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https://www.readbyqxmd.com/read/27909684/traditional-versus-3-rna-seq-in-a-non-model-species
#1
Sophie Tandonnet, Tatiana Teixeira Torres
One limitation of the widely used RNA-seq method is that long transcripts are represented by more reads than shorter transcripts, resulting in a biased estimation of expression levels. The 3' RNA-seq method, which yields only one sequence per transcript, bypasses this limitation. Here, RNA was extracted from two samples, in which we expected to find differentially expressed genes. Each was processed by both traditional and 3' RNA-seq protocols. Both methods yielded similar differentially expressed genes and estimated expression levels in a comparable way, confirming they both represent valid tools for RNA-seq analysis...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#2
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
https://www.readbyqxmd.com/read/27909059/the-role-of-the-histone-methyltransferase-enhancer-of-zeste-homolog-2-ezh2-in-the-pathobiological-mechanisms-underlying-inflammatory-bowel-disease-ibd
#3
Olga F Sarmento, Phyllis A Svingen, Yuning Xiong, Zhifu Sun, Adebowale O Bamidele, Angela J Mathison, Thomas C Smyrk, Asha A Nair, Michelle M Gonzalez, Mary R Sagstetter, Saurabh Baheti, Dermot P B McGovern, Jessica J Friton, Konstantinos A Papadakis, Goel Gautam, Ramnik J Xavier, Raul A Urrutia, William A Faubion
Regulatory T (Treg) cells expressing the transcription factor FOXP3 play a pivotal role in maintaining immunologic self-tolerance. We and others have previously shown that EZH2 is recruited to the FOXP3 promoter and its targets in Treg cells. To further address the role for EZH2 in Treg cellular function, we have now generated mice that lack EZH2 specifically in Treg cells (EZH2ΔFOXP3+). We find that EZH2 deficiency in FOXP3+ T cells results in lethal multi-organ autoimmunity. We further demonstrate that EZH2ΔFOXP3+ T cells lack a regulatory phenotype in vitro and secrete pro-inflammatory cytokines...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27909050/notch-pathway-is-activated-via-genetic-and-epigenetic-alterations-and-is-a-therapeutic-target-in-clear-cell-renal-cancer
#4
Tushar D Bhagat, Yiyu Zou, Shizeng Huang, Jihwan Park, Matthew B Palmer, Caroline Hu, Wejuan Li, Niraj Shenoy, Orsolya Giricz, Gaurav Choudhary, Yiting Yu, Yi-An Ko, Maria C Izquierdo, Ae Seo Deok Park, Nishanth Vallumsetla, Remi Laurence, Robert Lopez, Masako Suzuki, James Pullman, Justin Kaner, Benjamin Gartrell, A Ari Hakimi, John M Greally, Bharvin Patel, Karim Benhadji, Kith Pradhan, Amit Verma, Katalin Susztak
Clear cell renal cell carcinoma (CCRCC) is an incurable malignancy in advanced stages and needs newer therapeutic targets. Transcriptomic analysis of CCRCCs and matched microdissected renal tubular controls revealed overexpression of NOTCH ligands and receptors in tumor tissues. Examination of the TCGA RNA-seq dataset also revealed widespread activation of NOTCH pathway in a large cohort of CCRCC samples. Samples with NOTCH pathway activation were also clinically distinct and were associated with better overall survival...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27908741/resolving-interspecific-relationships-within-evolutionarily-young-lineages-using-rna-seq-data-an-example-from-pedicularis-section-cyathophora-orobanchaceae
#5
Hong-Juan Wang, Wei-Tao Li, Ya-Nan Liu, Fu-Sheng Yang, Xiao-Quan Wang
Phylogenomics has shown great potential in resolving evolutionary relationships at different taxonomical levels. However, it remains controversial whether all orthologous genes under different selective pressures can be concatenated for phylogenomic reconstruction. Here we used sect. Cyathophora of Pedicularis, one of the most species-rich genera of angiosperms in the alpine and arctic regions of the Northern Hemisphere, as a model to investigate the efficiency of RNA-seq in resolving relationships of closely related congeneric species...
November 28, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27907167/infusion-advancing-discovery-of-fusion-genes-and-chimeric-transcripts-from-deep-rna-sequencing-data
#6
Konstantin Okonechnikov, Aki Imai-Matsushima, Lukas Paul, Alexander Seitz, Thomas F Meyer, Fernando Garcia-Alcalde
Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind of analysis, however, is complicated by native trans-splicing events, the splicing-induced complexity of the transcriptome and biases and artefacts introduced in experiments and data analysis. There are a number of tools available for the detection of fusions from RNA-seq data; however, certain differences in specificity and sensitivity between commonly used approaches have been found...
2016: PloS One
https://www.readbyqxmd.com/read/27907116/rnai-mediated-functional-analysis-of-bursicon-genes-related-to-adult-cuticle-formation-and-tanning-in-the-honeybee-apis-mellifera
#7
Claudinéia Pereira Costa, Moysés Elias-Neto, Tiago Falcon, Rodrigo Pires Dallacqua, Juliana Ramos Martins, Marcia Maria Gentile Bitondi
Bursicon is a heterodimeric neurohormone that acts through a G protein-coupled receptor named rickets (rk), thus inducing an increase in cAMP and the activation of tyrosine hydroxylase, the rate-limiting enzyme in the cuticular tanning pathway. In insects, the role of bursicon in the post-ecdysial tanning of the adult cuticle and wing expansion is well characterized. Here we investigated the roles of the genes encoding the bursicon subunits during the adult cuticle development in the honeybee, Apis mellifera...
2016: PloS One
https://www.readbyqxmd.com/read/27907096/global-deletion-of-tspo-does-not-affect-the-viability-and-gene-expression-profile
#8
Huaishan Wang, Kangle Zhai, Yingchao Xue, Jia Yang, Qi Yang, Yi Fu, Yu Hu, Fang Liu, Weiqing Wang, Lianxian Cui, Hui Chen, Jianmin Zhang, Wei He
Translocator Protein (18kDa, TSPO) is a mitochondrial outer membrane transmembrane protein. Its expression is elevated during inflammation and injury. However, the function of TSPO in vivo is still controversial. Here, we constructed a TSPO global knockout (KO) mouse with a Cre-LoxP system that abolished TSPO protein expression in all tissues and showed normal phenotypes in the physiological condition. The birth rates of TSPO heterozygote (Het) x Het or KO x KO breeding were consistent with Mendel's Law, suggesting a normal viability of TSPO KO mice at birth...
2016: PloS One
https://www.readbyqxmd.com/read/27907090/forkhead-box-c1-regulates-human-primary-keratinocyte-terminal-differentiation
#9
Lianghua Bin, Liehua Deng, Hengwen Yang, Leqing Zhu, Xiao Wang, Michael G Edwards, Brittany Richers, Donald Y M Leung
The epidermis serves as a critical protective barrier between the internal and external environment of the human body. Its remarkable barrier function is established through the keratinocyte (KC) terminal differentiation program. The transcription factors specifically regulating terminal differentiation remain largely unknown. Using a RNA-sequencing (RNA-seq) profiling approach, we found that forkhead box c 1 (FOXC1) was significantly up-regulated in human normal primary KC during the course of differentiation...
2016: PloS One
https://www.readbyqxmd.com/read/27907077/transcriptome-and-multivariable-data-analysis-of-corynebacterium-glutamicum-under-different-dissolved-oxygen-conditions-in-bioreactors
#10
Yang Sun, Wenwen Guo, Fen Wang, Feng Peng, Yankun Yang, Xiaofeng Dai, Xiuxia Liu, Zhonghu Bai
Dissolved oxygen (DO) is an important factor in the fermentation process of Corynebacterium glutamicum, which is a widely used aerobic microbe in bio-industry. Herein, we described RNA-seq for C. glutamicum under different DO levels (50%, 30% and 0%) in 5 L bioreactors. Multivariate data analysis (MVDA) models were used to analyze the RNA-seq and metabolism data to investigate the global effect of DO on the transcriptional distinction of the substance and energy metabolism of C. glutamicum. The results showed that there were 39 and 236 differentially expressed genes (DEGs) under the 50% and 0% DO conditions, respectively, compared to the 30% DO condition...
2016: PloS One
https://www.readbyqxmd.com/read/27906584/effects-of-the-transforming-growth-factor-beta-signaling-pathway-on-the-differentiation-of-chicken-embryonic-stem-cells-into-male-germ-cells
#11
Yani Zhang, Yingjie Wang, Qisheng Zuo, Dong Li, Wenhui Zhang, Chao Lian, Beibei Tang, Tianrong Xiao, Man Wang, Kehua Wang, Bichun Li
The objectives of the present study were to screen for key gene and signaling pathways involved in the production of male germ cells in poultry and to investigate the effects of the transforming growth factor beta (TGF-β) signaling pathway on the differentiation of chicken embryonic stem cells (ESCs) into male germ cells. The ESCs, primordial germ cells, and spermatogonial stem cells (SSCs) were sorted using flow cytometry for RNA sequencing (RNA-seq) technology. Male chicken ESCs were induced using 40 ng/mL of bone morphogenetic protein 4 (BMP4)...
November 2016: Cellular Reprogramming
https://www.readbyqxmd.com/read/27906043/exosomes-play-an-important-role-in-the-process-of-psoralen-reverse-multidrug-resistance-of-breast-cancer
#12
Xiaohong Wang, Chengfeng Xu, Yitong Hua, Leitao Sun, Kai Cheng, Zhongming Jia, Yong Han, Jianli Dong, Yuzhen Cui, Zhenlin Yang
BACKGROUND: Release of exosomes have been shown to play critical roles in drug resistance by delivering cargo. Targeting the transfer of exosomes from resistant cells to sensitive cells may be an approach to overcome some cases of drug resistance. METHOD: In this study, we investigated the potential role of exosomes in the process of psoralen reverse multidrug resistance of MCF-7/ADR cells. Exosomes were isolated by differential centrifugation of culture media from MCF-7/ADR cells (ADR/exo) and MCF-7 parental cells (S/exo)...
December 1, 2016: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/27905880/the-lair-a-resource-for-exploratory-analysis-of-published-rna-seq-data
#13
Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted, Lior Pachter
Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is difficult to use in practice. We introduce a series of tools for processing and analyzing RNA-Seq data in the Sequence Read Archive, that together have allowed us to build an easily extendable resource for analysis of data underlying published papers. Our system makes the exploration of data easily accessible and usable without technical expertise...
December 1, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27904804/mining-snps-in-extracellular-vesicular-transcriptome-of-trypanosoma-cruzi-a-step-closer-to-early-diagnosis-of-neglected-chagas-disease
#14
Pallavi Gaur, Anoop Chaturvedi
One of the newest and strongest members of intercellular communicators, the Extracellular vesicles (EVs) and their enclosed RNAs; Extracellular RNAs (exRNAs) have been acknowledged as putative biomarkers and therapeutic targets for various diseases. Although a very deep insight has not been possible into the physiology of these vesicles, they are believed to be involved in cell-to-cell communication and host-pathogen interactions. EVs might be significantly helpful in discovering biomarkers for possible target identification as well as prognostics, diagnostics and developing vaccines...
2016: PeerJ
https://www.readbyqxmd.com/read/27903987/mapping-heterogeneity-in-patient-derived-melanoma-cultures-by-single-cell-rna-seq
#15
Tobias Gerber, Edith Willscher, Henry Loeffler-Wirth, Lydia Hopp, Dirk Schadendorf, Manfred Schartl, Ulf Anderegg, Gray Camp, Barbara Treutlein, Hans Binder, Manfred Kunz
Recent technological advances in single-cell genomics make it possible to analyze cellular heterogeneity of tumor samples. Here, we applied single-cell RNA-seq to measure the transcriptomes of 307 single cells cultured from three biopsies of three different patients with a BRAF/NRAS wild type, BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant melanoma metastasis, respectively. Analysis based on self-organizing maps identified sub-populations defined by multiple gene expression modules involved in proliferation, oxidative phosphorylation, pigmentation and cellular stroma...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27903900/autoregulation-of-mbnl1-function-by-exon-1-exclusion-from-mbnl1-transcript
#16
Patryk Konieczny, Ewa Stepniak-Konieczna, Katarzyna Taylor, Łukasz J Sznajder, Krzysztof Sobczak
Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed that MBNL1 binds to MBNL1 exon 1 (e1) encoding both the major part of 5'UTR and an amino-terminal region of MBNL1 protein. We tested several hypotheses regarding the possible autoregulatory function of MBNL1 binding to its own transcript...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902792/rascaf-improving-genome-assembly-with-rna-sequencing-data
#17
Li Song, Dhruv S Shankar, Liliana Florea
Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations. Gene structure information from RNA sequences can be used to improve the completeness and contiguity of an assembly, but bioinformatics methods have been lacking. Rascaf is a highly efficient tool leveraging long-range continuity information from intron spanning RNA sequencing (RNA-seq) read pairs to detect new contig connections. It determines a heaviest path in an exon block graph that simultaneously represents a gene and the underlying contig relationships...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902686/genomic-characterization-of-metformin-hepatic-response
#18
Marcelo R Luizon, Walter L Eckalbar, Yao Wang, Stacy L Jones, Robin P Smith, Megan Laurance, Lawrence Lin, Paul J Gallins, Amy S Etheridge, Fred Wright, Yihui Zhou, Cliona Molony, Federico Innocenti, Sook Wah Yee, Kathleen M Giacomini, Nadav Ahituv
Metformin is used as a first-line therapy for type 2 diabetes (T2D) and prescribed for numerous other diseases. However, its mechanism of action in the liver has yet to be characterized in a systematic manner. To comprehensively identify genes and regulatory elements associated with metformin treatment, we carried out RNA-seq and ChIP-seq (H3K27ac, H3K27me3) on primary human hepatocytes from the same donor treated with vehicle control, metformin or metformin and compound C, an AMP-activated protein kinase (AMPK) inhibitor (allowing to identify AMPK-independent pathways)...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27901120/complete-genome-sequence-and-transcriptomic-analysis-of-a-novel-marine-strain-bacillus-weihaiensis-reveals-the-mechanism-of-brown-algae-degradation
#19
Yueming Zhu, Peng Chen, Yunjuan Bao, Yan Men, Yan Zeng, Jiangang Yang, Jibin Sun, Yuanxia Sun
A novel marine strain representing efficient degradation ability toward brown algae was isolated, identified, and assigned to Bacillus weihaiensis Alg07. The alga-associated marine bacteria promote the nutrient cycle and perform important functions in the marine ecosystem. The de novo sequencing of the B. weihaiensis Alg07 genome was carried out. Results of gene annotation and carbohydrate-active enzyme analysis showed that the strain harbored enzymes that can completely degrade alginate and laminarin, which are the specific polysaccharides of brown algae...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900601/rna-seq-expression-analysis-of-enteric-neuron-cells-with-rotenone-treatment-and-prediction-of-regulated-pathways
#20
Qiang Guan, Xijin Wang, Yanyan Jiang, Lijuan Zhao, Zhiyu Nie, Lingjing Jin
The enteric nervous system (ENS) is involved in the initiation and development of the pathological process of Parkinson's disease (PD). The effect of rotenone on the ENS may trigger the progression of PD through the central nervous system (CNS). In this study, we used RNA-sequencing (RNA-seq) analysis to examine differential expression genes (DEGs) and pathways induced by in vitro treatment of rotenone in the enteric nervous cells isolated from rats. We identified 45 up-regulated and 30 down-regulated genes...
November 30, 2016: Neurochemical Research
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