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https://www.readbyqxmd.com/read/28938616/identification-of-potential-cancer-related-pseudogenes-in-lung-adenocarcinoma-based-on-cerna-hypothesis
#1
Yunzhen Wei, Zhiqiang Chang, Cheng Wu, Yinling Zhu, Kun Li, Yan Xu
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28936668/rna-seq-data-analysis-protocol-combining-in-house-and-publicly-available-data
#2
Marc W Schmid
Comparing gene expression profiles measured in a wide range of different tissue types, at different developmental stages, or under different environmental conditions can yield valuable insights into the mechanisms of cell/tissue specification and differentiation, or identify cell/tissue-type specific responses to environmental stimuli. Critical for such comparisons is the identical processing of data from different sources. This may also include the integration of a novel data set into an existing collection of data sets (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28931675/comparative-transcriptomics-highlights-the-role-of-the-ap1-transcription-factor-in-the-host-response-to-ebolavirus
#3
James W Wynne, Shawn Todd, Victoria Boyd, Mary Tachedjian, Reuben Klein, Brian Shiell, Megan Dearnley, Alexander J McAuley, Amanda P Woon, Anthony W Purcell, Glenn A Marsh, Michelle L Baker
Ebolavirus and Marburgvirus comprise two genera of negative-sense single-stranded RNA viruses that cause severe hemorrhagic fevers in humans. Despite considerable research efforts, the molecular events following Ebola virus (EBOV) infection are poorly understood. With the view of identifying host factors that underpin EBOV pathogenesis, we compared the transcriptomes of EBOV-infected human, pig and bat kidney cells using an RNAseq approach. Despite a significant difference in viral transcription/replication between the cell lines, all cells responded to EBOV infection through a robust induction of extracellular growth factors...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28928284/functional-and-evolutionary-insights-from-the-ciona-notochord-transcriptome
#4
Wendy M Reeves, Yuye Wu, Matthew J Harder, Michael T Veeman
The notochord of the ascidian Ciona consists of only 40 cells, and is a longstanding model for studying organogenesis in a small, simple embryo. Here, we perform RNAseq on flow-sorted notochord cells from multiple stages to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression and extensively validate the results by in situ hybridization. These genes are highly enriched for Gene Ontology terms related to the extracellular matrix, cell adhesion and cytoskeleton...
September 15, 2017: Development
https://www.readbyqxmd.com/read/28927943/laser-microdissection-a-powerful-tool-for-genomics-at-cell-level
#5
REVIEW
Claudia Bevilacqua, Bertrand Ducos
Laser microdissection (LM) has become considerably democratized over the last fifteen years. Instruments have evolved to offer more powerful and efficient lasers as well as new options for sample collection and preparation. Technological evolutions have also focused on the post-microdissection analysis capabilities, opening up investigations in all disciplines of experimental and clinical biology, thanks to the advent of new high-throughput methods of genome analysis, including RNAseq and proteomics, now globally known as microgenomics, i...
September 16, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/28924186/interactome-analysis-reveals-znf804a-a-schizophrenia-risk-gene-as-a-novel-component-of-protein-translational-machinery-critical-for-embryonic-neurodevelopment
#6
Y Zhou, F Dong, T A Lanz, V Reinhart, M Li, L Liu, J Zou, H S Xi, Y Mao
Recent genome-wide association studies identified over 100 genetic loci that significantly associate with schizophrenia (SZ). A top candidate gene, ZNF804A, was robustly replicated in different populations. However, its neural functions are largely unknown. Here we show in mouse that ZFP804A, the homolog of ZNF804A, is required for normal progenitor proliferation and neuronal migration. Using a yeast two-hybrid genome-wide screen, we identified novel interacting proteins of ZNF804A. Rather than transcriptional factors, genes involved in mRNA translation are highly represented in our interactome result...
September 19, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28922848/aggressive-behavior-in-silent-subtype-iii-pituitary-adenomas-may-depend-on-suppression-of-local-immune-response-a-whole-transcriptome-analysis
#7
Timothy E Richardson, Zhong-Jian Shen, Mohammed Kanchwala, Chao Xing, Alexander Filatenkov, Ping Shang, Samuel Barnett, Zahidur Abedin, James S Malter, Jack M Raisanen, Dennis K Burns, Charles L White, Kimmo J Hatanpaa
Silent subtype III pituitary adenomas (SS-3) are clinically nonfunctional adenomas that are more aggressive in terms of invasion and risk of recurrence than their conventional null cell counterparts. We previously showed that these tumors can be distinguished by immunohistochemistry based on the identification of a markedly enlarged and fragmented Golgi apparatus. To understand the molecular correlates of differential aggressiveness, we performed whole transcriptome sequencing (RNAseq) on 4 SS-3 and 4 conventional null cell adenomas...
October 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28922759/transcriptomic-and-metabolomics-responses-to-elevated-cell-wall-invertase-activity-during-tomato-fruit-set
#8
Lei Ru, Sonia Osorio, Lu Wang, Alisdair R Fernie, John W Patrick, Yong-Ling Ruan
Fruit set is a developmental transition from ovaries to fruitlets that determines yield potential. Cell wall invertase (CWIN) is essential for fruit and seed set, but the underlying molecular basis remains elusive. We addressed this issue by using CWIN-elevated transgenic tomato, focusing on ovaries and fruitlets at 2 d before and after anthesis, respectively. RNAseq analyses revealed that ovaries and fruitlets exhibited remarkable differences in their transcriptomic responses to elevated CWIN activity. Ovaries 2 d before anthesis were far more responsive to elevated CWIN activity compared with the fruitlets...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28919887/complete-circular-genome-sequence-and-temperature-independent-adaptation-to-anaerobiosis-of-listeria-weihenstephanensis-dsm-24698
#9
Elena Ferrari, Mathias C Walter, Christopher Huptas, Siegfried Scherer, Stefanie Müller-Herbst
The aim of this study was to analyze the adaptation of the environmental Listeria weihenstephanensis DSM 24698 to anaerobiosis. The complete circular genome sequence of this species is reported and the adaptation of L. weihenstephanensis DSM 24698 to oxygen availability was investigated by global transcriptional analyses via RNAseq at 18 and 34°C. A list of operons was created based on the transcriptional data. Forty-two genes were upregulated anaerobically and 62 genes were downregulated anaerobically. The oxygen dependent gene expression of selected genes was further validated via qPCR...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28915793/the-cacao-criollo-genome-v2-0-an-improved-version-of-the-genome-for-genetic-and-functional-genomic-studies
#10
X Argout, G Martin, G Droc, O Fouet, K Labadie, E Rivals, J M Aury, C Lanaud
BACKGROUND: Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. METHODS: We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome...
September 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28904646/participation-in-a-year-long-cure-embedded-into-major-core-genetics-and-cellular-and-molecular-biology-laboratory-courses-results-in-gains-in-foundational-biological-concepts-and-experimental-design-skills-by-novice-undergraduate-researchers
#11
Marcy A Peteroy-Kelly, Matthew R Marcello, Erika Crispo, Zafir Buraei, Daniel Strahs, Marisa Isaacson, Leslie Jaworski, David Lopatto, David Zuzga
This two-year study describes the assessment of student learning gains arising from participation in a year-long curriculum consisting of a classroom undergraduate research experience (CURE) embedded into second-year, major core Genetics and Cellular and Molecular Biology (CMB) laboratory courses. For the first course in our CURE, students used micro-array or RNAseq analyses to identify genes important for environmental stress responses by Saccharomyces cerevisiae. The students were tasked with creating overexpressing mutants of their genes and designing their own original experiments to investigate the functions of those genes using the overexpression and null mutants in the second CURE course...
2017: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28902868/discovery-of-numerous-novel-small-genes-in-the-intergenic-regions-of-the-escherichia-coli-o157-h7-sakai-genome
#12
Sarah M Hücker, Zachary Ardern, Tatyana Goldberg, Andrea Schafferhans, Michael Bernhofer, Gisle Vestergaard, Chase W Nelson, Michael Schloter, Burkhard Rost, Siegfried Scherer, Klaus Neuhaus
In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value...
2017: PloS One
https://www.readbyqxmd.com/read/28902852/genome-wide-chromatin-mapping-with-size-resolution-reveals-a-dynamic-sub-nucleosomal-landscape-in-arabidopsis
#13
Daniel Antony Pass, Emily Sornay, Angela Marchbank, Margaret R Crawford, Konrad Paszkiewicz, Nicholas A Kent, James A H Murray
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28900252/profiling-of-the-metabolic-transcriptome-via-single-molecule-molecular-inversion-probes
#14
Tessa de Bitter, Carlijn van de Water, Corina van den Heuvel, Carolien Zeelen, Astrid Eijkelenboom, Bastiaan Tops, Egbert Oosterwijk, Dimitar Kolev, Peter Mulders, Mark Ter Laan, Sanne van Lith, William Leenders
Cancer-specific metabolic alterations are of high interest as therapeutic targets. These alterations vary between tumor types, and to employ metabolic targeting to its fullest potential there is a need for robust methods that identify candidate targetable metabolic pathways in individual cancers. Currently, such methods include (13)C-tracing studies and mass spectrometry/ magnetic resonance spectroscopic imaging. Due to high cost and complexity, such studies are restricted to a research setting. We here present the validation of a novel technique of metabolic profiling, based on multiplex targeted next generation sequencing of RNA with single molecule molecular inversion probes (smMIPs), designed to measure activity of and mutations in genes that encode metabolic enzymes...
September 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28890721/development-and-application-of-transcriptome-derived-microsatellites-in-actinidia-eriantha-actinidiaceae
#15
Rui Guo, Jacob B Landis, Michael J Moore, Aiping Meng, Shuguang Jian, Xiaohong Yao, Hengchang Wang
Actinidia eriantha Benth. is a diploid perennial woody vine native to China and is recognized as a valuable species for commercial kiwifruit improvement with high levels of ascorbic acid as well as having been used in traditional Chinese medicine. Due to the lack of genomic resources for the species, microsatellite markers for population genetics studies are scarce. In this study, RNASeq was conducted on fruit tissue of A. eriantha, yielding 5,678,129 reads with a total output of 3.41 Gb. De novo assembly yielded 69,783 non-redundant unigenes (41...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28889014/transcriptomic-and-morphological-analyses-of-litopenaeus-vannamei-intestinal-barrier-in-response-to-vibrio-paraheamolyticus-infection-reveals-immune-response-signatures-and-structural-disruption
#16
Cancan Qi, Lei Wang, Mei Liu, Keyong Jiang, Mengqiang Wang, Wei Zhao, Baojie Wang
The white shrimp Litopenaeus vannamei has been greatly impacted by Vibrio infection. In this study, we investigated the intestinal barrier response of L vannamei following challenge with Vibrio parahaemolyticus E1, by examining morphological changes and transcriptome expression levels. A total of 16,4420 unigenes were obtained from RNAseq data after quality control and assembly, and 4646 differentially expressed genes (DEGs) were identified following Vibrio challenge, of which 2469 unigenes were significantly up-regulated and 2177 were significantly down-regulated...
September 6, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28888037/myc-drives-overexpression-of-telomerase-rna-htr-terc-in-prostate-cancer
#17
Javier A Baena-Del Valle, Qizhi Zheng, David M Esopi, Michael Rubenstein, Gretchen K Hubbard, Maria C Moncaliano, Andrew Hruszkewycz, Ajay Vaghasia, Srinivasan Yegnasubramanian, Sarah J Wheelan, Alan K Meeker, Christopher M Heaphy, Mindy K Graham, Angelo M De Marzo
Telomerase consists of at least two essential elements, an RNA component hTR or TERC that contains the template for telomere DNA addition, and a catalytic reverse transcriptase (TERT). While expression of TERT has been considered the key rate limiting component for telomerase activity, increasing evidence suggests an important role for the regulation of TERC in telomere maintenance and perhaps other functions in human cancer. By using three orthogonal methods including RNAseq, RT-qPCR, and an analytically validated chromogenic RNA in situ hybridization assay, we report consistent overexpression of TERC in prostate cancer...
September 9, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28887464/rnaseq-revealed-the-important-gene-pathways-controlling-adaptive-mechanisms-under-waterlogged-stress-in-maize
#18
Kanika Arora, Kusuma Kumari Panda, Shikha Mittal, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta Kumar Dash, Nepolean Thirunavukkarasu
Waterlogging causes yield penalty in maize-growing countries of subtropical regions. Transcriptome analysis of the roots of a tolerant inbred HKI1105 using RNA sequencing revealed 21,364 differentially expressed genes (DEGs) under waterlogged stress condition. These 21,364 DEGs are known to regulate important pathways including energy-production, programmed cell death (PCD), aerenchyma formation, and ethylene responsiveness. High up-regulation of invertase (49-fold) and hexokinase (36-fold) in roots explained the ATP requirement in waterlogging condition...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886042/domestication-reduces-alternative-splicing-expression-variations-in-sorghum
#19
Vincent Ranwez, Audrey Serra, David Pot, Nathalie Chantret
Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession...
2017: PloS One
https://www.readbyqxmd.com/read/28881797/upregulation-of-long-noncoding-rna-hoxa-as3-promotes-tumor-progression-and-predicts-poor-prognosis-in-glioma
#20
Fan Wu, Chuanbao Zhang, Jinquan Cai, Fan Yang, Tingyu Liang, Xiaoyan Yan, Haoyuan Wang, Wen Wang, Jing Chen, Tao Jiang
Long noncoding RNAs (lncRNAs) have recently emerged as new potentially promising therapeutic targets in many cancers. However, their prognostic value and biological functions associated with glioma remain to be elucidated. Here, High-throughput RNAseq was performed to detect the expression profiles of lncRNAs in 325 human glioma tissues. It was shown that a novel lncRNA HOXA-AS3 was one of the most significantly upregulated lncRNAs in glioma tissues. Quantitative PCR further verified the increased expression of HOXA-AS3 in patient samples and glioma cell lines...
August 8, 2017: Oncotarget
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