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no-coding RNA

Jakob Trendel, Thomas Schwarzl, Rastislav Horos, Ananth Prakash, Alex Bateman, Matthias W Hentze, Jeroen Krijgsveld
Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here, we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs) and to identify hundreds of protein-RNA interfaces...
December 1, 2018: Cell
Saby George, Antonios Papanicolau-Sengos, Felicia L Lenzo, Jeffrey M Conroy, Mary Nesline, Sarabjot Pabla, Sean T Glenn, Blake Burgher, Jonathan Andreas, Vincent Giamo, Moachun Qin, Yirong Wang, Lorenzo Galluzzi, Carl Morrison
We report the immunological profile of a patient with upper-tract urothelial carcinoma experiencing stable disease on pembrolizumab for 20 months. The tumor exhibited extensive infiltration by CD8+ cytotoxic T lymphocytes, low-to-moderate mutational burden, no PD-L1 staining by commercially available immunohistochemical assays, but amplification of CD274 (coding for PD-L1) and/or PDCD1LG2 (encoding PD-L2) by fluorescence in situ hybridization. RNA-seq revealed multiple biomarkers of an ongoing immune response and compensatory immune evasion, including moderate PD-L1 levels coupled with robust PD-L2 expression...
2018: Oncoimmunology
Steven T Pittenger, Victoria L Schaal, Dalia Moore, Rahul S Guda, Sneh Koul, Sowmya V Yelamanchili, Rick A Bevins, Gurudutt Pendyala
Previous research has established sex differences associated with nicotine intake, however a significant gap in knowledge remains regarding the molecular mechanisms that govern these differences at the transcriptional level. One critical regulator of transcription are microRNAs (miRNAs). miRNAs are a family of non-coding RNAs that regulate an array of important biological functions altered in several disease states, including neuroadaptive changes within the brain associated with drug dependence. We examined the prefrontal cortex (PFC) from male and female Sprague-Dawley rats following self-administration (22 days) of nicotine or yoked saline controls using next generation RNA-Sequencing (RNA-Seq) technology and found an array of miRNAs to be significantly and differentially regulated by nicotine self-administration...
November 30, 2018: Scientific Reports
Ching-Ching Yeh, Jun-Liang Luo, Nam Nhut Phan, Yi-Chun Cheng, Lu-Ping Chow, Mong-Hsun Tsai, Eric Y Chuang, Liang-Chuan Lai
Hypoxia plays a crucial role in the aggressiveness of solid tumors by driving multiple signaling pathways. Recently, long non-coding RNA (lncRNA) has been reported to promote or inhibit tumor aggressiveness by regulating gene expression. Previous studies in our laboratory found that the lncRNA NDRG1-OT1 is significantly up-regulated under hypoxia and inhibits its target gene NDRG1 at both the mRNA and protein levels. At the protein level, NDRG1-OT1 increases NDRG1 degradation via ubiquitin-mediated proteolysis...
November 30, 2018: RNA Biology
Chen Zhang, Wei Wu, Honglan Zhu, Xiaoming Yu, Yinli Zhang, Xue Ye, Hongyan Cheng, Ruiqiong Ma, Heng Cui, Jianjun Luo, Jing Guan, Xiaohong Chang
Endometriosis (EM) is a mysterious and complicated disease that has been found to be multifactorial. Recent studies demonstrated that long noncoding RNAs (lncRNAs) play an important role in the pathogenesis of EM. However, the functional and biological mechanisms of lncRNAs in EM remain unknown. Here, we performed microarray analyses to compare the lncRNA expression profiles of 4 paired ectopic endometrial (EC) tissues and eutopic endometrial (EU) tissues from patients with ovarian EM. A novel lncRNA, CCDC144NL-AS1, was identified as being potentially functional...
November 28, 2018: Biology of Reproduction
Elahe Seyed Hosseini, Marziyeh Alizadeh Zarei, Sadegh Babashah, Roohollah Nakhaei Sistani, Majid Sadeghizadeh, Hamad Haddad Kashani, Javad Amini Mahabadi, Fatemeh Izadpanah, Mohhamad Ali Atlasi, Hossein Nikzad
Drug resistance remains a major challenge in the treatment of patients with ovarian cancer. Therefore, the development of new anticancer drugs is a clinical priority to develop more effective therapies. New approaches to improve clinical outcomes and limit the toxicity of anticancer drugs focus on chemoprevention. The aim of this study was to determine the effects of dendrosomal nanocurcumin (DNC) and oxaliplatin (Oxa) and their combination on cell death and apoptosis induction in human ovarian carcinoma cell lines analyzed by MTT assay and flow cytometry, respectively...
November 26, 2018: Cell Biology and Toxicology
Madhusudhana R Janga, Devendra Pandeya, LeAnne M Campbell, Kranti Konganti, Stephany Toinga Villafuerte, Lorraine Puckhaber, Alan Pepper, Robert D Stipanovic, Jodi A Scheffler, Keerti S Rathore
In seeds and other parts of cultivated, tetraploid cotton (Gossypium hirsutum L.), multicellular groups of cells lysigenously form dark glands containing toxic terpenoids such as gossypol that defend the plant against pests and pathogens. Using RNA-seq analysis of embryos from near-isogenic glanded (Gl2 Gl2 Gl3 Gl3 ) versus glandless (gl2 gl2 gl3 gl3 ) plants, we identified 33 genes that expressed exclusively or at higher levels in embryos just prior to gland formation in glanded plants. Virus Induced Gene Silencing against three gene pairs led to significant reductions in the number of glands in the leaves, and significantly lower levels of gossypol and related terpenoids...
November 22, 2018: Plant Biotechnology Journal
S John Liu, Daniel A Lim
Long non-coding RNAs (lncRNAs) have emerged as important regulators of cell biology. The mechanisms by which lncRNAs function are likely numerous, and most are poorly understood. Currently, the mechanisms of functional lncRNAs include those that directly involve the lncRNA transcript, the process of their own transcription and splicing, and even underlying transcriptional regulatory elements within the genomic DNA that encodes the lncRNA As our understanding of lncRNA biology evolves, so have the methods that are utilized to elucidate their functions...
November 21, 2018: EMBO Reports
Mingming Chen, Xin Li, Xiaojuan Zhang, Yan Li, Junxing Zhang, Minhui Liu, Linlin Zhang, Xiangbin Ding, Xinfeng Liu, Hong Guo
Accumulating evidence suggests that long non-coding RNAs (lncRNAs) play a crucial role in regulating skeletal muscle myogenesis, a highly coordinated multistep biological process. However, most studies of lncRNAs have focused on humans, mouse, and other model animals. In this study, we identified a novel lncRNA, named lncKBTBD10, located in the nucleus and involved in the proliferation and differentiation of bovine skeletal muscle satellite cells. Prediction of coding potential and in vitro translation system illustrated that lncKBTBD10 has no encoding capability...
November 21, 2018: In Vitro Cellular & Developmental Biology. Animal
Jared P May, Xuefeng Yuan, Erika Sawicki, Anne E Simon
Nonsense-mediated decay (NMD) is a host RNA control pathway that removes aberrant transcripts with long 3' untranslated regions (UTRs) due to premature termination codons (PTCs) that arise through mutation or defective splicing. To maximize coding potential, RNA viruses often contain internally located stop codons that should also be prime targets for NMD. Using an agroinfiltration-based NMD assay in Nicotiana benthamiana, we identified two segments conferring NMD-resistance in the carmovirus Turnip crinkle virus (TCV) genome...
November 19, 2018: PLoS Pathogens
Yingshan Han, Thibault Mesplède
The Zika virus (ZIKV) infection results in severe neurological complications and has emerged as a threat to public health worldwide. No drugs or vaccines are available for use in the clinic and the need for novel and effective therapeutic agents is urgent. Areas covered: This review describes the latest progress of antiviral development for the treatment of ZIKV infection; it primarily focuses on the literature describing 20 potential anti-ZIKV drugs/agents currently being tested in vivo or in clinical trials...
December 2018: Expert Opinion on Investigational Drugs
Jussi Hepojoki, Satu Hepojoki, Teemu Smura, Leonóra Szirovicza, Eva Dervas, Barbara Prähauser, Lisbeth Nufer, Elisabeth M Schraner, Olli Vapalahti, Anja Kipar, Udo Hetzel
The family Arenaviridae comprises three genera, Mammarenavirus, Reptarenavirus and the most recently added Hartmanivirus. Arenaviruses have a bisegmented genome with ambisense coding strategy. For mammarenaviruses and reptarenaviruses the L segment encodes the Z protein (ZP) and the RNA-dependent RNA polymerase, and the S segment encodes the glycoprotein precursor and the nucleoprotein. Herein we report the full length genome and characterization of Haartman Institute snake virus-1 (HISV-1), the putative type species of hartmaniviruses...
November 2018: PLoS Pathogens
Hui Peng, Yi Zheng, Zhixun Zhao, Tao Liu, Jinyan Li
Motivation: CRISPR/Cas9 is driving a broad range of innovative applications from basic biology to biotechnology and medicine. One of its current issues is the effect of off-target editing that should be critically resolved and should be completely avoided in the ideal use of this system. Results: We developed an ensemble learning method to detect the off-target sites of a single guide RNA (sgRNA) from its thousands of genome-wide candidates. Nucleotide mismatches between on-target and off-target sites have been studied recently...
September 1, 2018: Bioinformatics
Kirsten Bentley, Jonathan P Cook, Andrew K Tuplin, David J Evans
The hepatitis C virus RNA genome possesses a variety of conserved structural elements, in both coding and non-coding regions, that are important for viral replication. These elements are known or predicted to modulate key life cycle events, such as translation and genome replication, some involving conformational changes induced by long-range RNA-RNA interactions. One such element is SLVI, a stem-loop (SL) structure located towards the 5' end of the core protein-coding region. This element forms an alternative RNA-RNA interaction with complementary sequences in the 5' untranslated regions that are independently involved in the binding of the cellular microRNA 122 (miR122)...
2018: PeerJ
Svetlana Vakkilainen, Riikka Mäkitie, Paula Klemetti, Helena Valta, Mervi Taskinen, Eystein Sverre Husebye, Outi Mäkitie
Background: Mutations in RMRP , encoding a non-coding RNA molecule, underlie cartilage-hair hypoplasia (CHH), a syndromic immunodeficiency with multiple pathogenetic mechanisms and variable phenotype. Allergy and asthma have been reported in the CHH population and some patients suffer from autoimmune (AI) diseases. Objective: We explored AI and allergic manifestations in a large cohort of Finnish patients with CHH and correlated clinical features with laboratory parameters and autoantibodies. Methods: We collected clinical and laboratory data from patient interviews and hospital records...
2018: Frontiers in Immunology
Patrick Lypaczewski, Johanna Hoshizaki, Wen-Wei Zhang, Laura-Isobel McCall, John Torcivia-Rodriguez, Vahan Simonyan, Amanpreet Kaur, Ken Dewar, Greg Matlashewski
Leishmania donovani is responsible for visceral leishmaniasis, a neglected and lethal parasitic disease with limited treatment options and no vaccine. The study of L. donovani has been hindered by the lack of a high-quality reference genome and this can impact experimental outcomes including the identification of virulence genes, drug targets and vaccine development. We therefore generated a complete genome assembly by deep sequencing using a combination of second generation (Illumina) and third generation (PacBio) sequencing technologies...
November 8, 2018: Scientific Reports
Zhaojing Chen, Michael G Bemben, Debra A Bemben
MicroRNAs (miRNAs) are short, non-coding RNA molecules that fine tune posttranscriptional protein expression. Aging is accompanied by progressive declines in muscle mass and strength, and in bone mineral density (BMD). Although miRNAs in pathology have been extensively studied, the role of circulating miRNAs (c-miRNAs) in osteoporosis and sarcopenia has to date not been well understood. The purpose of this study was to examine the difference in bone and muscle specific c-miRNAs in postmenopausal women based on their bone and muscle status, and to determine the associations between these specific c-miRNAs and muscle and bone variables...
November 5, 2018: Bone
Jinglin Li, Xingming Jiang, Zhenglong Li, Lining Huang, Yuanshi Zhou, Yueping Liu, Yunfu Cui
LncRNAs are a group of noncoding RNAs that are >200 nucleotides in length. These RNAs have no significant protein-coding potential due to the lack of obvious open reading frames. To date, accumulating evidence has demonstrated that dysregulation of lncRNAs exhibits indispensable roles in the pathological processes of human cancers. These RNAs function as either oncogenes or tumor suppressor genes to regulate proliferation, migration and invasion of cancer cells. GHET1, a prominent oncogenic lncRNA, is highly expressed in diverse malignancies...
November 3, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
J T Guidry, J E Myers, M Bienkowska-Haba, W K Songock, X Ma, M Shi, C O Nathan, J M Bodily, M J Sapp, R S Scott
Epstein-Barr virus (EBV) is implicated in the pathogenesis of human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OSCC). EBV-associated cancers harbor a latent EBV infection characterized by a lack of viral replication and the expression of viral oncogenes. Cellular changes promoted by HPV are comparable to those shown to facilitate EBV latency, though whether HPV-positive cells support a latent EBV infection has not been demonstrated. Using a model of direct EBV infection into HPV16-immortalized tonsillar cells grown in organotypic raft culture, we showed robust EBV replication in HPV-negative rafts but little to no replication in HPV-immortalized rafts...
October 31, 2018: Journal of Virology
Ying Li, Yu-Dong Liu, Shi-Ling Chen, Xin Chen, De-Sheng Ye, Xing-Yu Zhou, Jing Zhe, Jun Zhang
STUDY QUESTION: Is there a specific mechanism underlying the association between lung adenocarcinoma transcript 1 (MALAT1) and endometriosis-related infertility? SUMMARY ANSWER: The down-regulation of MALAT1 in endometriosis granulosa cells (GCs) may have an adverse effect on the growth and development of oocytes by inhibiting GC proliferation, due to cell cycle-dependent mechanisms that enhance P21 expression through activation of the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) pathway...
October 27, 2018: Molecular Human Reproduction
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