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https://www.readbyqxmd.com/read/28108657/risearch2-suffix-array-based-large-scale-prediction-of-rna-rna-interactions-and-sirna-off-targets
#1
Ferhat Alkan, Anne Wenzel, Oana Palasca, Peter Kerpedjiev, Anders Frost Rudebeck, Peter F Stadler, Ivo L Hofacker, Jan Gorodkin
Intermolecular interactions of ncRNAs are at the core of gene regulation events, and identifying the full map of these interactions bears crucial importance for ncRNA functional studies. It is known that RNA-RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. Here, we present RIsearch2, a large-scale RNA-RNA interaction prediction tool that enables quick localization of potential near-complementary RNA-RNA interactions between given query and target sequences...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28093925/hypermethylation-of-antisense-long-noncoding-rnas-in-acute-lymphoblastic-leukemia
#2
Gerald Arthur, Md Almamun, Kristen Taylor
AIM: Long noncoding RNAs serve critical regulatory functions highly specific for a tissue and its developmental stage. Antisense long ncRNA (AS-lncRNA) methylation changes in acute lymphoblastic leukemia (ALL) versus normal pre-B-cell lymphoblasts were evaluated to identify potential differential methylation in this group of genes. MATERIALS & METHODS: The methylome of ALL and normal lymphoblasts was examined by the methylated CpG island recovery assay followed by NGS...
January 17, 2017: Epigenomics
https://www.readbyqxmd.com/read/28090611/performance-of-nano-assembly-logic-gates-with-a-dna-multi-hairpin-motif
#3
Lulu Zhang, Annie M Bluhm, Kuan-Jen Chen, Nicholas E Larkey, Sean M Burrows
DNA nano-assemblies have far-reaching implications for molecular computers. Boolean logic gates made from DNA respond to specific combinations of chemical or molecular inputs. In complex samples an assortment of other chemicals and molecules may interfere with the gate's recognition and response mechanisms. For logic gates to accept an increasing number of inputs, while maintaining selectivity, their design must only respond when specific input combinations are available simultaneously. Here we present proof-of-principle for a fluorescent-based nano-assembly logic gate for three inputs...
January 16, 2017: Nanoscale
https://www.readbyqxmd.com/read/28077569/rain-rna-protein-association-and-interaction-networks
#4
Alexander Junge, Jan C Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T Workman, Lars Juhl Jensen, Jan Gorodkin
Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA-RNA and ncRNA-protein interactions and its integration with the STRING database of protein-protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28069878/malat1-is-associated-with-poor-response-to-oxaliplatin-based-chemotherapy-in-colorectal-cancer-patients-and-promotes-chemoresistance-through-ezh2
#5
Peilong Li, Xin Zhang, Haiyan Wang, Lili Wang, Tong Liu, Lutao Du, Yongmei Yang, Chuanxin Wang
A major reason for oxaliplatin chemoresistance in colorectal cancer (CRC) is the acquisition of epithelial-mesenchymal transition (EMT) in cancer cells. The long non-coding RNA, MALAT1, is a highly conserved nuclear ncRNA and a key regulator of metastasis development in several cancers. However, its role in oxaliplatin-induced metastasis and chemo-resistance is not well known. In this study, we aim to investigate the prognostic and therapeutic role of MALAT1 in CRC patients receiving oxaliplatin-based therapy, and further explore the potential transcriptional regulation through interaction with EZH2 based on the established HT29 oxaliplatin-resistant cells...
January 9, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28058582/genome-wide-dna-methylation-patterns-analysis-of-noncoding-rnas-in-temporal-lobe-epilepsy-patients
#6
Wenbiao Xiao, Yuze Cao, Hongyu Long, Zhaohui Luo, Shuyu Li, Na Deng, Jianjian Wang, Xiaoyan Lu, Tianfeng Wang, Shangwei Ning, Lihua Wang, Bo Xiao
Temporal lobe epilepsy (TLE) is the most common form of adult epilepsy and frequently evolving drug resistance. Although there is growing consensus that noncoding ribonucleic acids (ncRNAs) are modulators of TLE, the knowledge about the deoxyribonucleic acid (DNA) methylation patterns of ncRNAs in TLE remains limited. In the current study, we constructed DNA methylation profiles from 30 TLE patients and 30 healthy controls for ncRNAs, primarily focusing on long ncRNAs (lncRNAs) and microRNAs (miRNAs), by reannotating data of DNA methylation BeadChip...
January 5, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28029658/the-inhibition-of-45a-ncrna-expression-reduces-tumor-formation-affecting-tumor-nodules-compactness-and-metastatic-potential-in-neuroblastoma-cells
#7
Ilaria Penna, Arianna Gigoni, Delfina Costa, Serena Vella, Debora Russo, Alessandro Poggi, Federico Villa, Antonella Brizzolara, Claudio Canale, Andrea Mescola, Antonio Daga, Claudio Russo, Mario Nizzari, Tullio Florio, Paola Menichini, Aldo Pagano
We recently reported the in vitro over-expression of 45A, a RNA polymerase III-transcribed non-coding (nc)RNA, that perturbs the intracellular content of FE65L1 affecting cell proliferation rate, short-term response to genotoxic stress, substrate adhesion capacity and, ultimately, increasing the tumorigenic potential of human neuroblastoma cells. In this work, to deeply explore the mechanism by which 45A ncRNA contributes to cancer development, we targeted in vitro and in vivo 45A levels by the stable overexpression of antisense 45A RNA...
December 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/28013268/rna-g-quadruplexes-emerging-mechanisms-in-disease
#8
Anne Cammas, Stefania Millevoi
RNA G-quadruplexes (G4s) are formed by G-rich RNA sequences in protein-coding (mRNA) and non-coding (ncRNA) transcripts that fold into a four-stranded conformation. Experimental studies and bioinformatic predictions support the view that these structures are involved in different cellular functions associated to both DNA processes (telomere elongation, recombination and transcription) and RNA post-transcriptional mechanisms (including pre-mRNA processing, mRNA turnover, targeting and translation). An increasing number of different diseases have been associated with the inappropriate regulation of RNA G4s exemplifying the potential importance of these structures on human health...
December 23, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28011477/long-noncoding-rna-panda-positively-regulates-proliferation-of-osteosarcoma-cells
#9
Yojiro Kotake, Taiki Goto, Madoka Naemura, Yasutoshi Inoue, Haruna Okamoto, Keiichiro Tahara
BACKGROUND: A long noncoding RNA, p21-associated ncRNA DNA damage-activated (PANDA), associates with nuclear transcription factor Y subunit alpha (NF-YA) and inhibits its binding to promoters of apoptosis-related genes, thereby repressing apoptosis in normal human fibroblasts. Here, we show that PANDA is involved in regulating proliferation in the U2OS human osteosarcoma cell line. MATERIALS AND METHODS: U2OS cells were transfected with siRNAs against PANDA 72 h later and they were subjected to reverse transcription-polymerase chain reaction (RT-PCR), quantitative RT-PCR and cell-cycle analysis...
January 2017: Anticancer Research
https://www.readbyqxmd.com/read/28005467/defining-the-purity-of-exosomes-required-for-diagnostic-profiling-of-small-rna-suitable-for-biomarker-discovery
#10
Camelia Quek, Shayne A Bellingham, Chol-Hee Jung, Benjamin J Scicluna, Mitch C Shambrook, Robyn A Sharples, Lesley Cheng, Andrew F Hill
Small non-coding RNAs (ncRNA), including microRNAs (miRNA), enclosed in exosomes are being utilised for biomarker discovery in disease. Two common exosome isolation methods involve differential ultracentrifugation or differential ultracentrifugation coupled with Optiprep gradient fractionation. Generally, the incorporation of an Optiprep gradient provides better separation and increased purity of exosomes. The question of whether increased purity of exosomes is required for small ncRNA profiling, particularly in diagnostic and biomarker purposes, has not been addressed and highly debated...
December 22, 2016: RNA Biology
https://www.readbyqxmd.com/read/27995975/rna-activation-of-haploinsufficient-foxg1-gene-in-murine-neocortex
#11
Cristina Fimiani, Elisa Goina, Qin Su, Guangping Gao, Antonello Mallamaci
More than one hundred distinct gene hemizygosities are specifically linked to epilepsy, mental retardation, autism, schizophrenia and neuro-degeneration. Radical repair of these gene deficits via genome engineering is hardly feasible. The same applies to therapeutic stimulation of the spared allele by artificial transactivators. Small activating RNAs (saRNAs) offer an alternative, appealing approach. As a proof-of-principle, here we tested this approach on the Rett syndrome-linked, haploinsufficient, Foxg1 brain patterning gene...
December 20, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27990832/-non-coding-rna-from-useless-to-essential
#12
(no author information available yet)
Whole-genome sequencing analyses revealed that the majority of the human genome is transcribed and identified thousands of protein non-coding transcripts. Non-coding RNAs (ncRNAs) are divided into two main groups: small and long ncRNAs. This review is focused on the regulatory ncRNAs mainly on microRNAs and long ncRNAs. These ncRNAs regulate gene expression at the transcriptional and post-transcriptional levels. In this context, ncRNAs are involved in the regulation of most cellular processes and their deregulation has serious impacts on the phenotype...
2016: Casopís Lékar̆ů C̆eských
https://www.readbyqxmd.com/read/27990175/the-development-of-non-coding-rna-ontology
#13
Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A Blake, Dejing Dou, Weili Huang, Darren A Natale, Alan Ruttenberg, Jun Huan, Michael T Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J Strachan, Nisansa de Silva, Mohan Vamsi Kasukurthi, Vikash Kumar Jha, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M Borchert, Ming Tan
Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data...
2016: International Journal of Data Mining and Bioinformatics
https://www.readbyqxmd.com/read/27988178/a-novel-protein-coding-potential-of-long-intergenic-non-coding-rnas-lincrnas-in-the-kinetoplastid-protozoan-parasite-leishmania-major
#14
Harsh Pawar, Kalpana Pai, Milind S Patole
Cutaneous leishmaniasis (CL) is caused by a kinetoplastid protozoan parasite Leishmania major, as a skin ulcer at the site of the sandfly bite. CL is curable and in most cases ulcers heal spontaneously within three to six months leaving a scar and disfiguration. Complete genome of L. major was reported in 2005 at the very initial phase of kinetoplastid parasite genome sequencing project. Presently, L. major genome is most studied and comprehensively annotated genome and therefore, it is being used as a reference genome for annotating recently sequenced Leishmanial genomes...
December 14, 2016: Acta Tropica
https://www.readbyqxmd.com/read/27965463/ameloblastoma-rna-profiling-uncovers-a-distinct-non-coding-rna-signature
#15
Haleh Davanian, Anangi Balasiddaiah, Robert Heymann, Magnus Sundström, Poppy Redenström, Mikael Silfverberg, David Brodin, Matti Sällberg, Sven Lindskog, Carina Kruger Weiner, Margaret Chen
Ameloblastoma of the jaws remains the top difficult to treat odontogenic tumour and has a high recurrence rate. New evidence suggests that non-coding RNAs (ncRNAs) play a critical role in tumourgenesis and prognosis of cancer. However, ameloblastoma ncRNA expression data is lacking. Here we present the first report of ameloblastoma ncRNA signatures. A total of 95 ameloblastoma cases and a global array transcriptome technology covering > 285.000 full-length transcripts were used in this two-step analysis...
December 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27939377/draft-genome-of-a-south-african-strain-of-pectobacterium-carotovorum-subsp-brasiliense
#16
Khayalethu Ntushelo, Joseph Mafofo
The draft genome of Pectobacterium carotovorum subsp. brasiliense (Pcb) which causes blackleg of potato was submitted to the NCBI and released with reference number NZ_LGRF00000000.1. The estimated genome size based on the draft genome assembly is 4,820,279bp from 33 contigs ranging in length from 444 to 1,660,019 nucleotides. The genome annotation showed 4250 putative genes, 4114 CDS and 43 pseudo-genes. Three complete rRNA gene species were detected: nine 5S, one 16S and one 23S. Other partial rRNA gene fragments were also identified, nine 16S rRNA and three 23S rRNA...
January 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/27930710/urb-rip-an-adaptable-and-efficient-approach-for-immunoprecipitation-of-rnas-and-associated-rnas-proteins
#17
Kyle A Cottrell, Sergej Djuranovic
Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application...
2016: PloS One
https://www.readbyqxmd.com/read/27928018/expression-of-the-antisense-to-latency-transcript-long-noncoding-rna-in-kaposi-s-sarcoma-associated-herpesvirus
#18
Jason M Schifano, Kathleen Corcoran, Hemant Kelkar, Dirk P Dittmer
: The regulation of latency is central to herpesvirus biology. Recent transcriptome-wide surveys have uncovered evidence for promiscuous transcription across the entirety of the Kaposi sarcoma-associated herpesvirus genome and postulated the existence of multiple viral long noncoding RNAs (lncRNAs). NextGen sequencing studies are highly dependent on the specific experimental approach and particular algorithms of analysis, and therefore benefit from independent confirmation of the results...
December 7, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27924586/rna-sequencing-analysis-of-salivary-extracellular-rna
#19
Blanca Majem, Feng Li, Jie Sun, David T W Wong
Salivary biomarkers for disease detection, diagnostic and prognostic assessments have become increasingly well established in recent years. In this chapter we explain the current leading technology that has been used to characterize salivary non-coding RNAs (ncRNAs) from the extracellular RNA (exRNA) fraction: HiSeq from Illumina® platform for RNA sequencing. Therefore, the chapter is divided into two main sections regarding the type of the library constructed (small and long ncRNA libraries), from saliva collection, RNA extraction and quantification to cDNA library generation and corresponding QCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924038/farna-knowledgebase-of-inferred-functions-of-non-coding-rna-transcripts
#20
Tanvir Alam, Mahmut Uludag, Magbubah Essack, Adil Salhi, Haitham Ashoor, John B Hanks, Craig Kapfer, Katsuhiko Mineta, Takashi Gojobori, Vladimir B Bajic
Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate...
October 24, 2016: Nucleic Acids Research
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