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small RNA sequencing

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https://www.readbyqxmd.com/read/28445988/specific-up-regulation-of-p21-by-a-small-active-rna-sequence-suppresses-human-colorectal-cancer-growth
#1
Lu-Lu Wang, Hui-Hui Guo, Yun Zhan, Chen-Lin Feng, Shuai Huang, Yan-Xing Han, Wen-Sheng Zheng, Jian-Dong Jiang
The double stranded small active RNA (saRNA)- p21-saRNA-322 inhibits tumor growth by stimulating the p21 gene expression. We focused our research of p21-saRNA-322 on colorectal cancer because 1) p21 down-regulation is a signature abnormality of the cancer, and 2) colorectal cancer might be a suitable target for in situ p21-saRNA-322 delivery. The goal of the present study is to learn the activity of p21-saRNA-322 in colorectal cancer. Three human colorectal cancer cell lines, HCT-116, HCT-116 (p53-/-) and HT-29 were transfected with the p21-saRNA-322...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445987/context-dependent-mir-204-and-mir-211-affect-the-biological-properties-of-amelanotic-and-melanotic-melanoma-cells
#2
Marianna Vitiello, Andrea Tuccoli, Romina D'Aurizio, Samanta Sarti, Laura Giannecchini, Simone Lubrano, Andrea Marranci, Monica Evangelista, Silvia Peppicelli, Chiara Ippolito, Ivana Barravecchia, Elena Guzzolino, Valentina Montagnani, Michael Gowen, Elisa Mercoledi, Alberto Mercatanti, Laura Comelli, Salvatore Gurrieri, Lawrence W Wu, Omotayo Ope, Keith Flaherty, Genevieve M Boland, Marc R Hammond, Lawrence Kwong, Mario Chiariello, Barbara Stecca, Gao Zhang, Alessandra Salvetti, Debora Angeloni, Letizia Pitto, Lido Calorini, Giovanna Chiorino, Marco Pellegrini, Meenhard Herlyn, Iman Osman, Laura Poliseno
Despite increasing amounts of experimental evidence depicting the involvement of non-coding RNAs in cancer, the study of BRAFV600E-regulated genes has thus far focused mainly on protein-coding ones. Here, we identify and study the microRNAs that BRAFV600E regulates through the ERK pathway.By performing small RNA sequencing on A375 melanoma cells and a vemurafenib-resistant clone that was taken as negative control, we discover miR-204 and miR-211 as the miRNAs most induced by vemurafenib. We also demonstrate that, although belonging to the same family, these two miRNAs have distinctive features...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28444389/smithrnas-could-mitochondria-bend-nuclear-regulation
#3
Andrea Pozzi, Federico Plazzi, Liliana Milani, Fabrizio Ghiselli, Marco Passamonti
Typically, animal mitochondria have very compact genomes, with few short intergenic regions, and no introns. Hence, it may seem that there is little space for unknown functions in mitochondrial DNA (mtDNA). However, mtDNA can also operate through RNA interference, as small non coding RNAs (sncRNAs) produced by mtDNA have already been proposed for humans. We sequenced sncRNA libraries from isolated mitochondria of Ruditapes philippinarum (Mollusca Bivalvia) gonads, a species with doubly uniparental inheritance of mitochondria (DUI), and identified several putative sncRNAs of mitochondrial origin...
April 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28443131/a-bioinformatics-based-alternative-mrna-splicing-code-that-may-explain-some-disease-mutations-is-conserved-in-animals
#4
Wen Qu, Pablo Cingolani, Barry R Zeeberg, Douglas M Ruden
Deep sequencing of cDNAs made from spliced mRNAs indicates that most coding genes in many animals and plants have pre-mRNA transcripts that are alternatively spliced. In pre-mRNAs, in addition to invariant exons that are present in almost all mature mRNA products, there are at least 6 additional types of exons, such as exons from alternative promoters or with alternative polyA sites, mutually exclusive exons, skipped exons, or exons with alternative 5' or 3' splice sites. Our bioinformatics-based hypothesis is that, in analogy to the genetic code, there is an "alternative-splicing code" in introns and flanking exon sequences, analogous to the genetic code, that directs alternative splicing of many of the 36 types of introns...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28442386/arginine-deiminase-pathway-provides-atp-and-boosts-growth-of-the-gas-fermenting-acetogen-clostridium-autoethanogenum
#5
Kaspar Valgepea, Kim Q Loi, James B Behrendorff, Renato de S P Lemgruber, Manuel Plan, Mark P Hodson, Michael Köpke, Lars K Nielsen, Esteban Marcellin
Acetogens are attractive organisms for the production of chemicals and fuels from inexpensive and non-food feedstocks such as syngas (CO, CO2 and H2). Expanding their product spectrum beyond native compounds is dictated by energetics, particularly ATP availability. Acetogens have evolved sophisticated strategies to conserve energy from reduction potential differences between major redox couples, however, this coupling is sensitive to small changes in thermodynamic equilibria. To accelerate the development of strains for energy-intensive products from gases, we used a genome-scale metabolic model (GEM) to explore alternative ATP-generating pathways in the gas-fermenting acetogen Clostridium autoethanogenum...
April 22, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28441451/two-featured-series-of-rrna-derived-rna-fragments-rrfs-constitute-a-novel-class-of-small-rnas
#6
Ze Chen, Yu Sun, Xiaojun Yang, Zhenfeng Wu, Kaifei Guo, Xiaoran Niu, Qingsong Wang, Jishou Ruan, Wenjun Bu, Shan Gao
In this study, we reported two featured series of rRNA-derived RNA fragments (rRFs) from the small RNA sequencing (sRNA-seq) data of Amblyomma testudinarium using the Illunima platform. Two series of rRFs (rRF5 and rRF3) were precisely aligned to the 5' and 3' ends of the 5.8S and 28S rRNA gene. The rRF5 and rRF3 series were significantly more highly expressed than the rRFs located in the body of the rRNA genes. These series contained perfectly aligned reads, the lengths of which varied progressively with 1-bp differences...
2017: PloS One
https://www.readbyqxmd.com/read/28441426/identification-of-genes-associated-with-dissociation-of-cognitive-performance-and-neuropathological-burden-multistep-analysis-of-genetic-epigenetic-and-transcriptional-data
#7
Charles C White, Hyun-Sik Yang, Lei Yu, Lori B Chibnik, Robert J Dawe, Jingyun Yang, Hans-Ulrich Klein, Daniel Felsky, Alfredo Ramos-Miguel, Konstantinos Arfanakis, William G Honer, Reisa A Sperling, Julie A Schneider, David A Bennett, Philip L De Jager
INTRODUCTION: The molecular underpinnings of the dissociation of cognitive performance and neuropathological burden are poorly understood, and there are currently no known genetic or epigenetic determinants of the dissociation. METHODS AND FINDINGS: "Residual cognition" was quantified by regressing out the effects of cerebral pathologies and demographic characteristics on global cognitive performance proximate to death. To identify genes influencing residual cognition, we leveraged neuropathological, genetic, epigenetic, and transcriptional data available for deceased participants of the Religious Orders Study (n = 492) and the Rush Memory and Aging Project (n = 487)...
April 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28439835/the-uea-small-rna-workbench-a-suite-of-computational-tools-for-small-rna-analysis
#8
Irina Mohorianu, Matthew Benedict Stocks, Christopher Steven Applegate, Leighton Folkes, Vincent Moulton
RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439833/srnatoolboxvm-small-rna-analysis-in-a-virtual-machine
#9
Cristina Gómez-Martín, Ricardo Lebrón, Antonio Rueda, José L Oliver, Michael Hackenberg
High-throughput sequencing (HTS) data for small RNAs (noncoding RNA molecules that are 20-250 nucleotides in length) can now be routinely generated by minimally equipped wet laboratories; however, the bottleneck in HTS-based research has shifted now to the analysis of such huge amount of data. One of the reasons is that many analysis types require a Linux environment but computers, system administrators, and bioinformaticians suppose additional costs that often cannot be afforded by small to mid-sized groups or laboratories...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439831/predicting-functional-microrna-mrna-interactions
#10
Zixing Wang, Yin Liu
MicroRNAs (miRNAs) are small RNA molecules that play key regulatory roles in general biological processes and disease pathogenesis. These small RNA molecules interact with their target mRNAs to induce mRNA degradation and/or inhibit the translation of mRNAs into proteins. Therefore, identifying miRNA targets is an essential step to fully understand the regulatory effects of miRNAs. Here, we describe a regularized regression approach that integrates the sequence information with the miRNA and mRNA expression profiles for detecting miRNA targets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439825/small-rna-profiling-by-next-generation-sequencing-using-high-definition-adapters
#11
Martina Billmeier, Ping Xu
Small RNAs (sRNAs) as key regulators of gene expression play fundamental roles in many biological processes. Next-generation sequencing (NGS) has become an important tool for sRNA discovery and profiling. However, NGS data often show bias for or against certain sequences which is mainly caused by adapter oligonucleotides that are ligated to sRNAs more or less efficiently by RNA ligases. In order to reduce ligation bias, High-definition (HD) adapters for the Illumina sequencing platform were developed. However, a large amount of direct 5' and 3' adapter ligation products are often produced when the current commercially available kits are used for cloning with HD adapters...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439823/high-throughput-rt-qpcr-for-the-analysis-of-circulating-micrornas
#12
Geok Wee Tan, Lu Ping Tan
Reverse transcription followed by real-time or quantitative polymerase chain reaction (RT-qPCR) is the gold standard for validation of results from transcriptomic profiling studies such as microarray and RNA sequencing. The current need for most studies, especially biomarker studies, is to evaluate the expression levels or fold changes of many transcripts in a large number of samples. With conventional low to medium throughput qPCR platforms, many qPCR plates would have to be run and a significant amount of RNA input per sample will be required to complete the experiments...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439397/transcriptomic-analysis-of-maternally-provisioned-cues-for-phenotypic-plasticity-in-the-annual-killifish-austrofundulus-limnaeus
#13
Amie L Romney, Jason E Podrabsky
BACKGROUND: Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifish Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause...
2017: EvoDevo
https://www.readbyqxmd.com/read/28438123/small-rna-sequencing-reveals-a-role-for-sugarcane-mirnas-and-their-targets-in-response-to-sporisorium-scitamineum-infection
#14
Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo, Youxiong Que
BACKGROUND: Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The present study was the first to use two sugarcane genotypes, YA05-179 (smut-resistant) and ROC22 (smut-susceptible), to identify differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing. RESULTS: The predicted target gene number corresponding to known differentially expressed miRNAs in YA05-179 was less than that in ROC22, however most of them were in common...
April 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28437139/protection-against-common-bean-rust-conferred-by-a-gene-silencing-method
#15
Bret Cooper, Kimberly B Campbell
Rust disease of the dry bean plant, Phaseolus vulgaris, is caused by the fungus Uromyces appendiculatus. The fungus acquires its nutrients and energy from bean leaves using a specialized cell structure, the haustorium, through which it secretes effector proteins that contribute to pathogenicity by defeating the plant immune system. Candidate effectors have been identified by DNA sequencing and motif analysis, and some candidates have been observed in infected leaves by mass spectrometry. To assess their roles in pathogenicity, we have inserted small fragments of genes for five candidates into bean pod mottle virus...
April 24, 2017: Phytopathology
https://www.readbyqxmd.com/read/28436950/mre11-stability-is-regulated-by-ck2-dependent-interaction-with-r2tp-complex
#16
P von Morgen, K Burdova, T G Flower, N J O'Reilly, S J Boulton, S J Smerdon, L Macurek, Z Hořejší
The MRN (MRE11-RAD50-NBS1) complex is essential for repair of DNA double-strand breaks and stalled replication forks. Mutations of the MRN complex subunit MRE11 cause the hereditary cancer-susceptibility disease ataxia-telangiectasia-like disorder (ATLD). Here we show that MRE11 directly interacts with PIH1D1, a subunit of heat-shock protein 90 cochaperone R2TP complex, which is required for the assembly of large protein complexes, such as RNA polymerase II, small nucleolar ribonucleoproteins and mammalian target of rapamycin complex 1...
April 24, 2017: Oncogene
https://www.readbyqxmd.com/read/28435243/peripheral-leukocyte-micrornas-as-novel-biomarkers-for-copd
#17
Ruiying Wang, Jianying Xu, Hu Liu, Zhiping Zhao
COPD is a multifactorial disease caused by environmental determinants as well as genetic risk factors. The prevalence and mortality of COPD continue to increase, and underdiagnosis of COPD remains a critical issue. Previous reports investigated promising microRNAs (miRNAs) to reveal the molecular mechanism for the development of COPD; however, diagnostic and therapeutic markers for COPD have not yet been found. For this study, 20 representative COPD patients were separated into four groups based on increasing severity (A, B, C, and D) and compared to six healthy controls...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/28433608/toward-biotechnology-in-space-high-throughput-instruments-for-in-situ-biological-research-beyond-earth
#18
REVIEW
Fathi Karouia, Kianoosh Peyvan, Andrew Pohorille
Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites...
April 19, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28433417/mechanistic-insights-into-epigenetic-modulation-of-ethanol-consumption
#19
Igor Ponomarev, Claire E Stelly, Hitoshi Morikawa, Yuri A Blednov, R Dayne Mayfield, R Adron Harris
There is growing evidence that small-molecule inhibitors of epigenetic modulators, such as histone deacetylases (HDAC) and DNA methyltransferases (DNMT), can reduce voluntary ethanol consumption in animal models, but molecular and cellular processes underlying this behavioral effect are poorly understood. We used C57BL/6J male mice to investigate the effects of two FDA-approved drugs, decitabine (a DNMT inhibitor) and SAHA (an HDAC inhibitor), on ethanol consumption using two tests: binge-like drinking in the dark (DID) and chronic intermittent every other day (EOD) drinking...
March 12, 2017: Alcohol
https://www.readbyqxmd.com/read/28433053/the-envelope-proteins-of-the-bunyavirales
#20
Pablo Guardado-Calvo, Félix A Rey
The Bunyavirales Order encompasses nine families of enveloped viruses containing a single-stranded negative-sense RNA genome divided into three segments. The small (S) and large (L) segments encode proteins participating in genome replication in the infected cell cytoplasm. The middle (M) segment encodes the viral glycoproteins Gn and Gc, which are derived from a precursor polyprotein by host cell proteases. Entry studies are available only for a few viruses in the Order, and in each case they were shown to enter cells via receptor-mediated endocytosis...
2017: Advances in Virus Research
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