecular functions in cardio-protection...
July 14, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28716709/isolation-and-characterization-of-the-5-flanking-region-of-the-human-pdxk-gene
#18
ShuoHao Huang, ZhengQing Liu, ZhenQiao Ma, JianYun Zhang, LongQuan Huang
Pyridoxal kinase is a key enzyme for the biosynthesis of pyridoxal 5'-phosphate. Pyridoxal 5'-phosphate is the catalytically active form of vitamin B6, and acts as a cofactor in >140 different enzyme reactions. It is still unknown how the kinase synthesis is regulated in the cells, and nothing has been reported about the gene promoter. In the present study, based on the bioinformatics analysis of the 5'-flanking region of the human PDXK gene, we cloned the promoter region by PCR. Through the construction of a series of luciferase expression vectors containing the human PDXK promoter region, we characterized the promoter in terms of its structure and function...
July 14, 2017: Gene
https://www.readbyqxmd.com/read/28716136/up-regulation-of-cdk16-by-multiple-mechanisms-in-hepatocellular-carcinoma-promotes-tumor-progression
#19
Yitao Wang, Xian Qin, Tao Guo, Pengpeng Liu, Ping Wu, Zhisu Liu
BACKGROUND: Hepatocellular carcinoma (HCC) remains difficult to cure due to lack of effective treatment and the molecular mechanisms are complex and not completely understood. In this study, We investigated the role of CDK16 in tumor progression of HCC. METHODS: We interrogated the expression level of CDK16 by polymerase chain reaction and immunohistochemistry(IHC) and studied its clinical significance. The functional role of CDK16 on HCC was studied via gain and loss of function in vitro and in vivo...
July 17, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28716052/%C3%AE-arrestin1-mediated-acetylation-of-gli1-regulates-hedgehog-gli-signaling-and-modulates-self-renewal-of-shh-medulloblastoma-cancer-stem-cells
#20
Evelina Miele, Agnese Po, Federica Begalli, Laura Antonucci, Angela Mastronuzzi, Carlo Efisio Marras, Andrea Carai, Danilo Cucchi, Luana Abballe, Zein Mersini Besharat, Giuseppina Catanzaro, Paola Infante, Lucia Di Marcotullio, Gianluca Canettieri, Enrico De Smaele, Isabella Screpanti, Franco Locatelli, Elisabetta Ferretti
BACKGROUND: Aberrant Sonic Hedgehog/Gli (Hh/Gli) signaling pathway is a critical regulator of Sonic hedgehog medulloblastoma (SHH-MB). Cancer stem cells (CSCs), thought to be largely responsible for tumor initiation, maintenance, dissemination and relapse, have been identified in SHH-MB. Since we previously demonstrated that Hh/Gli signaling controls CSCs features in SHH-MB and that in these tumors miR-326 is down regulated, here we investigated whether there is a functional link between Hh/Gli signaling and miR-326...
July 17, 2017: BMC Cancer
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