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https://www.readbyqxmd.com/read/28732356/the-circrna-interactome-innovative-hallmarks-of-the-intra-and-extracellular-radiation-response
#1
Valerie Bríd O'Leary, Jan Smida, Martina Matjanovski, Corinna Brockhaus, Klaudia Winkler, Simone Moertl, Saak Victor Ovsepian, Michael John Atkinson
Generated by Quaking (QKI), circular RNAs (circRNAs) are newly recognised non-coding RNA (ncRNA) members characterised by tissue specificity, increased stability and enrichment within exosomes. Studies have shown that ionizing radiation (IR) can influence ncRNA transcription. However, it is unknown whether circRNAs or indeed QKI are regulated by IR. Microarray circRNA profiling and next generation sequencing revealed that circRNA expression was altered by low and medium dose exposure sourced predominantly from genes influencing the p53 pathway...
July 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28716689/brg1-and-smarcal1-transcriptionally-co-regulate-drosha-dgcr8-and-dicer-in-response-to-doxorubicin-induced-dna-damage
#2
Ketki Patne, Radhakrishnan Rakesh, Vijendra Arya, Upasana Bedi Chanana, Ramesh Sethy, Pynskhem Bok Swer, Rohini Muthuswami
Recent investigations have emphasized the role of miRNA biogenesis proteins in the synthesis of non-coding RNA when double-strand DNA breaks are induced by ionizing radiations. However, the role of these ncRNA and their regulation in response to doxorubicin-induced DNA damage is not known. In this paper, BRG1 and SMARCAL1, members of the ATP-dependent chromatin remodelling family, are shown to co-regulate the transcription of DROSHA, DGCR8, and DICER in response to double-strand DNA breaks induced by doxorubicin...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28701522/yeast-non-coding-rna-interaction-network
#3
Simona Panni, Ananth Prakash, Alex Bateman, Sandra Orchard
This article describes the creation of the first expert manually curated non-coding RNA interaction networks for S. cerevisiae. The RNA-RNA and RNA-protein interaction networks have been carefully extracted from the experimental literature and made available through the IntAct database (www.ebi.ac.uk/intact). We provide an initial network analysis and compare their properties to the much larger protein-protein interaction network. We find that the proteins that bind to ncRNAs in the network contain only a small proportion of classical RNA binding domains...
July 12, 2017: RNA
https://www.readbyqxmd.com/read/28699365/activating-the-chromatin-by-non-coding-rnas
#4
Nihay Laham-Karam, Pia Laitinen, Tiia A Turunen, Seppo Ylä-Herttuala
SIGNIFICANCE: The extent and breadth of transcription has recently been uncovered and this has revealed an extensive array of non-coding RNAs (ncRNAs). The biological role and significance of these ncRNAs have been realised and to date it appears that ncRNA may have many important regulatory functions. ncRNAs are multifaceted and they induce a complexity of different types of transcriptional and post-transcriptional regulation including gene activation. Recent Advances: Association of ncRNAs with gene activation is an important finding...
July 12, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28698797/new-technologies-accelerate-the-exploration-of-non-coding-rnas-in-horticultural-plants
#5
REVIEW
Degao Liu, Ritesh Mewalal, Rongbin Hu, Gerald A Tuskan, Xiaohan Yang
Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28698299/neat1-is-a-p53-inducible-lincrna-essential-for-transformation-suppression
#6
Stephano S Mello, Carolyn Sinow, Nitin Raj, Pawel K Mazur, Kathryn Bieging-Rolett, Daniela Kenzelmann Broz, Jamie F Conklin Imam, Hannes Vogel, Laura D Wood, Julien Sage, Tetsuro Hirose, Shinichi Nakagawa, John Rinn, Laura D Attardi
The p53 gene is mutated in over half of all cancers, reflecting its critical role as a tumor suppressor. Although p53 is a transcriptional activator that induces myriad target genes, those p53-inducible genes most critical for tumor suppression remain elusive. Here, we leveraged p53 ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) and RNA-seq (RNA sequencing) data sets to identify new p53 target genes, focusing on the noncoding genome. We identify Neat1, a noncoding RNA (ncRNA) constituent of paraspeckles, as a p53 target gene broadly induced by mouse and human p53 in different cell types and by diverse stress signals...
July 11, 2017: Genes & Development
https://www.readbyqxmd.com/read/28679390/lncrna-ancr-regulates-the-cell-growth-of-osteosarcoma-by-interacting-with-ezh2-and-affecting-the-expression-of-p21-and-p27
#7
Fei Zhang, Hao Peng
BACKGROUND: Osteosarcoma (OS) is one of the most common malignant tumors developed in the bone. EZH2 has been found to play pivotal roles in the development of various cancers. LncRNA-ANCR (anti-differentiation ncRNA) has been reported to interact with EZH2 and regulated osteoblast differentiation. Our study aimed to investigate the effect of lncRNA-ANCR on the tumorigenesis of osteosarcoma and explore the underlying molecular mechanism. METHODS: RT-PCR was performed to detect the messenger RNA (mRNA) levels of lncRNA-ANCR, EZH2, p21, and p27 in OS tissues and cell lines...
July 5, 2017: Journal of Orthopaedic Surgery and Research
https://www.readbyqxmd.com/read/28669734/inhibition-of-mir-664a-interferes-with-the-migration-of-osteosarcoma-cells-via-modulation-of-meg3
#8
Yunus Sahin, Zekiye Altan, Kaifee Arman, Esra Bozgeyik, Meltem Koruk Ozer, Ahmet Arslan
Osteosarcoma is the most common primary bone tumor in children and adolescents. Understanding the basic molecular mechanisms in developing cancer can be helpful in developing alternative treatment strategies. The relationship between dysregulated non-coding RNAs' (ncRNA) expression level and osteosarcoma was detected. Among those ncRNAs, the expression levels of miR-664a were detected to be upregulated and MEG3 long non-coding RNA levels were detected to be downregulated in osteosarcoma tissue and cell lines...
June 29, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28652179/non-coding-rna-regulation-of-t-cell-biology-implications-for-age-associated-cardiovascular-diseases
#9
REVIEW
Jose Coelho-Lima, Ioakim Spyridopoulos
Prevalence of age-associated cardiovascular diseases (CVD) has dramatically increased as a result of improvements in life expectancy. Chronic inflammation is a shared pathophysiological feature of age-associated CVDs, indicating a role for the immune system in the onset and development of CVDs. Indeed, ageing elicits profound changes in both the cardiovascular and immune system, especially in the T cell compartment. Although such changes have been well described at the cellular level, the molecular mechanisms underlying immune-mediated cardiovascular ageing remain largely unexplored...
June 23, 2017: Experimental Gerontology
https://www.readbyqxmd.com/read/28645654/epigenome-dysregulation-in-cholangiocarcinoma
#10
REVIEW
Colm J O'Rourke, Patricia Munoz-Garrido, Esmeralda L Aguayo, Jesper B Andersen
Epigenomics is a fast-evolving field of research that has lately attracted considerable interest, mainly due to the reversibility of epigenetic marks. Clinically, among solid tumors, the field is still limited. In cholangiocarcinoma (CCA) it is well known that the epigenetic landscape is deregulated both during carcinogenesis and disease progression as a consequence of aberrant mechanisms leading to genome instability. In this article, we will briefly review the molecular alterations that have been described in the transformation of normal cholangiocytes into malignant derivatives, focusing on the role of non-coding RNA (ncRNA) interactions, DNA methylation, post-translational modifications (PTMs) of histones and chromatin remodeling complexes...
June 20, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28643459/construction-of-competitive-endogenous-rna-network-reveals-regulatory-role-of-long-non-coding-rnas-in-type-2-diabetes-mellitus
#11
Zijing Lin, Xinyu Li, Xiaorong Zhan, Lijie Sun, Jie Gao, Yan Cao, Hui Qiu
Increasing epidemic of type 2 diabetes mellitus (T2DM) and its comorbidities makes it urgent to understand the pathogenesis and regulatory mechanism. However, little is known about the regulatory role of lncRNAs in diabetes. Here, we constructed a T2DM-related competitive endogenous RNA (ceRNA) network (DMCN) to explore biological function of lncRNAs during the development of diabetes mellitus. This network contained 351 nodes including 98 mRNAs, 86 microRNAs and 167 lncRNAs. Functional analysis showed that the mRNAs in DMCN were annotated into some diabetes-related pathways...
June 23, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28641521/lncrna-hotair-polymorphisms-association-with-cancer-susceptibility-in-different-tumor-types
#12
Gerardo Botti, Francesca Collina, Giosuè Scognamiglio, Gabriella Aquino, Margherita Cerrone, Giuseppina Liguori, Vincenzo Gigantino, Maria Gabriella Malzone, Monica Cantile
Single nucleotide polymorphisms (SNPs) in non coding RNAs (ncRNA) molecules affect gene and protein expression and generate genetic variability influencing the risk of tumor diseases. HOTAIR is locates at the heart of the cell memory gene program and represents a prototype of long non coding RNA (LncRNA) due to its capacity to regulate in-trans a distant chromosome landscape. Aberrant expression of HOTAIR is frequently associated with pathogenesis and mostly with metastatic progression of several human cancers...
June 21, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28634583/circular-rnas-biogenesis-function-and-role-in-human-diseases
#13
REVIEW
John Greene, Anne-Marie Baird, Lauren Brady, Marvin Lim, Steven G Gray, Raymond McDermott, Stephen P Finn
Circular RNAs (circRNAs) are currently classed as non-coding RNA (ncRNA) that, unlike linear RNAs, form covalently closed continuous loops and act as gene regulators in mammals. They were originally thought to represent errors in splicing and considered to be of low abundance, however, there is now an increased appreciation of their important function in gene regulation. circRNAs are differentially generated by backsplicing of exons or from lariat introns. Unlike linear RNA, the 3' and 5' ends normally present in an RNA molecule have been joined together by covalent bonds leading to circularization...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28634418/long-noncoding-rnas-as-biomarkers-in-cancer
#14
REVIEW
Luka Bolha, Metka Ravnik-Glavač, Damjan Glavač
Long noncoding RNAs (lncRNAs) are a relatively well-characterized class of noncoding RNA (ncRNA) molecules, involved in the regulation of various cell processes, including transcription, intracellular trafficking, and chromosome remodeling. Their deregulation has been associated with the development and progression of various cancer types, the fact which makes them suitable as biomarkers for cancer diagnosis and prognosis. In recent years, detection of cancer-associated lncRNAs in body fluids of cancer patients has proven itself as an especially valuable method to effectively diagnose cancer...
2017: Disease Markers
https://www.readbyqxmd.com/read/28629929/interactions-between-micrornas-and-long-non-coding-rnas-in-cardiac-development-and-repair
#15
REVIEW
Alessio Rotini, Ester Martínez-Sarrà, Enrico Pozzo, Maurilio Sampaolesi
Non-coding RNAs (ncRNAs) are emerging players in muscle regulation. Based on their length and differences in molecular structure, ncRNAs are subdivided into several categories including small interfering RNAs, stable non-coding RNAs, microRNAs (miRs), long non-coding RNAs (lncRNAs), and circular RNAs. miRs and lncRNAs are able to post-transcriptionally regulate many genes and bring into play several traits simultaneously due to a myriad of different targets. Recent studies have emphasized their importance in cardiac regeneration and repair...
June 17, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28629776/unveiling-the-non-repair-face-of-the-base-excision-repair-pathway-in-rna-processing-a-missing-link-between-dna-repair-and-gene-expression
#16
REVIEW
Giulia Antoniali, Matilde Clarissa Malfatti, Gianluca Tell
The Base Excision Repair (BER) pathway, initially studied as a mere DNA repair pathway, has been later found to be implicated in the expression of cancer related genes in human. For several years, this intricate involvement in apparently different processes represented a mystery, which we now are starting to unveil. The BER handles simple alkylation and oxidative lesions arising from both endogenous and exogenous sources, including cancer therapy agents. Surprisingly, BER pathway involvement in transcriptional regulation, immunoglobulin variability and switch recombination, RNA metabolism and nucleolar function is astonishingly consolidating...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28602844/primate-specific-long-non-coding-rnas-and-micrornas
#17
REVIEW
Hassaan Mehboob Awan, Abdullah Shah, Farooq Rashid, Ge Shan
Non-coding RNAs (ncRNAs) are critical regulators of gene expression in essentially all life forms. Long ncRNAs (lncRNAs) and microRNAs (miRNAs) are two important RNA classes possessing regulatory functions. Up to date, many primate-specific ncRNAs have been identified and investigated. Their expression specificity to primate lineage suggests primate-specific roles. It is thus critical to elucidate the biological significance of primate or even human-specific ncRNAs, and to develop potential ncRNA-based therapeutics...
June 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28587571/expression-profiling-of-lncrnas-mirnas-and-mrnas-and-their-differential-expression-in-leiomyoma-using-next-generation-rna-sequencing
#18
Tsai-Der Chuang, Omid Khorram
The objective of this study was to identify the expression profile of long noncoding RNAs (lncRNAs) with concurrent assessment of microRNA (miRNA) and messenger RNA (mRNA) profiles in leiomyomas and paired myometrium using next-generation RNA sequencing and assembly of RNA transcripts. Total RNA was isolated from leiomyoma and paired myometrium (N = 8) and samples from 3 pairs were subjected to RNA sequencing. Normalized assembly of over 48 000 lncRNAs resulted in identification of 45 936 lncRNAs. Of these lncRNAs, 22 148 representing overlapping, intergenic, intronic, and antisense subtypes were expressed in all paired tissues, with 5941 (2813 up- and 3128 downregulated at ≥1...
January 1, 2017: Reproductive Sciences
https://www.readbyqxmd.com/read/28575517/comprehensive-classification-of-the-pin-domain-like-superfamily
#19
Dorota Matelska, Kamil Steczkiewicz, Krzysztof Ginalski
PIN-like domains constitute a widespread superfamily of nucleases, diverse in terms of the reaction mechanism, substrate specificity, biological function and taxonomic distribution. Proteins with PIN-like domains are involved in central cellular processes, such as DNA replication and repair, mRNA degradation, transcription regulation and ncRNA maturation. In this work, we identify and classify the most complete set of PIN-like domains to provide the first comprehensive analysis of sequence-structure-function relationships within the whole PIN domain-like superfamily...
May 31, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28553651/a-review-on-recent-computational-methods-for-predicting-noncoding-rnas
#20
REVIEW
Yi Zhang, Haiyun Huang, Dahan Zhang, Jing Qiu, Jiasheng Yang, Kejing Wang, Lijuan Zhu, Jingjing Fan, Jialiang Yang
Noncoding RNAs (ncRNAs) play important roles in various cellular activities and diseases. In this paper, we presented a comprehensive review on computational methods for ncRNA prediction, which are generally grouped into four categories: (1) homology-based methods, that is, comparative methods involving evolutionarily conserved RNA sequences and structures, (2) de novo methods using RNA sequence and structure features, (3) transcriptional sequencing and assembling based methods, that is, methods designed for single and pair-ended reads generated from next-generation RNA sequencing, and (4) RNA family specific methods, for example, methods specific for microRNAs and long noncoding RNAs...
2017: BioMed Research International
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