scholarly journals Gene expression of settled and metamorphosed Orbicella faveolata during establishment of symbiosis

2017 ◽  
Author(s):  
Aubrie O'Rourke ◽  
Aki Ohdera ◽  
Shinichi Sunagawa ◽  
Erika M Diaz-Almeyda ◽  
Michael K DeSalvo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nutrient Metabolism ◽  
Transcriptomic Response ◽  
Tropical Oceans ◽  
Expression Of Genes ◽  
Expression Studies ◽  
Genome Wide ◽  
Orbicella Faveolata ◽  
Algal Symbiosis ◽  
Differential Gene

Corals rely on a symbiosis with dinoflagellate algae (Symbiodinium spp.) to thrive in nutrient poor tropical oceans. However, the coral-algal symbiosis can break down during bleaching events, potentially leading to coral death. While genome-wide expression studies have shown the genes associated with the breakdown of this partnership, the full conglomerate of genes responsible for the establishment and maintenance of a healthy symbiosis remains unknown. Results from previous studies suggested little transcriptomic change associated with the establishment of symbiosis. We examined the transcriptomic response of the coral Orbicella faveolata in the presence (symbiotic) and absence (aposymbiotic) of Symbiodinium minutum, one of its associated symbionts. 9 days post-metamorphic aposymbiotic coral polyps of O. faveolata were compared to symbiotic coral polyps and the subsequent differential gene expression between control and treatment was quantified using cDNA microarray technology. Coral polyps exhibited differential expression of genes associated with nutrient metabolism and development, providing insight into control of pathways as a result of symbiosis driving early polyp growth. Furthermore, genes associated with lysosomal fusion were also upregulated, suggesting host regulation of symbiont densities soon after infection.

scholarly journals Gene expression of settled and metamorphosed Orbicella faveolata during establishment of symbiosis

2017 ◽  
Author(s):  
Aubrie O'Rourke ◽  
Aki Ohdera ◽  
Shinichi Sunagawa ◽  
Erika M Diaz-Almeyda ◽  
Michael K DeSalvo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nutrient Metabolism ◽  
Transcriptomic Response ◽  
Tropical Oceans ◽  
Expression Of Genes ◽  
Expression Studies ◽  
Genome Wide ◽  
Orbicella Faveolata ◽  
Algal Symbiosis ◽  
Differential Gene

Corals rely on a symbiosis with dinoflagellate algae (Symbiodinium spp.) to thrive in nutrient poor tropical oceans. However, the coral-algal symbiosis can break down during bleaching events, potentially leading to coral death. While genome-wide expression studies have shown the genes associated with the breakdown of this partnership, the full conglomerate of genes responsible for the establishment and maintenance of a healthy symbiosis remains unknown. Results from previous studies suggested little transcriptomic change associated with the establishment of symbiosis. We examined the transcriptomic response of the coral Orbicella faveolata in the presence (symbiotic) and absence (aposymbiotic) of Symbiodinium minutum, one of its associated symbionts. 9 days post-metamorphic aposymbiotic coral polyps of O. faveolata were compared to symbiotic coral polyps and the subsequent differential gene expression between control and treatment was quantified using cDNA microarray technology. Coral polyps exhibited differential expression of genes associated with nutrient metabolism and development, providing insight into control of pathways as a result of symbiosis driving early polyp growth. Furthermore, genes associated with lysosomal fusion were also upregulated, suggesting host regulation of symbiont densities soon after infection.

scholarly journals RNAlater and flash freezing storage methods nonrandomly influence observed gene expression in RNAseq experiments

2018 ◽  
Author(s):  
Courtney N. Passow ◽  
Thomas J. Y. Kono ◽  
Bethany A. Stahl ◽  
James B. Jaggard ◽  
Alex C. Keene ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liquid Nitrogen ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gc Content ◽  
Gene Expression Profiles ◽  
Expression Studies ◽  
Genome Wide ◽  
Differential Gene ◽  
Genome Wide Gene Expression

AbstractRNA-sequencing is a popular next-generation sequencing technique for assaying genome-wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field-based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Flash freezing in liquid nitrogen can be impractical, particularly for field collections. RNAlater is a solution for stabilizing tissue for longer-term storage as it rapidly permeates tissue to protect cellular RNA. In this study, we assessed genome-wide expression patterns in 30 day old fry collected from the same brood at the same time point that were flash-frozen in liquid nitrogen and stored at −80°C or submerged and stored in RNAlater at room temperature, simulating conditions of fieldwork. We show that sample storage is a significant factor influencing observed differential gene expression. In particular, genes with elevated GC content exhibit higher observed expression levels in liquid nitrogen flash-freezing relative to RNAlater-storage. Further, genes with higher expression in RNAlater relative to liquid nitrogen experience disproportionate enrichment for functional categories, many of which are involved in RNA processing. This suggests that RNAlater may elicit a physiological response that has the potential to bias biological interpretations of expression studies. The biases introduced to observed gene expression arising from mimicking many field-based studies are substantial and should not be ignored.

scholarly journals Genome-Wide Analysis of Differential Gene Expression and Splicing in Excitatory Neurons and Interneuron Subtypes

2019 ◽  
Vol 40 (5) ◽  
pp. 958-973 ◽  
Author(s):  
Melanie A. Huntley ◽  
Karpagam Srinivasan ◽  
Brad A. Friedman ◽  
Tzu-Ming Wang ◽  
Ada X. Yee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Excitatory Neurons ◽  
Differential Gene

scholarly journals Single-Cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in Control and Aneurysmal Human Aortic Tissue

Circulation ◽  
2020 ◽  
Vol 142 (14) ◽  
pp. 1374-1388
Author(s):  
Yanming Li ◽  
Pingping Ren ◽  
Ashley Dawson ◽  
Hernan G. Vasquez ◽  
Waleed Ageedi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Aortic Wall ◽  
Genome Wide Association ◽  
Aortic Tissue ◽  
Sequencing Data ◽  
Genome Wide ◽  
Single Cell Rna Sequencing ◽  
Differential Gene

Background: Ascending thoracic aortic aneurysm (ATAA) is caused by the progressive weakening and dilatation of the aortic wall and can lead to aortic dissection, rupture, and other life-threatening complications. To improve our understanding of ATAA pathogenesis, we aimed to comprehensively characterize the cellular composition of the ascending aortic wall and to identify molecular alterations in each cell population of human ATAA tissues. Methods: We performed single-cell RNA sequencing analysis of ascending aortic tissues from 11 study participants, including 8 patients with ATAA (4 women and 4 men) and 3 control subjects (2 women and 1 man). Cells extracted from aortic tissue were analyzed and categorized with single-cell RNA sequencing data to perform cluster identification. ATAA-related changes were then examined by comparing the proportions of each cell type and the gene expression profiles between ATAA and control tissues. We also examined which genes may be critical for ATAA by performing the integrative analysis of our single-cell RNA sequencing data with publicly available data from genome-wide association studies. Results: We identified 11 major cell types in human ascending aortic tissue; the high-resolution reclustering of these cells further divided them into 40 subtypes. Multiple subtypes were observed for smooth muscle cells, macrophages, and T lymphocytes, suggesting that these cells have multiple functional populations in the aortic wall. In general, ATAA tissues had fewer nonimmune cells and more immune cells, especially T lymphocytes, than control tissues did. Differential gene expression data suggested the presence of extensive mitochondrial dysfunction in ATAA tissues. In addition, integrative analysis of our single-cell RNA sequencing data with public genome-wide association study data and promoter capture Hi-C data suggested that the erythroblast transformation-specific related gene( ERG ) exerts an important role in maintaining normal aortic wall function. Conclusions: Our study provides a comprehensive evaluation of the cellular composition of the ascending aortic wall and reveals how the gene expression landscape is altered in human ATAA tissue. The information from this study makes important contributions to our understanding of ATAA formation and progression.

scholarly journals Generalised Anxiety Disorder – A Twin Study of Genetic Architecture, Genome-Wide Association and Differential Gene Expression

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0134865 ◽  
Author(s):  
Matthew N. Davies ◽  
Serena Verdi ◽  
Andrea Burri ◽  
Maciej Trzaskowski ◽  
Minyoung Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Anxiety Disorder ◽  
Differential Gene Expression ◽  
Twin Study ◽  
Genetic Architecture ◽  
Genome Wide Association ◽  
Generalised Anxiety Disorder ◽  
Genome Wide ◽  
Differential Gene

scholarly journals Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast

Genetics ◽  
2020 ◽  
Vol 214 (3) ◽  
pp. 651-667 ◽  
Author(s):  
Marco Di Stefano ◽  
Francesca Di Giovanni ◽  
Vasilisa Pozharskaia ◽  
Mercè Gomar-Alba ◽  
Davide Baù ◽  
...  
Keyword(s):  
Gene Expression ◽  
Budding Yeast ◽  
Nuclear Organization ◽  
Nuclear Periphery ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
3D Genome ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Chromosome Fusions

The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.

Genome-Wide Differential Gene Expression Profiles in Broiler Chickens with Gangrenous Dermatitis

2012 ◽  
Vol 56 (4) ◽  
pp. 670-679 ◽  
Author(s):  
Duk Kyung Kim ◽  
Hyun S. Lillehoj ◽  
Kyung Woo Lee ◽  
Seung Ik Jang ◽  
Anthony P. Neumann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Broiler Chickens ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Genome Wide ◽  
Differential Gene
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