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https://www.readbyqxmd.com/read/27903230/glucocorticoid-receptor-interacting-co-regulators-putative-candidates-for-future-drug-targeting-therapy
#1
Alessia Di Silvestre, Marianna Lucafò, Sara De Iudicibus, Alessandro Ventura, Stefano Martelossi, Gabriele Stocco, Giuliana Decorti
Glucocorticoids (GCs) are largely used in different inflammatory, autoimmune and proliferative diseases. To date their mechanism of action is not completely clear and more studies are necessary, in particular to explain the great interindividual variability in clinical response. In this panorama the glucocorticoid receptor (GR) has an important role: in fact it regulates the pharmacological response thanks to the capability to interact with different molecules (DNA, RNA, ncRNA and proteins) that are known to influence its activity...
November 29, 2016: Mini Reviews in Medicinal Chemistry
https://www.readbyqxmd.com/read/27899618/rna-seq-mixology-designing-realistic-control-experiments-to-compare-protocols-and-analysis-methods
#2
Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie
Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression control studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise that is atypical of regular studies. To achieve a more realistic noise structure, we generated a RNA-sequencing mixture experiment using two cell lines of the same cancer type. Variability was added by extracting RNA from independent cell cultures and degrading particular samples...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899613/nsdna-a-manually-curated-database-of-experimentally-supported-ncrnas-associated-with-nervous-system-diseases
#3
Jianjian Wang, Yuze Cao, Huixue Zhang, Tianfeng Wang, Qinghua Tian, Xiaoyu Lu, Xiaoyan Lu, Xiaotong Kong, Zhaojun Liu, Ning Wang, Shuai Zhang, Heping Ma, Shangwei Ning, Lihua Wang
The Nervous System Disease NcRNAome Atlas (NSDNA) (http://www.bio-bigdata.net/nsdna/) is a manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDs represent a common group of disorders, some of which are characterized by high morbidity and disabilities. The pathogenesis of NSDs at the molecular level remains poorly understood. ncRNAs are a large family of functionally important RNA molecules. Increasing evidence shows that diverse ncRNAs play a critical role in various NSDs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27881904/long-noncoding-rnas-in-metabolic-syndrome-related-disorders
#4
REVIEW
Magdalena Losko, Jerzy Kotlinowski, Jolanta Jura
Ribonucleic acids (RNAs) are very complex and their all functions have yet to be fully clarified. Noncoding genes (noncoding RNA, sequences, and pseudogenes) comprise 67% of all genes and they are represented by housekeeping noncoding RNAs (transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and small nucleolar RNA (snoRNA)) that are engaged in basic cellular processes and by regulatory noncoding RNA (short and long noncoding RNA (ncRNA)) that are important for gene expression/transcript stability...
2016: Mediators of Inflammation
https://www.readbyqxmd.com/read/27881537/complete-genome-sequence-of-mycobacterium-chimaera-strain-ah16
#5
Nabeeh A Hasan, Jennifer R Honda, Rebecca M Davidson, L Elaine Epperson, Matthew J Bankowski, Edward D Chan, Michael Strong
Mycobacterium chimaera is a nontuberculous mycobacterial species that causes cardiovascular, pulmonary, and postsurgical infections. Here, we report the first complete genome sequence of M. chimaera This genome is 6.33 Mbp, with a G+C content of 67.56%, and encodes 4,926 protein-coding genes, as well as 74 tRNAs, one ncRNA, and three rRNA genes.
November 23, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27878945/regulatory-non-coding-rnas-in-acute-myocardial-infarction
#6
REVIEW
Yuan Guo, Fei Luo, Qiong Liu, Danyan Xu
Acute myocardial infarction (AMI) is one of the most common cardiovascular diseases that leads to high mortality and morbidity globally. Various therapeutic targets for AMI have been investigated in recent years, including the non-coding RNAs (ncRNAs). NcRNAs, a class of RNA molecules that typically do not code proteins, are divided into several subgroups. Among them, microRNAs (miRNAs) are widely studied for their modulation of several pathological aspects of AMI, including cardiomyocyte apoptosis, inflammation, angiogenesis and fibrosis...
November 23, 2016: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/27876851/the-genome-transcriptome-and-proteome-of-the-nematode-steinernema-carpocapsae-evolutionary-signatures-of-a-pathogenic-lifestyle
#7
Alejandra Rougon-Cardoso, Mitzi Flores-Ponce, Hilda Eréndira Ramos-Aboites, Christian Eduardo Martínez-Guerrero, You-Jin Hao, Luis Cunha, Jonathan Alejandro Rodríguez-Martínez, Cesaré Ovando-Vázquez, José Roberto Bermúdez-Barrientos, Cei Abreu-Goodger, Norberto Chavarría-Hernández, Nelson Simões, Rafael Montiel
The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode's genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27865480/biofluids-cell-mechanics-and-epigenetics-flow-induced-epigenetic-mechanisms-of-endothelial-gene-expression
#8
Peter F Davies, Elisabetta Manduchi, Juan M Jiménez, Yi-Zhou Jiang
Epigenetics is the regulation of gene expression (transcription) in response to changes in the cell environment through genomic modifications that largely involve the non-coding fraction of the human genome and that cannot be attributed to modification of the primary DNA sequence. Epigenetics is dominant in establishing cell fate and positioning during programmed embryonic development. However the same pathways are used by mature postnatal and adult mammalian cells during normal physiology and are implicated in disease mechanisms...
November 11, 2016: Journal of Biomechanics
https://www.readbyqxmd.com/read/27862321/ptenp1-a-natural-sponge-of-mir-21-mediates-pten-expression-to-inhibit-the-proliferation-of-oral-squamous-cell-carcinoma
#9
Ling Gao, Wenhao Ren, Linmei Zhang, Shaoming Li, Xinjuan Kong, Hao Zhang, Jianwei Dong, Guangfeng Cai, Changxiong Jin, Danqing Zheng, Keqian Zhi
PTENp1, non-coding RNA (ncRNA) pseudogene, is involved in oral squamous cell carcinoma (OSCC). The precise effects mediated by PTENp1 transcripts within intricate regulatory networks involving molecular interactions with ancestral gene PTEN and tumorigenicity in OSCC remain unclear. Here, we found that PTENp1 was aberrantly expressed in OSCC. There was a positive correlation between the expression levels of PTENp1 and PTEN. Further, we showed that PTENp1 acted as a competing endogenous RNA that protects PTEN transcripts from being inhibited by miR-21, and consequently inhibited proliferation and colony formation and triggered S-G2/M cell cycle arrest through the AKT pathway...
November 15, 2016: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/27853310/non-coding-rnas-match-the-deleted-genomic-regions-in-humans
#10
Boseon Byeon, Igor Kovalchuk
RNA is transcribed from DNA, and therefore, there should be no RNA transcript from the deleted DNA region. Our study attempted to analyse whether any RNA cache that maps the deleted regions is present in human cells. Using data from the 1000 genome project, we selected 41 CEPH (CEU) and 38 Yoruba (YRI) samples that included the data for the entire genome sequence and ncRNA and mRNA sequences. Aligning the ncRNA reads against the genomic DNA in individual samples has revealed that 229 out of 1114 homozygous deletions have ncRNA reads that map to them...
November 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27826551/noncoding-rna-regulation-of-dopamine-signaling-in-diseases-of-the-central-nervous-system
#11
REVIEW
William T Carrick, Brandi Burks, Murray J Cairns, Jannet Kocerha
Dopaminergic neurotransmission mediates a majority of the vital central nervous system functions. Disruption of these synaptic events provokes a multitude of neurological pathologies, including Parkinson's, schizophrenia, depression, and addiction. Growing evidence supports a key role for noncoding RNA (ncRNA) regulation in the synapse. This review will discuss the role of both short and long ncRNAs in dopamine signaling, including bioinformatic examination of the pathways they target. Specifically, we focus on the contribution of ncRNAs to dopaminergic dysfunction in neurodegenerative as well as psychiatric disease...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27825925/molecular-mechanism-of-dna-topoisomerase-i-dependent-rdna-silencing-sir2p-recruitment-at-ribosomal-genes
#12
Anna D'Alfonso, Francesca Di Felice, Valentina Carlini, Christine M Wright, Marla I Hertz, Mary-Ann Bjornsti, Giorgio Camilloni
Saccharomyces cerevisiae sir2Δ or top1Δ mutants exhibit similar phenotypes involving ribosomal DNA, including (i) loss of transcriptional silencing, resulting in non-coding RNA hyperproduction from cryptic RNA polymerase II promoters; (ii) alterations in recombination; and (iii) a general increase in histone acetylation. Given the distinct enzymatic activities of Sir2 and Top1 proteins, a histone deacetylase and a DNA topoisomerase, respectively, we investigated whether genetic and/or physical interactions between the two proteins could explain the shared ribosomal RNA genes (rDNA) phenotypes...
November 5, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27818589/metastasis-associated-long-noncoding-rnas-in-gastrointestinal-cancer-implications-for-novel-biomarkers-and-therapeutic-targets
#13
REVIEW
Fei-Fei Zhang, Yu-Hao Luo, Hui Wang, Liang Zhao
Long non-coding RNAs (lncRNAs), a newly discovered class of ncRNA molecules, have been widely accepted as crucial regulators of various diseases including cancer. Increasing numbers of studies have demonstrated that lncRNAs are involved in diverse physiological and pathophysiological processes, such as cell cycle progression, chromatin remodeling, gene transcription, and posttranscriptional processing. Aberrant expression of lncRNAs frequently occurs in gastrointestinal cancer and plays emerging roles in cancer metastasis...
October 21, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/27817751/novel-insight-into-triple-negative-breast-cancers-the-emerging-role-of-angiogenesis-and-antiangiogenic-therapy
#14
Cornelia Braicu, Roxana Chiorean, Alexandru Irimie, Sergiu Chira, Ciprian Tomuleasa, Emilian Neagoe, Angelo Paradiso, Patriciu Achimas-Cadariu, Vladimir Lazar, Ioana Berindan-Neagoe
Triple-negative breast cancer (TNBC) is a heterogeneous group of tumours characterised by lack of expression of oestrogen-, progesterone- and human epidermal growth factor receptors. TNBC, which represents approximately 15% of all mammary tumours, has a poor prognosis because of an aggressive behaviour and the lack of specific treatment. Accordingly, TNBC has become a major focus of research into breast cancer and is now classified into several molecular subtypes, each with a different prognosis. Pathological angiogenesis occurs at a late stage in the proliferation of TNBC and is associated with invasion and metastasis; there is an association with metabolic syndrome...
November 7, 2016: Expert Reviews in Molecular Medicine
https://www.readbyqxmd.com/read/27815509/long-non-coding-rnas-lncrnas-in-skeletal-and-cardiac-muscle-potential-therapeutic-and-diagnostic-targets
#15
REVIEW
Julie R McMullen, Brian G Drew
The recent discovery that thousands of RNAs are transcribed by the cell but are never translated into protein, highlights a significant void in our current understanding of how transcriptional networks regulate cellular function. This is particularly astounding when we consider that over 75% of the human genome is transcribed into RNA, but only approximately 2% of RNA is translated into known proteins. This raises the question as to what function the other so-called 'non-coding RNAs' (ncRNAs) are performing in the cell...
December 1, 2016: Clinical Science (1979-)
https://www.readbyqxmd.com/read/27812951/the-vision-and-challenges-of-the-gene-ontology
#16
Suzanna E Lewis
The overarching goal of the Gene Ontology (GO) Consortium is to provide researchers in biology and biomedicine with all current functional information concerning genes and the cellular context under which these occur. When the GO was started in the 1990s surprisingly little attention had been given to how functional information about genes was to be uniformly captured, structured in a computable form, and made accessible to biologists. Because knowledge of gene, protein, ncRNA, and molecular complex roles is continuously accumulating and changing, the GO needed to be a dynamic resource, accurately tracking ongoing research results over time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27810413/noncoding-rnas-in-the-development-diagnosis-and-prognosis-of-colorectal-cancer
#17
REVIEW
Mingjiao Weng, Di Wu, Chao Yang, Haisheng Peng, Guangyu Wang, Tianzhen Wang, Xiaobo Li
More than 90% of the human genome is actively transcribed, but less than 2% of the total genome encodes protein-coding RNA, and thus, noncoding RNA (ncRNA) is a major component of the human transcriptome. Recently, ncRNA was demonstrated to play important roles in multiple biological processes by directly or indirectly interfering with gene expression, and the dysregulation of ncRNA is associated with a variety of diseases, including cancer. In this review, we summarize the function and mechanism of miRNA, long intergenic ncRNA, and some other types of ncRNAs, such as small nucleolar RNA, circular ncRNA, pseudogene RNA, and even protein-coding mRNA, in the progression of colorectal cancer (CRC)...
October 14, 2016: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/27803687/emerging-putative-associations-between-non-coding-rnas-and-protein-coding-genes-in-neuropathic-pain-added-value-from-reusing-microarray-data
#18
Hemalatha B Raju, Nicholas F Tsinoremas, Enrico Capobianco
Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27800139/the-effect-of-microrna-375-overexpression-an-inhibitor-of-helicobacter-pylori-induced-carcinogenesis-on-lncrna-sox2ot
#19
Mohammad Shafiee, Seyed Ahmad Aleyasin, Seyed Javad Mowla, Mohammad Vasei, Seyed Amir Yazdanparast
BACKGROUND: Helicobacter pylori is a major human pathogenic bacterium in gastric mucosa. Although the association between gastric cancer and H. pylori has been well-established, the molecular mechanisms underlying H. pylori-induced carcinogenesis are still under investigation. MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression at the posttranscriptional level. Recently, studies have revealed that miRNAs are involved in immune response and host cell response to bacteria...
September 2016: Jundishapur Journal of Microbiology
https://www.readbyqxmd.com/read/27794554/rnacentral-a-comprehensive-database-of-non-coding-rna-sequences
#20
(no author information available yet)
RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species...
October 28, 2016: Nucleic Acids Research
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