Read by QxMD icon Read

miRNA next generation sequencing

Sheng Xu, Yumei Jiang, Ning Wang, Bing Xia, Yilong Jiang, Xiaodan Li, Zhengzhi Zhang, Yikui Li, Ren Wang
BACKGROUND: Lycoris aurea is a medicine-valuable and ornamental herb widely distributed in China. Former studied have showed that methyl jasmonate (MJ) treatment could increase the content of glanthamine-a worldwide medicine for symptomatic treatment of Alzheimer's disease in genus Lycoris plants. To explore the possible role of miRNAs in the regulation of jasmonic acid signaling pathway and uncover their potential correlations, we investigated the expression profiles of small RNAs (sRNAs) and their targets in Lycoris aurea, with MJ treatment by using next-generation deep sequencing...
October 10, 2016: BMC Genomics
Ivan Kel, Zisong Chang, Nadia Galluccio, Margherita Romeo, Stefano Beretta, Luisa Diomede, Alessandra Mezzelani, Luciano Milanesi, Christoph Dieterich, Ivan Merelli
The interpretation of genome-wide association study is difficult, as it is hard to understand how polymorphisms can affect gene regulation, in particular for trans-regulatory elements located far from their controlling gene. Using RNA or protein expression data as phenotypes, it is possible to correlate their variations with specific genotypes. This technique is usually referred to as expression Quantitative Trait Loci (eQTLs) analysis and only few packages exist for the integration of genotype patterns and expression profiles...
September 22, 2016: Molecular BioSystems
Chandni V Jain, Philip Jessmon, Brian A Kilburn, Meritxell Jodar, Edward Sendler, Stephen A Krawetz, D Randall Armant
INTRODUCTION: The growth factor HBEGF is upregulated post-transcriptionally in the low O2 environment of the human placenta during the first 10 weeks of pregnancy. We have examined the possible roles of HBEGF turnover and micro-RNA (miRNA) in its regulation by O2 in human first trimester trophoblast. METHODS: HTR-8/SVneo trophoblast cells were cultured at 2% or 20% O2. The cells were transfected with a dual luciferase reporter construct (psiCHECK-2) containing no insert (control), the HBEGF 3' untranslated region (3'UTR), or sub-regions of the 3'UTR, as well as with siRNA for DGCR8...
2016: PloS One
Ajay Kumar Dixit, Anne E Sarver, Zuobiao Yuan, John George, Usman Barlass, Hassam Cheema, Archana Sareen, Sulagna Banerjee, Vikas Dudeja, Rajinder K Dawra, Subbaya Subramanian, Ashok K Saluja
In the current study, we have characterized the global miRNA expression profile in mouse pancreatic acinar cells and during acute pancreatitis using next-generation RNA-Sequencing. We identified 324 known and 6 novel miRNAs being expressed in mouse pancreatic acinar cells. At basal state, miR-148a-3p, miR-375-3p, miR-217-5p, miR-200a-3p were among the most abundantly expressed whereas, miR-24-5p and miR-421-3p were least abundant. Treatment of acinar cells with caerulein (100 nM) and taurolithocholic acid 3-sulfate [TLC-S (250 μM)] induced numerous changes in miRNA expression profile...
September 29, 2016: American Journal of Physiology. Gastrointestinal and Liver Physiology
Thomas Tsiloulis, Joshua Pike, David Powell, Fernando J Rossello, Benedict J Canny, Ruth C R Meex, Matthew J Watt
Adipocytes are major regulators of metabolism and endurance exercise training improves adipocyte function; however, the molecular mechanisms that regulate chronic adaptive responses remain unresolved. microRNAs (miRNAs) influence adipocyte differentiation and metabolism. Accordingly, we aimed to determine whether adipocyte miRNA expression is responsive to exercise training and to identify exercise-responsive miRNAs that influence adipocyte metabolism. Next generation sequencing was used to profile miRNA expression of adipocytes that were isolated from subcutaneous abdominal (ABD) and gluteofemoral (GF) adipose tissue of overweight men before and after 6 wk of endurance exercise training...
September 28, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Maciej Pietrzak, Audrey Papp, Amanda Curtis, Samuel K Handelman, Maria Kataki, Douglas W Scharre, Grzegorz Rempala, Wolfgang Sadee
Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative disorder in the elderly. The development and progression of DLB remain unclear. In this study we used next generation sequencing to assess RNA expression profiles and cellular processes associated with DLB in the anterior cingulate cortex, a brain region affected by DLB pathology. The expression measurements were made in autopsy brain tissues from 8 DLB subjects and 10 age-matched controls using AmpliSeq technology with ion torrent sequencing...
October 28, 2016: Biochemical and Biophysical Research Communications
Jun Luo, Junying Liu, Hehe Liu, Tao Zhang, Jiwen Wang, Hua He, Chunchun Han
The bursa of Fabricius (BF) is a central humoral immune organ belonging to avian specifically. Recent studies had suggested that miRNAs were active regulators involved in the immune processes. This study was to investigate the possible differences of the BF at miRNA level between two genetically disparate duck breeds. Using Illumina next-generation sequencing, the data showed that there were 66 differentially expressed miRNAs and 28 novel miRNAs in bursa. A set of abundant miRNAs (i.e., let-7, miR-146a-5p, miR-21-5p, miR-17~92) which involved in immunity and disease were detected and the predicted target genes of the novel miRNAs were associated with duck high anti-adversity ability...
September 16, 2016: Asian-Australasian Journal of Animal Sciences
Jing Gong, Chunjie Liu, Wei Liu, Yu Xiang, Lixia Diao, An-Yuan Guo, Leng Han
RNA editing is a widespread post-transcriptional mechanism that can make a single base change on specific nucleotide sequence in an RNA transcript. RNA editing events can result in missense codon changes and modulation of alternative splicing in mRNA, and modification of regulatory RNAs and their binding sites in noncoding RNAs. Recent computational studies accurately detected more than 2 million A-to-I RNA editing sites from next-generation sequencing (NGS). However, the vast majority of these RNA editing sites have unknown functions and are in noncoding regions of the genome...
September 19, 2016: Nucleic Acids Research
Yu Kakimoto, Masayuki Tanaka, Hiroshi Kamiguchi, Eriko Ochiai, Motoki Osawa
MicroRNAs (miRNAs) are small non-coding RNAs responsible for fine-tuning of gene expression at post-transcriptional level. The alterations in miRNA expression levels profoundly affect human health and often lead to the development of severe diseases. Currently, high throughput analyses, such as microarray and deep sequencing, are performed in order to identify miRNA biomarkers, using archival patient tissue samples. MiRNAs are more robust than longer RNAs, and resistant to extreme temperatures, pH, and formalin-fixed paraffin-embedding (FFPE) process...
2016: PloS One
Barbara Tanno, Gabriele Babini, Simona Leonardi, Paola Giardullo, Ilaria De Stefano, Emanuela Pasquali, Andrea Ottolenghi, Michael J Atkinson, Anna Saran, Mariateresa Mancuso
It has historically been accepted that incorrectly repaired DNA double strand breaks (DSBs) are the principal lesions of importance regarding mutagenesis, and long-term biological effects associated with ionizing radiation. However, radiation may also cause dysregulation of epigenetic processes that can lead to altered gene function and malignant transformation, and epigenetic alterations are important causes of miRNAs dysregulation in cancer.Patched1 heterozygous (Ptch1+/-) mice, characterized by aberrant activation of the Sonic hedgehog (Shh) signaling pathway, are a well-known murine model of spontaneous and radiation-induced medulloblastoma (MB), a common pediatric brain tumor originating from neural granule cell progenitors (GCPs)...
September 10, 2016: Oncotarget
Pierre J Lyons, Louise Govaere, Nicolas Crapoulet, Kenneth B Storey, Pier Jr Morin
Significant physiological and biochemical changes are observed in freeze-tolerant insects when confronted with cold temperatures. These insects have adapted to winter by retreating into a hypometabolic state of diapause and implementing cryoprotective mechanisms that allow them to survive whole body freezing. MicroRNAs (miRNAs), a family of short ribonucleic acids, are emerging as likely molecular players underlying the process of cold adaptation. Unfortunately, the data is sparse concerning the signature of miRNAs that are modulated following cold exposure in the freeze-tolerant goldenrod gall fly Eurosta solidaginis...
September 4, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
Shiho Hoshina, Tsuyoshi Sekizuka, Michiyo Kataoka, Hideki Hasegawa, Hiromichi Hamada, Makoto Kuroda, Harutaka Katano
Exosomes are small vesicles released from cells, into which microRNAs (miRNA) are specifically sorted and accumulated. Two gamma-herpesviruses, Kaposi sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV), encode miRNAs in their genomes and express virus-encoded miRNAs in cells and exosomes. However, there is little information about the detailed distribution of virus-encoded miRNAs in cells and exosomes. In this study, we thus identified virus- and host-encoded miRNAs in exosomes released from KSHV- or EBV-infected lymphoma cell lines and compared them with intracellular miRNAs using a next-generation sequencer...
2016: PloS One
Jess Morhayim, Jeroen van de Peppel, Eric Braakman, Elwin W J C Rombouts, Mariette N D Ter Borg, Amel Dudakovic, Hideki Chiba, Bram C J van der Eerden, Marc H Raaijmakers, Andre J van Wijnen, Jan J Cornelissen, Johannes P van Leeuwen
Osteolineage cells represent one of the critical bone marrow niche components that support maintenance of hematopoietic stem and progenitor cells (HSPCs). Recent studies demonstrate that extracellular vesicles (EVs) regulate stem cell development via horizontal transfer of bioactive cargo, including microRNAs (miRNAs). Using next-generation sequencing we show that human osteoblast-derived EVs contain highly abundant miRNAs specifically enriched in EVs, including critical regulators of hematopoietic proliferation (e...
2016: Scientific Reports
Yadong Yang, Nan Ding, Xunong Dong, Xiangdong Fang
Next-generation sequencing technologies have greatly accelerated the biological and medical progression. As one of the applications, miRNA-Seq is invaluable in detecting and characterizing genome-wide miRNAs of either too high or too low abundance. Besides, it can also be used in detecting novel miRNAs. Here, we describe an ab initio analysis of an example chronic myeloid leukemia miRNA sequencing data set to quantify the global expression of miRNAs, detect differential expression and novel miRNAs, and predict target genes...
2016: Methods in Molecular Biology
Vincenzo Marotta, Concetta Sciammarella, Annamaria Al Colao, Antongiulio Faggiano
Although cancer outcome results from the interplay between genetics and environment, researchers are making a great effort for applying molecular biology in the prognostication of differentiated thyroid cancer (DTC). Nevertheless, role of molecular characterization in the prognostic setting of DTC is still nebulous. Among the most common and well-characterized genetic alterations related to DTC, including mutations of BRAF and RAS and RET rearrangements, BRAFV600E is the only showing unequivocal association with clinical outcome...
August 30, 2016: Endocrine-related Cancer
Katherine A Sanders, Miles C Benton, Rod A Lea, Vicki E Maltby, Susan Agland, Nathan Griffin, Rodney J Scott, Lotti Tajouri, Jeannette Lechner-Scott
BACKGROUND: Immunoactivation is less evident in secondary progressive MS (SPMS) compared to relapsing-remitting disease. MicroRNA (miRNA) expression is integral to the regulation of gene expression; determining their impact on immune-related cell functions, especially CD4+ T cells, during disease progression will advance our understanding of MS pathophysiology. This study aimed to compare miRNA profiles of CD4+ T cells from SPMS patients to healthy controls (HC) using whole miRNA transcriptome next-generation sequencing (NGS)...
2016: Clinical Epigenetics
Sarah Seashols-Williams, Carolyn Lewis, Chelsea Calloway, Nerissa Peace, Ariana Harrison, Christina Hayes-Nash, Samantha Fleming, Qianni Wu, Zendra E Zehner
microRNAs (miRNAs) are small noncoding RNAs that regulate cellular processes through modulation of proteins at the translational level. They tend to be highly stable as compared to other RNA species due to their small size and protection by protein and/or lipid matrices. Thus, it is likely that miRNAs, when fully evaluated, will make excellent candidates for body fluid identification. miRNA analysis of body fluids has been the subject of some recent interest in the forensic community. In this study, small RNAs were isolated from individual donations of eight forensically relevant biological fluids (blood, semen, vaginal fluid, menstrual blood, saliva, urine, feces, and perspiration) and subjected to next generation sequencing using the Illumina Hi-Seq platform...
August 25, 2016: Electrophoresis
Yuanyuan Wang, Xingyi Guo, Michael J Bray, Zhiyong Ding, Zhongming Zhao
BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer. Recent large-scale next-generation sequencing analyses reveal that PBRM1 is the second most frequently mutated gene harboring many truncated mutations and has a suspected tumor suppressor role in ccRCC. However, the biological consequences of PBRM1 somatic mutations (e.g., truncated mutations) that drive tumor progression in ccRCC remain unclear. METHODS: In this study, we proposed an integrative genomics approach to explore the functional consequences of PBRM1 truncated mutations in ccRCC by incorporating somatic mutations, mRNA expression, DNA methylation, and microRNA (miRNA) expression profiles from The Cancer Genome Atlas (TCGA)...
August 22, 2016: BMC Genomics
Jai-Hong Cheng, Ching-Jen Wang, Shi-Hao Su, Chien-Yiu Huang, Shan-Ling Hsu
Extracorporeal shockwave therapy (ESWT) has shown chondroprotective effects on the initiation of the osteoarthritis (OA) changes of the rat knee. This study evaluated 69 significant expressed profiles of microRNA (miRNA) in the articular cartilage and subchondral bone after ESWT. There were 118 target genes identified for miRNAs of interest in articular cartilage and 214 target genes in subchondral bone by next generation sequencing (NGS). In principal component analysis (PCA), the relationships of miRNA expression in bone and cartilage were improved after ESWT...
August 17, 2016: Oncotarget
Shay Ben-Shachar, Henit Yanai, Hadas Sherman Horev, Hofit Elad, Liran Baram, Ofer Issakov, Hagit Tulchinsky, Metsada Pasmanik-Chor, Noam Shomron, Iris Dotan
BACKGROUND: Gene expression alterations are associated with disease behavior in inflammatory bowel disease (IBD). microRNAs (miRNAs) are dominant in the regulation of gene expression, and may affect IBD phenotype. Our aim was to assess mucosal miRNA expression in IBD and the correlation with intestinal inflammation. METHODS: We performed a large-scale analysis of ileal mucosal miRNA. Biopsies were retrieved from patients with ileal Crohn's disease (CD), unoperated ulcerative colitis (UC) patients, UC patients after pouch surgery, and normal controls (NC)...
2016: PloS One
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"