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https://www.readbyqxmd.com/read/28088069/nuclear-pore-complexes-and-regulation-of-gene-expression
#1
REVIEW
Marcela Raices, Maximiliano A D'Angelo
Nuclear pore complexes (NPCs), are large multiprotein channels that penetrate the nuclear envelope connecting the nucleus to the cytoplasm. Accumulating evidence shows that besides their main role in regulating the exchange of molecules between these two compartments, NPCs and their components also play important transport-independent roles, including gene expression regulation, chromatin organization, DNA repair, RNA processing and quality control, and cell cycle control. Here, we will describe the recent findings about the role of these structures in the regulation of gene expression...
January 11, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28087842/novel-determinants-of-mammalian-primary-microrna-processing-revealed-by-systematic-evaluation-of-hairpin-containing-transcripts-and-human-genetic-variation
#2
Christine Anne Roden, Jonathan Gaillard, Shaveta Kanoria, William Rennie, Syndi Barish, Jijun Cheng, Wen Pan, Jun Liu, Chris Cotsapas, Ye Ding, Jun Lu
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36+/-3nt is optimal for pri-miRNA processing...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28087716/the-piggybac-transposon-derived-genes-tpb1-and-tpb6-mediate-essential-transposon-like-excision-during-the-developmental-rearrangement-of-key-genes-in-tetrahymena-thermophila
#3
Chao-Yin Cheng, Janet M Young, Chih-Yi Gabriela Lin, Ju-Lan Chao, Harmit S Malik, Meng-Chao Yao
Ciliated protozoans perform extreme forms of programmed somatic DNA rearrangement during development. The model ciliate Tetrahymena thermophila removes 34% of its germline micronuclear genome from somatic macronuclei by excising thousands of internal eliminated sequences (IESs), a process that shares features with transposon excision. Indeed, piggyBac transposon-derived genes are necessary for genome-wide IES excision in both Tetrahymena (TPB2 [Tetrahymena piggyBac-like 2] and LIA5) and Paramecium tetraurelia (PiggyMac)...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087619/genome-wide-transcription-profiling-of-aerobic-and-anaerobic-escherichia-coli-biofilm-and-planktonic-cultures
#4
Bihter Bayramoglu, David Toubiana, Osnat Gillor
Many studies have described the response of the facultative anaerobe, Escherichia coli, to anaerobic conditions, yet they all investigated free-living (planktonic) cells because attempts to cultivate anaerobic E. coli biofilm were mostly unsuccessful. We challenged these findings and cultivated E. coli strain MG1655 biofilm under both aerobic and anaerobic conditions, characterizing the mature biofilm architecture and global gene expression profile. We used RNA sequencing technology to compare stationary phase planktonic cells with mature biofilm, cultured with and without oxygen...
January 12, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28087599/long-non-coding-rna-linc00092-acts-in-cancer-associated-fibroblasts-to-drive-glycolysis-and-progression-of-ovarian-cancer
#5
Linjie Zhao, Gaili Ji, Xiaobing Le, Chenlu Wang, Lian Xu, Min Feng, Yaguang Zhang, Huiliang Yang, Yu Xuan, Yanfei Yang, Lingzi Lei, Qilian Yang, Wayne Bond Lau, Bonnie Lau, Yi Chen, Xiangbing Deng, Shaohua Yao, Tao Yi, Xia Zhao, Yuquan Wei, Shengtao Zhou
The majority of patients with epithelial ovarian cancer are diagnosed at a late stage when peritoneal metastases exist, however, there is little knowledge of the metastatic process in this disease setting. In this study, we report the identification of the long non-coding RNA LINC00092 as a nodal driver of metastatic progression mediated by cancer-associated fibroblasts (CAF). Pro-metastatic properties of CAF in vitro and in vivo were found to associate with elevated expression of the chemokine CXCL14. In clinical specimens, elevated levels of CXCL14 in CAF also correlated with poor prognosis...
January 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28087495/comparative-analysis-of-variation-and-selection-in-the-hcv-genome
#6
Juan Ángel Patiño-Galindo, Fernando González-Candelas
Genotype 1 of the hepatitis C virus (HCV) is the most prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and CD8), and secondary protein structure...
January 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28086865/rnai-reveals-proteins-for-metabolism-and-protein-processing-associated-with-langat-virus-infection-in-ixodes-scapularis-black-legged-tick-ise6-cells
#7
Jeffrey M Grabowski, Monika Gulia-Nuss, Richard J Kuhn, Catherine A Hill
BACKGROUND: Tick-borne flaviviruses (TBFs) cause thousands of human cases of encephalitis worldwide each year, with some TBF infections progressing to hemorrhagic fever. TBFs are of medical and veterinary importance and strategies to reduce flavivirus transmission by the tick vector may have significant application. Analyses of the proteome of ISE6 cells derived from the black legged tick, Ixodes scapularis infected with the TBF, Langat virus (LGTV), have provided insights into proteins and cellular processes involved with LGTV infection...
January 13, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28086791/identification-of-functional-enolase-genes-of-the-silkworm-bombyx-mori-from-public-databases-with-a-combination-of-dry-and-wet-bench-processes
#8
Akira Kikuchi, Takeru Nakazato, Katsuhiko Ito, Yosui Nojima, Takeshi Yokoyama, Kikuo Iwabuchi, Hidemasa Bono, Atsushi Toyoda, Asao Fujiyama, Ryoichi Sato, Hiroko Tabunoki
BACKGROUND: Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated genes are included in these databases, which can prevent the correct interpretation of subsequent functional analyses. To address this problem, we used a combination of dry and wet bench processes to select functional genes from public databases. RESULTS: Enolase is an important glycolytic enzyme in all organisms...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086788/comprehensive-circrna-expression-profile-and-selection-of-key-circrnas-during-priming-phase-of-rat-liver-regeneration
#9
Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang, Cunshuan Xu
BACKGROUND: Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081468/role-of-mir-15a-in-intervertebral-disc-degeneration-through-targeting-map3k9
#10
Ping Cai, Ting Yang, Xingjie Jiang, Minghui Zheng, Gang Xu, Jianlong Xia
BACKGROUND: Accumulating evidence indicates that microRNAs are involved in various cellular processes, including cell proliferation, differentiation, apoptosis and metastasis. miR-15a is an important regulator of immune responses and angiogenesis, endogenous controls as well as potential targets and hallmarks of cancer. However, the role of miR-15a in intervertebral disc degeneration (IDD) has not been elucidated. METHODS: Total RNA was extracted from degenerative nucleus pulposus (NP) tissues of 20 patients with IDD and NP cells, respectively...
January 9, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28081283/transcriptome-analysis-of-peach-prunus-persica-l-batsch-during-the-late-stage-of-fruit-ripening
#11
H F Pan, Y Sheng, Z H Gao, H L Chen, Y J Qi, X K Yi, G H Qin, J Y Zhang
Fruit ripening is a complex developmental process, the details of which remain largely unknown in fleshy fruits. In this paper, the fruit flesh of two peach varieties, "Zhongyou9" (a nectarine; Prunus persica L. Batsch) and its mutant "Hongyu", was analyzed by RNA-seq technology during two stages of ripening at 20-day intervals. One hundred and eighty significant upregulated and two hundred and thirty-five downregulated genes were identified in the experiment. Many of these genes were related to plant hormones, chlorophyll breakdown, accumulation of aroma and flavor volatiles, and stress...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28079188/proteome-response-of-chicken-embryo-fibroblast-cells-to-recombinant-h5n1-avian-influenza-viruses-with-different-neuraminidase-stalk-lengths
#12
Yongtao Li, Fan Ming, Huimin Huang, Kelei Guo, Huanchun Chen, Meilin Jin, Hongbo Zhou
The variation on neuraminidase (NA) stalk region of highly pathogenic avian influenza H5N1 virus results in virulence change in animals. In our previous studies, the special NA stalk-motif of H5N1 viruses has been demonstrated to play a significant role in the high virulence and pathogenicity in chickens. However, the molecular mechanisms underlying the pathogenicity of viruses with different NA stalk remain poorly understood. This study presents a comprehensive characterization of the proteome response of chicken cells to recombinant H5N1 virus with stalk-short NA (rNA-wt) and the stalkless NA mutant virus (rSD20)...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28079179/transcriptome-and-network-analyses-in-saccharomyces-cerevisiae-reveal-that-amphotericin-b-and-lactoferrin-synergy-disrupt-metal-homeostasis-and-stress-response
#13
Chi Nam Ignatius Pang, Yu-Wen Lai, Leona T Campbell, Sharon C-A Chen, Dee A Carter, Marc R Wilkins
Invasive fungal infections are difficult to treat. The few available antifungal drugs have problems with toxicity or efficacy, and resistance is increasing. To overcome these challenges, existing therapies may be enhanced by synergistic combination with another agent. Previously, we found amphotericin B (AMB) and the iron chelator, lactoferrin (LF), were synergistic against a range of different fungal pathogens. This study investigates the mechanism of AMB-LF synergy, using RNA-seq and network analyses. AMB treatment resulted in increased expression of genes involved in iron homeostasis and ATP synthesis...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28079129/circrna_000203-enhances-the-expression-of-fibrosis-associated-genes-by-derepressing-targets-of-mir-26b-5p-col1a2-and-ctgf-in-cardiac-fibroblasts
#14
Chun-Mei Tang, Ming Zhang, Lei Huang, Zhi-Qin Hu, Jie-Ning Zhu, Zhen Xiao, Zhuo Zhang, Qiu-Xiong Lin, Xi-Long Zheng, Min -Yang, Shu-Lin Wu, Jian-Ding Cheng, Zhi-Xin Shan
Circular RNAs (circRNAs) participate in regulating gene expression in diverse biological and pathological processes. The present study aimed to investigate the mechanism underlying the modulation of circRNA_000203 on expressions of fibrosis-associated genes in cardiac fibroblasts. CircRNA_000203 was shown upregulated in the diabetic mouse myocardium and in Ang-II-induced mouse cardiac fibroblasts. Enforced-expression of circRNA_000203 could increase expressions of Col1a2, Col3a1 and α-SMA in mouse cardiac fibroblasts...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28079126/detecting-n-6-methyladenosine-sites-from-rna-transcriptomes-using-ensemble-support-vector-machines
#15
Wei Chen, Pengwei Xing, Quan Zou
As one of the most abundant RNA post-transcriptional modifications, N(6)-methyladenosine (m(6)A) involves in a broad spectrum of biological and physiological processes ranging from mRNA splicing and stability to cell differentiation and reprogramming. However, experimental identification of m(6)A sites is expensive and laborious. Therefore, it is urgent to develop computational methods for reliable prediction of m(6)A sites from primary RNA sequences. In the current study, a new method called RAM-ESVM was developed for detecting m(6)A sites from Saccharomyces cerevisiae transcriptome, which employed ensemble support vector machine classifiers and novel sequence features...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078618/decreased-tap63-and-%C3%AE-np63-mrna-levels-in-most-human-pituitary-adenomas-are-correlated-with-notch3-jagged1-relative-expression
#16
Lisiane Cervieri Mezzomo, Frederico Giacomoni Pesce, Josenel Maria Barcelos Marçal, Taiana Haag, Nelson Pires Ferreira, Julia Fernanda Semmelmann Pereira Lima, Carolina Garcia Soares Leães, Miriam Costa Oliveira, Maria Beatriz da Fonte Kohek
Despite recent advances in molecular genetics, the pituitary adenoma initiation, development, progress, and the molecular basis of their unique features are still poorly understood. In this sense, it is proposed that stem cell could be involved in pituitary adenoma tumorigenesis. It is suggested that TP63 has important functions in stem cells, and it may have interplay of TP63 and Notch and its ligand Jagged in this process. This study aimed to evaluate the distinct expression of TP63 isoforms (TAp63 and ΔNp63), as well as its correlation with Notch3 receptor and its ligand Jagged1 in human pituitary adenomas at the messenger RNA (mRNA) level...
January 11, 2017: Endocrine Pathology
https://www.readbyqxmd.com/read/28078562/myotonic-dystrophy-type-2-and-modifier-genes-an-update-on-clinical-and-pathomolecular-aspects
#17
REVIEW
Giovanni Meola, Rosanna Cardani
Myotonic dystrophy (DM) is the most common adult muscular dystrophy, characterized by autosomal dominant progressive myopathy, myotonia, and multiorgan involvement. To date, two distinct forms caused by similar mutations in two different genes have been identified: myotonic dystrophy type 1 (DM1) and myotonic dystrophy type 2 (DM2). Aberrant transcription and mRNA processing of multiple genes due to RNA-mediated toxic gain-of function has been suggested to cause the complex phenotype in DM1 and DM2. However, despite clinical and genetic similarities, DM1 and DM2 may be considered as distinct disorders...
January 11, 2017: Neurological Sciences
https://www.readbyqxmd.com/read/28078426/calreticulin-is-required-for-calcium-homeostasis-and-proper-pollen-tube-tip-growth-in-petunia
#18
Anna Suwińska, Piotr Wasąg, Przemysław Zakrzewski, Marta Lenartowska, Robert Lenartowski
Calreticulin is involved in stabilization of the tip-focused Ca (2+) gradient and the actin cytoskeleton arrangement and function that is required for several key processes driving Petunia pollen tube tip growth. Although the precise mechanism is unclear, stabilization of a tip-focused calcium (Ca(2+)) gradient seems to be critical for pollen germination and pollen tube growth. We hypothesize that calreticulin (CRT), a Ca(2+)-binding/buffering chaperone typically residing in the lumen of the endoplasmic reticulum (ER) of eukaryotic cells, is an excellent candidate to fulfill this role...
January 11, 2017: Planta
https://www.readbyqxmd.com/read/28077570/ktcnlncdb-a-first-platform-to-investigate-lncrnas-expressed-in-human-keratoconus-and-non-keratoconus-corneas
#19
Michał W Szcześniak, Michal Kabza, Justyna A Karolak, Malgorzata Rydzanicz, Dorota M Nowak, Barbara Ginter-Matuszewska, Piotr Polakowski, Rafal Ploski, Jacek P Szaflik, Marzena Gajecka
Keratoconus (KTCN, OMIM 148300) is a degenerative eye disorder characterized by progressive stromal thinning that leads to a conical shape of the cornea, resulting in optical aberrations and even loss of visual function. The biochemical background of the disease is poorly understood, which motivated us to perform RNA-Seq experiment, aimed at better characterizing the KTCN transcriptome and identification of long non-coding RNAs (lncRNAs) that might be involved in KTCN etiology. The in silico functional studies based on predicted lncRNA:RNA base-pairings led us to recognition of a number of lncRNAs possibly regulating genes with known or plausible links to KTCN...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077561/micrornas-stimulate-translation-initiation-mediated-by-hcv-like-ireses
#20
Chloé Mengardi, Taran Limousin, Emiliano P Ricci, Ricardo Soto-Rifo, Didier Decimo, Théophile Ohlmann
MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression by recognizing and hybridizing to a specific sequence generally located in the 3' untranslated region (UTR) of targeted mRNAs. miRNA-induced inhibition of translation occurs during the initiation step, most probably at the level of ribosome scanning. In this process, the RNA-induced silencing complex interacts both with PABP and the 43S pre-initiation complex to disrupt scanning of the 40S ribosome. However, in some specific cases, miRNAs can stimulate translation...
January 10, 2017: Nucleic Acids Research
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