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https://www.readbyqxmd.com/read/29244808/fgmd-a-novel-approach-for-functional-gene-module-detection-in-cancer
#1
Daeyong Jin, Hyunju Lee
With the increasing availability of multi-dimensional biological datasets for the same samples (i.e., gene expression, microRNAs, copy numbers, mutations, methylations), it has now become possible to systematically understand the regulatory mechanisms operating in a cancer cell. For this task, it is important to discover a set of co-expressed genes with functions, representing a so-called functional gene module, because co-expressed genes tend to be co-regulated by the same regulators, including transcription factors, microRNAs, and copy number aberrations...
2017: PloS One
https://www.readbyqxmd.com/read/29244760/impact-of-methods-on-the-measurement-of-mrna-turnover
#2
REVIEW
Takeo Wada, Attila Becskei
The turnover of the RNA molecules is determined by the rates of transcription and RNA degradation. Several methods have been developed to study RNA turnover since the beginnings of molecular biology. Here we summarize the main methods to measure RNA half-life: transcription inhibition, gene control, and metabolic labelling. These methods were used to detect the cellular activity of the mRNAs degradation machinery, including the exo-ribonuclease Xrn1 and the exosome. On the other hand, the study of the differential stability of mature RNAs has been hampered by the fact that different methods have often yielded inconsistent results...
December 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29244142/an-autofluorescence-based-method-for-the-isolation-of-highly-purified-ventricular-cardiomyocytes
#3
Veronica Larcher, Paolo Kunderfranco, Marco Vacchiano, Pierluigi Carullo, Marco Erreni, Irene Salamon, Federico Simone Colombo, Enrico Lugli, Marta Mazzola, Achille Anselmo, Gianluigi Condorelli
Aims: The aim of our study was to set up a simple and reliable isolation method of living ventricular cardiomyocytes (vCMs) for molecular and biological studies. Methods: A standard technique for the retrograde perfusion of an enzymatic solution was used to isolate cardiac cells from adult mouse heart. Fluorescence-activated cell sorting (FACS) on adult murine cardiac ventricle cells was performed, comparing the intrinsic autofluorescence in the FITC channel and the forward scatter (FSC) parameter in order to isolate highly fluorescent cells...
December 13, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/29244011/a-deep-learning-method-for-lincrna-detection-using-auto-encoder-algorithm
#4
Ning Yu, Zeng Yu, Yi Pan
BACKGROUND: RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the DNA sequences; (2) lincRNAs contain some conversed patterns/motifs tethered together by non-conserved regions...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29243374/molecular-classification-of-autofluorescence-excision-margins-in-oral-potentially-malignant-disorders
#5
Camile S Farah, Farzaneh Kordbacheh, Keziah John, Nigel Bennett, Simon A Fox
OBJECTIVE: To define molecular differences between autofluorescence and white light defined excision margins in oral potentially malignant disorders (OPMD) using transcriptome expression profiles. MATERIALS AND METHODS: Excisional biopsy specimens were taken from 11 patients at three different sites for each lesion: centre, white light margin, and autofluorescence margin. The lesions were diagnosed histopathologically as oral epithelial dysplasia, oral lichenoid dysplasia, oral lichen planus or other...
December 14, 2017: Oral Diseases
https://www.readbyqxmd.com/read/29242905/the-long-noncoding-rna-landscape-of-the-mouse-eye
#6
Weiwei Chen, Shuai Yang, Zhonglou Zhou, Xiaoting Zhao, Jiayun Zhong, Peter S Reinach, Dongsheng Yan
Purpose: Long noncoding RNAs (lncRNAs) are important regulators of diverse biological functions. However, an extensive in-depth analysis of their expression profile and function in mammalian eyes is still lacking. Here we describe comprehensive landscapes of stage-dependent and tissue-specific lncRNA expression in the mouse eye. Methods: Affymetrix transcriptome array profiled lncRNA signatures from six different ocular tissue subsets (i.e., cornea, lens, retina, RPE, choroid, and sclera) in newborn and 8-week-old mice...
December 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29242531/long-noncoding-rna-expression-profile-reveals-lncrnas-signature-associated-with-extracellular-matrix-degradation-in-kashin-beck-disease
#7
Cuiyan Wu, Huan Liu, Feng'e Zhang, Wanzhen Shao, Lei Yang, Yujie Ning, Sen Wang, Guanghui Zhao, Byeong Jae Lee, Mikko Lammi, Xiong Guo
Kashin-Beck disease (KBD) is a deformative, endemic osteochondropathy involving degeneration and necrosis of growth plates and articular cartilage. The pathogenesis of KBD is related to gene expression and regulation mechanisms, but long noncoding RNAs (lncRNAs) in KBD have not been investigated. In this study, we identified 316 up-regulated and 631 down-regulated lncRNAs (≥ 2-fold change) in KBD chondrocytes using microarray analysis, of which more than three-quarters were intergenic lncRNAs and antisense lncRNAs...
December 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29242366/the-landscape-of-human-mutually-exclusive-splicing
#8
Klas Hatje, Raza-Ur Rahman, Ramon O Vidal, Dominic Simm, Björn Hammesfahr, Vikas Bansal, Ashish Rajput, Michel Edwar Mickael, Ting Sun, Stefan Bonn, Martin Kollmar
Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA-Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold...
December 14, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/29242318/single-stranded-dna-and-rna-origami
#9
Dongran Han, Xiaodong Qi, Cameron Myhrvold, Bei Wang, Mingjie Dai, Shuoxing Jiang, Maxwell Bates, Yan Liu, Byoungkwon An, Fei Zhang, Hao Yan, Peng Yin
Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure...
December 15, 2017: Science
https://www.readbyqxmd.com/read/29241971/blocking-stemness-and-metastatic-properties-of-ovarian-cancer-cells-by-targeting-p70s6k-with-dendrimer-nanovector-based-sirna-delivery
#10
Jing Ma, Shashwati Kala, Susan Yung, Tak Mao Chan, Yu Cao, Yifan Jiang, Xiaoxuan Liu, Suzanne Giorgio, Ling Peng, Alice S T Wong
Metastasis is the cause of most (>90%) cancer deaths and currently lacks effective treatments. Approaches to understanding the biological process, unraveling the most effective molecular target(s), and implementing nanotechnology to increase the therapeutic index are expected to facilitate cancer therapy against metastasis. Here, we demonstrate the potential advantages of bringing these three approaches together through the rational design of a small interfering RNA (siRNA) that targets p70S6K in cancer stem cells (CSCs) in combination with dendrimer nanotechnology-based siRNA delivery...
November 16, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/29241531/lncrna-panct1-maintains-mouse-embryonic-stem-cell-identity-by-regulating-tobf1-recruitment-to-oct-sox-sequences-in-early-g1
#11
Debojyoti Chakraborty, Maciej Paszkowski-Rogacz, Nicolas Berger, Li Ding, Jovan Mircetic, Jun Fu, Vytautas Iesmantavicius, Chunaram Choudhary, Konstantinos Anastassiadis, A Francis Stewart, Frank Buchholz
Long noncoding RNAs (lncRNAs) have been implicated in diverse biological processes, including embryonic stem cell (ESC) maintenance. However, their functional mechanisms remain largely undefined. Here, we show that the lncRNA Panct1 regulates the transient recruitment of a putative X-chromosome-encoded protein A830080D01Rik, hereafter referred to as transient octamer binding factor 1 (TOBF1), to genomic sites resembling the canonical Oct-Sox motif. TOBF1 physically interacts with Panct1 and exhibits a cell-cycle-specific punctate localization in ESCs...
December 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/29241362/simplified-teixobactin-analogues-to-target-superbugs
#12
Ishwar Singh
Ishwar Singh speaks to Benjamin Walden, Commissioning Editor. Ishwar Singh is a Senior Lecturer in biological chemistry at the School of Pharmacy, University of Lincoln. Prior to Lincoln, he had held many prestigious fellowships such as the Alexander von Humboldt fellowship, Germany; and Senior Research Fellowship, DANIDA, Denmark and CSIR, India. He is an organic chemist. He has developed bioconjugations for DNA, RNA and polymer modifications. He is currently leading research in novel antimicrobials based on rational design against clinically important resistant bacteria (such as methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, mycobacteria, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa), biologics delivery, peptides, sequence-selective DNA cross linking, nanoparticles modifications for drug delivery and diagnostic applications...
December 15, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/29240998/orthogonality-and-burdens-of-heterologous-and-gate-gene-circuits-in-e-coli
#13
Qijun Liu, Jörg Schumacher, Xinyi Wan, Chunbo Lou, Baojun Wang
Synthetic biology approaches commonly introduce heterologous gene networks into a host to predictably program cells, with the expectation of the synthetic network being orthogonal to the host background. However, introduced circuits may interfere with the host's physiology, either indirectly by posing a metabolic burden and/or through unintended direct interactions between parts of the circuit with those of the host, affecting functionality. Here we used RNA-Seq transcriptome analysis to quantify the interactions between a representative heterologous AND gate circuit and the host Escherichia coli under various conditions including circuit designs and plasmid copy numbers...
December 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29240916/study-on-the-anti-endotoxin-effect-of-sinomenine-using-an-agilent-genome-array
#14
Yiyi Hu, Bin Li, Libin Wen, Kongwang He
Background: Endotoxin is a significant contributing factor underlying the occurrence of fever, diarrhea, inflammation, edema, coagulation, shock, and other syndromes associated with Gram-negative bacterial infections. To date, there is no effective treatment for endotoxemia. Aim: The aim of this study was to characterize differentially expressed genes in sinomenine-treated and LPS-induced endothelial cells by microarray analysis, and to determine the potential pharmacological activity of sinomenine...
December 12, 2017: QJM: Monthly Journal of the Association of Physicians
https://www.readbyqxmd.com/read/29240690/high-throughput-sequencing-of-small-rna-transcriptomes-in-maize-kernel-identifies-mirnas-involved-in-embryo-and-endosperm-development
#15
Lijuan Xing, Ming Zhu, Min Zhang, Wenzong Li, Haiyang Jiang, Junjie Zou, Lei Wang, Miaoyun Xu
Maize kernel development is a complex biological process that involves the temporal and spatial expression of many genes and fine gene regulation at a transcriptional and post-transcriptional level, and microRNAs (miRNAs) play vital roles during this process. To gain insight into miRNA-mediated regulation of maize kernel development, a deep-sequencing technique was used to investigate the dynamic expression of miRNAs in the embryo and endosperm at three developmental stages in B73. By miRNA transcriptomic analysis, we characterized 132 known miRNAs and six novel miRNAs in developing maize kernel, among which, 15 and 14 miRNAs were commonly differentially expressed between the embryo and endosperm at 9 days after pollination (DAP), 15 DAP and 20 DAP respectively...
December 14, 2017: Genes
https://www.readbyqxmd.com/read/29240458/genome-wide-analysis-of-uveal-melanoma-metastasis-associated-lncrnas-and-their-functional-network
#16
Binbin Xu, Ruiqi Ma, Hui Ren, Jiang Qian
Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Up to 50% of primary UM cases will develop distant metastasis, but no effective therapies are currently available. The present study aimed to characterize the expression profile of the long noncoding RNAs (lncRNAs) and screen the potential metastasis-associated lncRNAs in UM. A genome-wide analysis of the transcriptome was performed on 11 primary UM tissues (6 metastasized and 5 nonmetastasized) through RNA sequencing. A total of 40,878 lncRNAs were detected in UM, 4,983 of which were novel candidates...
December 14, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/29240300/genomic-origin-and-nuclear-localization-of-terra-telomeric-repeat-containing-rna-from-darkness-to-dawn
#17
REVIEW
Aurélie Diman, Anabelle Decottignies
Long non-coding RNAs, produced from distinct regions of the chromosomes, are emerging as new key players in several important biological processes. The long non-coding RNAs add a new layer of complexity to cellular regulatory pathways, from transcription to cellular trafficking or chromatin remodeling. More than 25 years ago, the discovery of a transcriptional activity at telomeres of protozoa ended the long-lasting belief that telomeres were transcriptionally silent. Since then, progressively accumulating evidences established that production of TElomeric Repeat-containing RNA (TERRA) was a general feature of eukaryotic cells...
December 14, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29239821/long-noncoding-rna-fezf1-as1-indicates-a-poor-prognosis-of-gastric-cancer-and-promotes-tumorigenesis-via-activation-of-wnt-signaling-pathway
#18
Xiaoli Wu, Peichen Zhang, Hua Zhu, Shi Li, Xiangjian Chen, Lingyan Shi
Long non-coding RNAs (lncRNAs) have been demonstrated that it plays very important role in development and progression of carcinomas. LncRNA FEZF1 antisense RNA 1 (FEZF1-AS1) has been proved to be implicated in tumor initiation and progression of various cancers, recently. Nevertheless, the biological function and clinical significance of lncRNA FEZF1-AS1 in gastric cancer (GC) are not clear enough. Here, we concentrated on the association of FEZF1-AS1 expression and clinicopathological factors in GC tissues and cells...
November 24, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29239719/live-cell-mapping-of-organelle-associated-rnas-via-proximity-biotinylation-combined-with-protein-rna-crosslinking
#19
Pornchai Kaewsapsak, David Michael Shechner, William Mallard, John L Rinn, Alice Y Ting
The spatial organization of RNA within cells is a crucial factor influencing a wide range of biological functions throughout all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we develop such a method, termed APEX-RIP, which combines peroxidase-catalyzed, spatially restricted in situ protein biotinylation with RNA-protein chemical crosslinking. We demonstrate that, using a single protocol, APEX-RIP can isolate RNAs from a variety of subcellular compartments, including the mitochondrial matrix, nucleus, cytosol, and endoplasmic reticulum (ER), with specificity and sensitivity that rival or exceed those of conventional approaches...
December 14, 2017: ELife
https://www.readbyqxmd.com/read/29239273/bioluminescent-high-throughput-succinate-detection-method-for-monitoring-the-activity-of-jmjc-histone-demethylases-and-fe-ii-2-oxoglutarate-dependent-dioxygenases
#20
Juliano Alves, Gediminas Vidugiris, Said A Goueli, Hicham Zegzouti
The modification of a diverse array of substrates by Fe(II)/2-oxoglutarate-dependent dioxygenases is central to the modulation of distinct biological processes such as epigenetics, hypoxic signaling, and DNA/RNA repair. Of these, JumonjiC domain-containing histone lysine demethylases (JMJCs) and prolyl hydroxylases are potential drug targets due to their relevance to human diseases. Thus, assays to interrogate this enzyme superfamily are needed to identify selective and potent inhibitors as leads for drug development and that could also be useful research tools...
December 1, 2017: SLAS Discovery
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