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Mozhgan Abasi, Zahra Bazi, Samira Mohammadi-Yeganeh, Masoud Soleimani, Vahid Haghpanah, Nosratollah Zargami, Hossein Ghanbarian
The small nuclear noncoding RNA (snRNA) 7SK is a highly conserved noncoding RNA of 331 nucleotides in animals, which is present in a nuclear ribonucleoprotein complex with proteins such as methylphosphate capping enzyme (MePCE), hexamethylene bisacetamide-inducible proteins 1 and 2 (HEXIM1 and HEXIM2) and La-related protein 7 (Larp7). Regulating the activity of the positive transcription elongation factor b (P-TEFb) is the key function of 7SK noncoding RNA. Recently, we have shown that 7SK snRNA over-expression reduces human embryonic kidney 293T cell line viability...
November 2016: Medical Oncology
Yolande F M Ramos, Ingrid Meulenbelt
PURPOSE OF REVIEW: The purpose of this review is to provide an update of recent advances in the established role of different layers of epigenetic control mechanism that are used by joint cells to ensure tissue homeostasis and cope with changing microenvironment (e.g. ageing or disease). RECENT FINDINGS: New studies have further strengthened the evidence that joint tissue cells highly dependent on epigenetic control mechanisms, such as methylation at CpG-sites, noncoding RNAs and histone modifications to assure phenotypic plasticity and respective tissue homeostasis...
October 5, 2016: Current Opinion in Rheumatology
Tao Shi, Kun Wang, Pingfang Yang
microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNAs in eukaryotes. However, under which circumstances different miRNAs/miRNA families exhibit different evolutionary trajectories in plants remains unclear. In this study, we sequenced the small RNAs and degradome from a basal eudicot, sacred lotus (Nelumbo nucifera or lotus), to identify miRNAs and their targets. Combining with public miRNAs, we predicted 57 pre-eudicot miRNA families from different evolutionary stages. We found that miRNA families featuring older age, higher copy and target number tend to show lower propensity for miRNA family loss (PGL) and stronger signature of purifying selection during divergence of temperate and tropical lotus...
October 15, 2016: Plant Journal: for Cell and Molecular Biology
Wei Lan, Min Li, Kaijie Zhao, Jin Liu, Fang-Xiang Wu, Yi Pan, Jianxin Wang
MOTIVATION: Increasing evidences have demonstrated that long noncoding RNAs (lncRNAs) play important roles in many human diseases. Therefore, predicting novel lncRNA-disease associations would contribute to dissect the complex mechanisms of disease pathogenesis. Some computational methods have been developed to infer lncRNA-disease associations. However, most of these methods infer lncRNA-disease associations only based on single data resource. RESULTS: In this paper, we propose a new computational method to predict lncRNA-disease associations by integrating multiple biological data resources...
October 14, 2016: Bioinformatics
Mark V Pinti, Quincy A Hathaway, John M Hollander
Heart failure (HF) is an endpoint resulting from a number of disease states. The prognosis for HF patients is poor with survival rates precipitously low. Energy metabolism is centrally linked to the development of HF and it involves the proteomic remodeling of numerous pathways, many of which are targeted to the mitochondrion. MicroRNA (miRNA) are noncoding RNAs that influence post-transcriptional gene regulation. MiRNA have garnered considerable attention for their ability to orchestrate changes to the transcriptome and ultimately the proteome, during HF...
October 14, 2016: American Journal of Physiology. Heart and Circulatory Physiology
Zhen-Hua Chen, Wen-Tao Wang, Wei Huang, Ke Fang, Yu-Meng Sun, Shu-Rong Liu, Xue-Qun Luo, Yue-Qin Chen
Increasing evidence has indicated that long noncoding RNAs (lncRNAs) are of great importance in different cell contexts. However, only a very small number of lncRNAs have been experimentally validated and functionally annotated during human hematopoiesis. Here, we report an lncRNA, HOTAIRM1, which is associated with myeloid differentiation and has pivotal roles in the degradation of oncoprotein PML-RARA and in myeloid cell differentiation by regulating autophagy pathways. We first revealed that HOTAIRM1 has different variants that are expressed at different levels in cells and that the expression pattern of HOTAIRM1 is closely related to that of the PML-RARA oncoprotein in acute promyelocytic leukemia (APL) patients...
October 14, 2016: Cell Death and Differentiation
E D Rosen
Insulin resistance is one of the defining features of type 2 diabetes and the metabolic syndrome and accompanies many other clinical conditions, ranging from obesity to lipodystrophy to glucocorticoid excess. Extraordinary efforts have gone into defining the mechanisms that underlie insulin resistance, with most attention focused on altered signalling as well as mitochondrial and endoplasmic reticulum stress. Here, nuclear mechanisms of insulin resistance, including transcriptional and epigenomic effects, will be discussed...
October 14, 2016: Journal of Internal Medicine
Pengmian Feng, Jidong Zhang, Hua Tang, Wei Chen, Hao Lin
Noncoding RNAs (ncRNAs) are implicated in various biological processes. Recent findings have demonstrated that the function of ncRNAs correlates with their provenance. Therefore, the recognition of ncRNAs from different organelle genomes will be helpful to understand their molecular functions. However, the weakness of experimental techniques limits the progress toward studying organellar ncRNAs and their functional relevance. As a complement of experiments, computational method provides an important choice to identify ncRNA in different organelles...
October 13, 2016: Interdisciplinary Sciences, Computational Life Sciences
Yan Zhou, Chenyan Zhao, Yabin Tian, Nan Xu, Youchun Wang
Hepatitis E virus (HEV) is a non-enveloped virus containing a single-stranded, positive-sense RNA genome of 7.2 kb, which consists of a 5' noncoding region, three open reading frames (ORFs), and a 3' noncoding region. ORF1 is diverse between genotypes and encodes the nonstructural proteins, which include the enzymes needed for virus replication. In addition to its role in virus replication, the function of ORF1 is relevant to viral adaption in cultured cells and may also relate to virus infection and HEV pathogenicity...
2016: Advances in Experimental Medicine and Biology
Yang Lin, Lijian Xu, Wei Wei, Xiaohui Zhang, Rongchao Ying
Long noncoding RNA (lncRNA) H19 has been reported to be upregulated in malignant digestive tumors, but its clinical relevance is not yet established. The meta-analysis was to investigate the association between H19 expression and pathological features of digestive system cancers. The databases of PubMed, EMBase, Web of Science, CNKI, and WanFang were searched for the related studies. A total of 478 patients from 6 studies were finally included. The meta-analysis showed that the patient group of high H19 expression had a higher risk of poorly differentiated grade, deep tumor invasion (T2 stage or more), lymph node metastasis, and advanced TNM stage than the group of low H19 expression, although there was no difference between them in terms of distant metastasis...
2016: BioMed Research International
Shamila D Alipoor, Esmaeil Mortaz, Johan Garssen, Masoud Movassaghi, Mehdi Mirsaeidi, Ian M Adcock
Exosomes are nanosized vesicles released from every cell in the body including those in the respiratory tract and lungs. They are found in most body fluids and contain a number of different biomolecules including proteins, lipids, and both mRNA and noncoding RNAs. Since they can release their contents, particularly miRNAs, to both neighboring and distal cells, they are considered important in cell-cell communication. Recent evidence has shown their possible importance in the pathogenesis of several pulmonary diseases...
2016: Mediators of Inflammation
Ruoxu Dou, Reiko Nishihara, Yin Cao, Tsuyoshi Hamada, Kosuke Mima, Atsuhiro Masuda, Yohei Masugi, Yan Shi, Mancang Gu, Wanwan Li, Annacarolina da Silva, Katsuhiko Nosho, Xuehong Zhang, Jeffrey A Meyerhardt, Edward L Giovannucci, Andrew T Chan, Charles S Fuchs, Zhi Rong Qian, Shuji Ogino
Experimental evidence suggests that the let-7 family of noncoding RNAs suppresses adaptive immune responses, contributing to immune evasion by the tumor. We hypothesized that the amount of let-7a and let-7b expression in colorectal carcinoma might be associated with limited T-lymphocyte infiltrates in the tumor microenvironment and worse clinical outcome. Utilizing the molecular pathological epidemiology resources of 795 rectal and colon cancers in two U.S.-nationwide prospective cohort studies, we measured tumor-associated let-7a and let-7b expression levels by quantitative reverse-transcription PCR, and CD3(+), CD8(+), CD45RO (PTPRC)(+), and FOXP3(+) cell densities by tumor tissue microarray immunohistochemistry and computer-assisted image analysis...
October 13, 2016: Cancer Immunology Research
Aline Koch, Dagmar Biedenkopf, Alexandra Furch, Lennart Weber, Oliver Rossbach, Eltayb Abdellatef, Lukas Linicus, Jan Johannsmeier, Lukas Jelonek, Alexander Goesmann, Vinitha Cardoza, John McMillan, Tobias Mentzel, Karl-Heinz Kogel
Meeting the increasing food and energy demands of a growing population will require the development of ground-breaking strategies that promote sustainable plant production. Host-induced gene silencing has shown great potential for controlling pest and diseases in crop plants. However, while delivery of inhibitory noncoding double-stranded (ds)RNA by transgenic expression is a promising concept, it requires the generation of transgenic crop plants which may cause substantial delay for application strategies depending on the transformability and genetic stability of the crop plant species...
October 2016: PLoS Pathogens
Winston Koh, Veronica Gonzalez, Sivaraman Natarajan, Robert Carter, Patrick O Brown, Charles Gawad
Circular RNAs comprise a poorly understood new class of noncoding RNA. In this study, we used a combination of targeted deletion, high-resolution splicing detection, and single-cell sequencing to deeply probe ASXL1 circular splicing. We found that efficient circular splicing required the canonical transcriptional start site and inverted AluSx elements. Sequencing-based interrogation of isoforms after ASXL1 overexpression identified promiscuous linear splicing between all exons, with the two most abundant non-canonical linear products skipping the exons that produced the circular isoforms...
2016: PloS One
Francesco P Marchese, Maite Huarte
No abstract text is available yet for this article.
October 13, 2016: Cell Cycle
Zofia Litwińska, Bogusław Machaliński
Chronic myeloid leukemia (CML) is a myeloproliferative disorder associated with clonal expansion of cancerous bone marrow stem cells. Tyrosine kinase inhibitors (TKIs) targeting Bcr-Abl oncoprotein are the first-line therapy for most CML patients, however, some are unresponsive to it or develop resistance. Recently, microRNAs (miRNAs) have been implicated in the progression of CML and the development of TKI resistance based on their important regulatory function in cell homeostasis. MicroRNAs are small noncoding RNAs that post-transcriptionally regulate gene expression...
October 13, 2016: Leukemia & Lymphoma
I-Cheng Ho, Shi-Chuen Miaw
IL-4 was first identified as a T cell-derived growth factor for B cells. Studies over the past several decades have markedly expanded our understanding of its cellular sources and function. In addition to T cells, IL-4 is produced by innate lymphocytes, such as NTK cells, and myeloid cells, such as basophils and mast cells. It is a signature cytokine of type 2 immune response but also has a nonimmune function. Its expression is tightly regulated at several levels, including signaling pathways, transcription factors, epigenetic modifications, microRNA, and long noncoding RNA...
2016: Advances in Experimental Medicine and Biology
Li Chen, David R Brigstock
Liver fibrosis occurs during chronic injury and represents, in large part, an exaggerated matrigenic output by hepatic stellate cells (HSCs) which become activated as a result of injury-induced signaling pathways in parenchymal and inflammatory cells (hepatocytes, macrophages, etc.). The molecular components in these pathways (e.g., CCN proteins) are modulated by transcription factors as well as by factors such as microRNAs (miRs) that act posttranscriptionally. MiRs are small (~23 nt) noncoding RNAs that regulate gene expression by specifically interacting with the 3' untranslated region (UTR) of target gene mRNA to repress translation or enhance mRNA cleavage...
2017: Methods in Molecular Biology
Fu Mei, Xu Kehui, Xu Wenming
Dicer, an RNAse III endonuclease, is critical for the biogenesis of small noncoding RNAs (microRNAs), including the biogenesis of microRNAs and small interfering RNAs, which transcriptionally and post-transcription ally regulate mRNA expression through binding to target mRNA and leading to subsequent mRNA degradation. Recent studies show that Dicer plays important roles in cell proliferation, differentiation and apoptosis. It has been attracted more and more attention in the reproductive field. In the male reproduction field, mouse model shows that Dicer is critical for the development of spermatogenic cell, sperm maturation, sperm motility and morphology...
July 20, 2016: Yi Chuan, Hereditas
Younguk Sun, Huimin Zhang, Majid Kazemian, Joseph M Troy, Christopher Seward, Xiaochen Lu, Lisa Stubbs
Mammalian genomes contain hundreds of genes transcribed by RNA Polymerase III (Pol III), encoding noncoding RNAs and especially the tRNAs specialized to carry specific amino acids to the ribosome for protein synthesis. In addition to this well-known function, tRNAs and their genes (tDNAs) serve a variety of other critical cellular functions. For example, tRNAs and other Pol III transcripts can be cleaved to yield small RNAs with potent regulatory activities. Furthermore, from yeast to mammals, active tDNAs and related "extra-TFIIIC" (ETC) loci provide the DNA scaffolds for the most ancient known mechanism of three-dimensional chromatin architecture...
October 6, 2016: Oncotarget
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