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Long none coding RNA

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https://www.readbyqxmd.com/read/28591699/genetic-heterogeneity-in-leiomyomas-of-deep-soft-tissue
#1
Ioannis Panagopoulos, Ludmila Gorunova, Marta Brunetti, Antonio Agostini, Hege Kilen Andersen, Ingvild Lobmaier, Bodil Bjerkehagen, Sverre Heim
Leiomyoma of deep soft tissue is a rare type of benign smooth muscle tumor that mostly occurs in the retroperitoneum or abdominal cavity of women, and about which very little genetic information exists. In the present study, eight leiomyomas of deep soft tissue were genetically analyzed. G-banding showed that three tumors carried rearrangements of the long arm of chromosome 12, three others had 8q rearrangements, the 7th tumor had deletion of the long arm of chromosome 7, del(7)(q22), and the 8th had aberrations of chromosome bands 3q21~23 and 11q21~22...
July 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28575155/dynamic-bm-multispecies-dynamic-bodymap-database-from-temporal-rna-seq-data
#2
Ya Cui, Xiaowei Chen, Yiwei Niu, Dongpeng Wang, Huaxia Luo, Zhen Fan, Dan Wang, Wei Wu, Xueyi Teng, Shunmin He, Jianjun Luo, Runsheng Chen
Biological processes, especially developmental processes, are often dynamic. Previous BodyMap projects for human and mouse have provided researchers with portals to tissue-specific gene expression, but these efforts have not included dynamic gene expression patterns. Over the past few years, substantial progress in our understanding of the molecular mechanisms of protein-coding and long noncoding RNA (lncRNA) genes in development processes has been achieved through numerous time series RNA sequencing (RNA-seq) studies...
June 1, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28476334/novel-spliced-variants-of-oct4-oct4c-and-oct4c1-with-distinct-expression-patterns-and-functions-in-pluripotent-and-tumor-cell-lines
#3
Mahshid Malakootian, Fatemeh Mirzadeh Azad, Parisa Naeli, Mohammad Pakzad, Youssef Fouani, Elham Taheri Bajgan, Hossein Baharvand, Seyed Javad Mowla
OCT4 is a major regulator of pluripotency which has several spliced variants and expressed pseudogenes. Here, we are reporting the existence of two additional novel spliced variants of OCT4, OCT4C and OCT4C1, which lack Exon1 (E1) but start at a novel exon (E0) located ∼14kb upstream of E2. OCT4C/C1 is highly expressed in ES and iPS cells, and their expression was sharply turned off, upon the induction of neural differentiation. The long non-coding RNA (lncRNA) PSORS1C3, is located ∼9kb downstream of the E0 of OCT4C/C1...
April 10, 2017: European Journal of Cell Biology
https://www.readbyqxmd.com/read/28288683/chromatin-landscapes-and-genetic-risk-for-juvenile-idiopathic-arthritis
#4
Lisha Zhu, Kaiyu Jiang, Karstin Webber, Laiping Wong, Tao Liu, Yanmin Chen, James N Jarvis
BACKGROUND: The transcriptomes of peripheral blood cells in children with juvenile idiopathic arthritis (JIA) have distinct transcriptional aberrations that suggest impairment of transcriptional regulation. To gain a better understanding of this phenomenon, we studied known JIA genetic risk loci, the majority of which are located in non-coding regions, where transcription is regulated and coordinated on a genome-wide basis. We examined human neutrophils and CD4 primary T cells to identify genes and functional elements located within those risk loci...
March 14, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28285723/epigenetic-aspects-of-rheumatoid-arthritis-contribution-of-non-coding-rnas
#5
REVIEW
Bogdan Kolarz, Maria Majdan
Since microRNA was discovered in the late 1990s the role of non-coding RNAs in the regulation of cellular processes has been confirmed. Intensive researches have revealed a number of subtypes of non-coding RNA. It has been proved that these molecules can influence each step of the development of cells and tissues. Moreover, researchers have found their expression change during disease development. In this article, we gathered the current results on the contribution of microRNA and long non-coding RNA in rheumatoid arthritis pathogenesis and their potential use in rheumatoid arthritis treatment...
June 2017: Seminars in Arthritis and Rheumatism
https://www.readbyqxmd.com/read/27890015/the-involvement-of-regulatory-non-coding-rnas-in-sepsis-a-systematic-review
#6
Jeffery Ho, Hung Chan, Sunny H Wong, Maggie H T Wang, Jun Yu, Zhangang Xiao, Xiaodong Liu, Gordon Choi, Czarina C H Leung, Wai T Wong, Zheng Li, Tony Gin, Matthew T V Chan, William K K Wu
BACKGROUND: Sepsis coincides with altered gene expression in different tissues. Accumulating evidence has suggested that microRNAs, long non-coding RNAs, and circular RNAs are important molecules involved in the crosstalk with various pathways pertinent to innate immunity, mitochondrial functions, and apoptosis. METHODS: We searched articles indexed in PubMed (MEDLINE), EMBASE and Europe PubMed Central databases using the Medical Subject Heading (MeSH) or Title/Abstract words ("microRNA", "long non-coding RNA", "circular RNA", "sepsis" and/or "septic shock") from inception to Sep 2016...
November 28, 2016: Critical Care: the Official Journal of the Critical Care Forum
https://www.readbyqxmd.com/read/27783602/local-regulation-of-gene-expression-by-lncrna-promoters-transcription-and-splicing
#7
Jesse M Engreitz, Jenna E Haines, Elizabeth M Perez, Glen Munson, Jenny Chen, Michael Kane, Patrick E McDonel, Mitchell Guttman, Eric S Lander
Mammalian genomes are pervasively transcribed to produce thousands of long non-coding RNAs (lncRNAs). A few of these lncRNAs have been shown to recruit regulatory complexes through RNA-protein interactions to influence the expression of nearby genes, and it has been suggested that many other lncRNAs can also act as local regulators. Such local functions could explain the observation that lncRNA expression is often correlated with the expression of nearby genes. However, these correlations have been challenging to dissect and could alternatively result from processes that are not mediated by the lncRNA transcripts themselves...
November 17, 2016: Nature
https://www.readbyqxmd.com/read/27611072/comprehensive-small-rna-seq-of-adeno-associated-virus-aav-infected-human-cells-detects-patterns-of-novel-non-coding-aav-rnas-in-the-absence-of-cellular-mirna-regulation
#8
Catrin Stutika, Mario Mietzsch, Andreas Gogol-Döring, Stefan Weger, Madlen Sohn, Wei Chen, Regine Heilbronn
Most DNA viruses express small regulatory RNAs, which interfere with viral or cellular gene expression. For adeno-associated virus (AAV), a small ssDNA virus with a complex biphasic life cycle miRNAs or other small regulatory RNAs have not yet been described. This is the first comprehensive Illumina-based RNA-Seq analysis of small RNAs expressed by AAV alone or upon co-infection with helper adenovirus or HSV. Several hotspots of AAV-specific small RNAs were detected mostly close to or within the AAV-ITR and apparently transcribed from the newly identified anti-p5 promoter...
2016: PloS One
https://www.readbyqxmd.com/read/27043436/efficient-translation-of-pelargonium-line-pattern-virus-rnas-relies-on-a-ted-like-3%C3%A2-translational-enhancer-that-communicates-with-the-corresponding-5%C3%A2-region-through-a-long-distance-rna-rna-interaction
#9
Marta Blanco-Pérez, Miryam Pérez-Cañamás, Leticia Ruiz, Carmen Hernández
Cap-independent translational enhancers (CITEs) have been identified at the 3´-terminal regions of distinct plant positive-strand RNA viruses belonging to families Tombusviridae and Luteoviridae. On the bases of their structural and/or functional requirements, at least six classes of CITEs have been defined whose distribution does not correlate with taxonomy. The so-called TED class has been relatively under-studied and its functionality only confirmed in the case of Satellite tobacco necrosis virus, a parasitic subviral agent...
2016: PloS One
https://www.readbyqxmd.com/read/26799454/regulating-infidelity-rna-mediated-recruitment-of-aid-to-dna-during-class-switch-recombination
#10
REVIEW
Lauren J DiMenna, Jayanta Chaudhuri
The mechanism by which the DNA deaminase activation-induced cytidine deaminase (AID) is specifically recruited to repetitive switch region DNA during class switch recombination is still poorly understood. Work over the past decade has revealed a strong link between transcription and RNA polymerase-associated factors in AID recruitment, yet none of these processes satisfactorily explain how AID specificity is affected. Here, we review a recent finding wherein AID is guided to switch regions not by a protein factor but by an RNA moiety, and especially one associated with a noncoding RNA that has been long thought of as being inert...
March 2016: European Journal of Immunology
https://www.readbyqxmd.com/read/26530187/differential-expression-analysis-of-human-endogenous-retroviruses-based-on-encode-rna-seq-data
#11
Kerstin Haase, Anja Mösch, Dmitrij Frishman
BACKGROUND: Human endogenous retroviruses (HERVs) are flanked by long terminal repeats (LTRs), which possess promoter activity and can therefore influence the expression of neighboring genes. HERV involvement in different types of cancer has already been thoroughly documented. However, so far there has been no systematic study of HERV expression patterns in a multitude of cell types in health and disease. In particular, the publication of the comprehensive ENCODE dataset has already facilitated many gene expression studies, but none so far focusing exclusively on HERVs...
2015: BMC Medical Genomics
https://www.readbyqxmd.com/read/26521025/transcriptome-sequencing-reveals-thousands-of-novel-long-non-coding-rnas-in-b-cell-lymphoma
#12
Akanksha Verma, Yanwen Jiang, Wei Du, Lauren Fairchild, Ari Melnick, Olivier Elemento
BACKGROUND: Gene profiling of diffuse large B cell lymphoma (DLBCL) has revealed broad gene expression deregulation compared to normal B cells. While many studies have interrogated well known and annotated genes in DLBCL, none have yet performed a systematic analysis to uncover novel unannotated long non-coding RNAs (lncRNA) in DLBCL. In this study we sought to uncover these lncRNAs by examining RNA-seq data from primary DLBCL tumors and performed supporting analysis to identify potential role of these lncRNAs in DLBCL...
2015: Genome Medicine
https://www.readbyqxmd.com/read/26506012/a-database-of-microrna-expression-patterns-in-xenopus-laevis
#13
Ayisha Ahmed, Nicole J Ward, Simon Moxon, Sara Lopez-Gomollon, Camille Viaut, Matthew L Tomlinson, Ilya Patrushev, Michael J Gilchrist, Tamas Dalmay, Dario Dotlic, Andrea E Münsterberg, Grant N Wheeler
MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides...
2015: PloS One
https://www.readbyqxmd.com/read/26410378/epigenetic-silencing-of-a-long-non-coding-rna-kiaa0495-in-multiple-myeloma
#14
Kwan Yeung Wong, Zhenhai Li, Xiaoqin Zhang, Gilberto Ka Kit Leung, Godfrey Chi-Fung Chan, Chor Sang Chim
In multiple myeloma, a long non-coding RNA, KIAA0495 (alias PDAM/TP73-AS1), had been found progressively downregulated from normal plasma cell to benign monoclonal gammopathy of undetermined significance to symptomatic myeloma. Herein, by methylation-specific PCR, the putative KIAA0495 promoter was found unmethylated in all healthy controls (N = 14) but methylated in 50 % of myeloma cell lines (N = 10). KIAA0495 methylation was shown inversely correlated with KIAA0495 expression. However, KIAA0495 methylation was detected in none of both primary myeloma samples at diagnosis (N = 61) and at relapse/progression (N = 16)...
2015: Molecular Cancer
https://www.readbyqxmd.com/read/26390953/age-dependent-differential-expression-profile-of-a-novel-intergenic-long-noncoding-rna-in-rat-brain
#15
Sukhleen Kour, Pramod C Rath
Long noncoding RNAs (lncRNAs) are ≥ 200 nt long, abundant class of non-protein coding RNAs that are transcribed in complex, sense- and antisense patterns from the intergenic and intronic regions of mammalian genome. Mammalian central nervous system constitutes the largest repertoire of noncoding transcripts that are known to be expressed in developmentally regulated and cell-type specific manners. Although many lncRNAs, functioning in the brain development and diseases are known, none involved in brain aging has been reported so far...
December 2015: International Journal of Developmental Neuroscience
https://www.readbyqxmd.com/read/26363523/age-dependent-differential-expression-profile-of-a-novel-intergenic-long-noncoding-rna-in-rat-brain
#16
Sukhleen Kour, Pramod C Rath
Long noncoding RNAs (lncRNAs) are ≥200 nt long, abundant class of non-protein coding RNAs that are transcribed in complex, sense- and antisense patterns from the intergenic and intronic regions of mammalian genome. Mammalian central nervous system constitutes the largest repertoire of noncoding transcripts that are known to be expressed in developmentally regulated and cell-type specific manners. Although many lncRNAs, functioning in the brain development and diseases are known, none involved in brain aging has been reported so far...
November 2015: International Journal of Developmental Neuroscience
https://www.readbyqxmd.com/read/26284247/microrna-diagnostic-perspective
#17
REVIEW
Omar Faruq, Andrea Vecchione
Biomarkers are biological measures of a biological state. An ideal marker should be safe and easy to measure, cost efficient, modifiable with treatment, and consistent across gender and ethnic groups. To date, none of the available biomarkers satisfy all of these criteria. In addition, the major limitations of these markers are low specificity, sensitivity, and false positive results. Recently identified, microRNAs (miRNAs) are endogenous, evolutionarily conserved small non-coding RNA (about 22-25 nt long), also known as micro-coordinators of gene expression, which have been shown to be an effective tools to study the biology of diseases and to have great potential as novel diagnostic and prognostic biomarkers with high specificity and sensitivity...
2015: Frontiers in Medicine
https://www.readbyqxmd.com/read/26048704/root-of-dictyostelia-based-on-213-universal-proteins
#18
Sanea Sheikh, Gernot Gloeckner, Hidekazu Kuwayama, Pauline Schaap, Hideko Urushihara, Sandra L Baldauf
Dictyostelia are common soil microbes that can aggregate when starved to form multicellular fruiting bodies, a characteristic that has also led to their long history of study and widespread use as model systems. Ribosomal RNA phylogeny of Dictyostelia identified four major divisions (Groups 1-4), none of which correspond to traditional genera. Group 1 was also tentatively identified as sister lineage to the other three Groups, although not consistently or with strong support. We tested the dictyostelid root using universal protein-coding genes identified by exhaustive comparison of six completely sequenced dictyostelid genomes, which include representatives of all four major molecular Groups...
November 2015: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/26043692/long-none-coding-rna-hottip-hoxa13-act-as-synergistic-role-by-decreasing-cell-migration-and-proliferation-in-hirschsprung-disease
#19
Hua Xie, Dongmei Zhu, Cao Xu, Hairong Zhu, Pingfa Chen, Hongxing Li, Xiang Liu, Yankai Xia, Weibing Tang
Long noncoding RNAs (lncRNAs) have been confirmed to be associated with various human diseases. However, whether they are associated with Hirschsprung disease (HSCR) progression remains unclear. In this study, we designed the experiment to explore the relationship between lncRNA HOTTIP and HOXA13, and their pathogenicity to HSCR. Quantitative real-time PCR and Western blot were performed to detect the levels of lncRNA, mRNAs, and proteins in colon tissues from 79 patients with HSCR and 79 controls. Small RNA interference transfection was used to study the function experiments in human 293T and SK-N-BE cell lines...
August 7, 2015: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/25821520/activation-of-an-endogenous-retrovirus-associated-long-non-coding-rna-in-human-adenocarcinoma
#20
Ewan A Gibb, René L Warren, Gavin W Wilson, Scott D Brown, Gordon A Robertson, Gregg B Morin, Robert A Holt
BACKGROUND: Long non-coding RNAs (lncRNAs) are emerging as molecules that significantly impact many cellular processes and have been associated with almost every human cancer. Compared to protein-coding genes, lncRNA genes are often associated with transposable elements, particularly with endogenous retroviral elements (ERVs). ERVs can have potentially deleterious effects on genome structure and function, so these elements are typically silenced in normal somatic tissues, albeit with varying efficiency...
2015: Genome Medicine
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