scholarly journals RNA-Seq reveals differential expression profile and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2019 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Hu Huang
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Expression Profile ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Insulin Signalling ◽  
Tca Cycle ◽  
Kegg Pathways ◽  
Insulin Signalling Pathway

Abstract Retinal degenerative diseases affect millions of people and are the leading cause of vision loss. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes that are involved in phototransduction, biosynthesis, folding of the rhodopsin molecule and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear. The molecular basis of the retinal pathologies defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we have analyzed the differential gene expression profile of retina from a wild-type zebrafish and pde6c mutant. The datasets were downloaded from the Sequence Read Archive (SRA), removed adaptors and unbiased bases and checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish and calculated gene expression. The differentially expressed genes (DEGs) were filtered based on the FDR (±4) and p-values (p<0.001). We performed gene annotation (Molecular function, biological process, cellular component), and functional pathways (KEGG pathway) for the DEGs. Our result showed that 216 up-regulated and 3527 down-regulated between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways like Phototransduction (12 genes), mRNA surveillance pathway (17 genes), Phagosome (25 genes), Glycolysis / Gluconeogenesis (15 genes), Adrenergic signalling in cardiomyocytes (29 genes), Ribosome (20 genes), Citrate cycle (TCA cycle) (8 genes), Insulin signalling pathway (24 genes), Oxidative phosphorylation (20 genes) and RNA transport (22 genes) pathways respectively. Much more of all the pathways genes were down-regulated, but fewer genes were up-regulated in retina mutant of zebrafish. Our data strongly indicate that the among these genes, above mentioned pathways genes as well as calcium-binding proteins, neural damage proteins, peptidase proteins, immunological proteins, and apoptosis proteins are mostly involved in retinal and neural degeneration that cause abnormalities in photoreceptors or RPE cells.

scholarly journals RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2019 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Adam Bouras ◽  
Hu Huang
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Tca Cycle ◽  
Kegg Pathways

Abstract Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6C (pde6c) mutant. The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the false discovery rate (FDR) (±4) and p-values (p < 0.001). We performed gene annotation (molecular function [MF], biological process [BP], cellular component [CC]) and determined the functional pathways Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the DEGs. Our result showed 216 upregulated and 3,527 downregulated genes between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways, such as the phototransduction (12 genes), mRNA surveillance (17 genes), phagosome (25 genes), glycolysis/gluconeogenesis (15 genes), adrenergic signaling in cardiomyocytes (29 genes), ribosome (20 genes), the citrate cycle (TCA cycle; 8 genes), insulin signaling (24 genes), oxidative phosphorylation (20 genes), and RNA transport (22 genes) pathways. Many more of all the pathway genes were downregulated, while fewer were upregulated in the retina of mutant zebrafish. Our data strongly indicate that, among these genes, the abovementioned pathways’ genes—as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins—are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.

scholarly journals RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2020 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Adam Bouras ◽  
Hu Huang
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Tca Cycle ◽  
Kegg Pathways

Abstract Background Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6c (pde6c) mutant. Results The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the false discovery rate (FDR) (±4) and p-values (p < 0.001). We performed gene annotation (molecular function [MF], biological process [BP], cellular component [CC]), and determined the functional pathways Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the DEGs. Our result showed 216 upregulated and 3,527 downregulated genes between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways, such as the phototransduction (12 genes), mRNA surveillance (17 genes), phagosome (25 genes), glycolysis/gluconeogenesis (15 genes), adrenergic signaling in cardiomyocytes (29 genes), ribosome (20 genes), the citrate cycle (TCA cycle; 8 genes), insulin signaling (24 genes), oxidative phosphorylation (20 genes), and RNA transport (22 genes) pathways. Many more of all the pathway genes were downregulated, while fewer were upregulated in the retina of mutant zebrafish. Conclusions Our data strongly indicate that, among these genes, the above-mentioned pathways’ genes as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.

scholarly journals RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2020 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Adam Bouras ◽  
Hu Huang
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Tca Cycle ◽  
Kegg Pathways

Abstract Background: Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6c (pde6c) mutant. Results: The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the false discovery rate (FDR) (±4) and p-values (p < 0.001). We performed gene annotation (molecular function [MF], biological process [BP], cellular component [CC]), and determined the functional pathways Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the DEGs. Our result showed 216 upregulated and 3,527 downregulated genes between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways, such as the phototransduction (12 genes), mRNA surveillance (17 genes), phagosome (25 genes), glycolysis/gluconeogenesis (15 genes), adrenergic signaling in cardiomyocytes (29 genes), ribosome (20 genes), the citrate cycle (TCA cycle; 8 genes), insulin signaling (24 genes), oxidative phosphorylation (20 genes), and RNA transport (22 genes) pathways. Many more of all the pathway genes were downregulated, while fewer were upregulated in the retina of mutant zebrafish. Conclusions: Our data strongly indicate that, among these genes, the above-mentioned pathways’ genes as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.

scholarly journals RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2019 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov(Former Corresponding Author) ◽  
Adam Bouras ◽  
Hu Huang(New Corresponding Author)
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Tca Cycle ◽  
Kegg Pathways

Abstract Background Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6C (pde6c) mutant. Results The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the false discovery rate (FDR) (±4) and p-values (p < 0.001). We performed gene annotation (molecular function [MF], biological process [BP], cellular component [CC]) and determined the functional pathways Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the DEGs. Our result showed 216 upregulated and 3,527 downregulated genes between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways, such as the phototransduction (12 genes), mRNA surveillance (17 genes), phagosome (25 genes), glycolysis/gluconeogenesis (15 genes), adrenergic signaling in cardiomyocytes (29 genes), ribosome (20 genes), the citrate cycle (TCA cycle; 8 genes), insulin signaling (24 genes), oxidative phosphorylation (20 genes), and RNA transport (22 genes) pathways. Many more of all the pathway genes were downregulated, while fewer were upregulated in the retina of mutant zebrafish. Conclusions Our data strongly indicate that, among these genes, the above-mentioned pathways’ genes as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.

scholarly journals Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii

2020 ◽  
Vol 8 (1) ◽  
pp. 102 ◽  
Author(s):  
Tangcheng Li ◽  
Liying Yu ◽  
Bo Song ◽  
Yue Song ◽  
Ling Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Acid Synthesis ◽  
Core Gene ◽  
Chromosome Conformation ◽  
Gene Set ◽  
Kegg Pathways ◽  
Expression Studies ◽  
Gene Expression Studies

Cataloging an accurate functional gene set for the Symbiodiniaceae species is crucial for addressing biological questions of dinoflagellate symbiosis with corals and other invertebrates. To improve the gene models of Fugacium kawagutii, we conducted high-throughput chromosome conformation capture (Hi-C) for the genome and Illumina combined with PacBio sequencing for the transcriptome to achieve a new genome assembly and gene prediction. A 0.937-Gbp assembly of F. kawagutii were obtained, with a N50 > 13 Mbp and the longest scaffold of 121 Mbp capped with telomere motif at both ends. Gene annotation produced 45,192 protein-coding genes, among which, 11,984 are new compared to previous versions of the genome. The newly identified genes are mainly enriched in 38 KEGG pathways including N-Glycan biosynthesis, mRNA surveillance pathway, cell cycle, autophagy, mitophagy, and fatty acid synthesis, which are important for symbiosis, nutrition, and reproduction. The newly identified genes also included those encoding O-methyltransferase (O-MT), 3-dehydroquinate synthase, homologous-pairing protein 2-like (HOP2) and meiosis protein 2 (MEI2), which function in mycosporine-like amino acids (MAAs) biosynthesis and sexual reproduction, respectively. The improved version of the gene set (Fugka_Geneset _V3) raised transcriptomic read mapping rate from 33% to 54% and BUSCO match from 29% to 55%. Further differential gene expression analysis yielded a set of stably expressed genes under variable trace metal conditions, of which 115 with annotated functions have recently been found to be stably expressed under three other conditions, thus further developing the “core gene set” of F. kawagutii. This improved genome will prove useful for future Symbiodiniaceae transcriptomic, gene structure, and gene expression studies, and the refined “core gene set” will be a valuable resource from which to develop reference genes for gene expression studies.

scholarly journals Forkhead transcription factor FOXO1 (FKHR)-dependent induction of PDK4 gene expression in skeletal muscle during energy deprivation

2003 ◽  
Vol 375 (2) ◽  
pp. 365-371 ◽  
Author(s):  
Tatsuo FURUYAMA ◽  
Kazuko KITAYAMA ◽  
Hitoshi YAMASHITA ◽  
Nozomu MORI
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Transcription Factor ◽  
Food Deprivation ◽  
Insulin Signalling ◽  
Pyruvate Dehydrogenase Kinase ◽  
C2c12 Cells ◽  
Glucocorticoid Treatment ◽  
Insulin Signalling Pathway ◽  
Energy Deprivation

A forkhead-type transcription factor, DAF-16, is located in the most downstream part of the insulin signalling pathway via PI3K (phosphoinositide 3-kinase). It is essential for the extension of life-span and is also involved in dauer formation induced by food deprivation in Caenorhabditis elegans. In the present study, we addressed whether or not FOXO members AFX, FKHR (forkhead homologue in rhabdomyosarcoma) and FKHRL1 (FKHR-like protein 1), mammalian counterparts of DAF-16, are involved in starvation stress. We found a remarkable selective induction of FKHR and FKHRL1 transcripts in skeletal muscle of mice during starvation. The induction of FKHR gene expression was observed at 6 h after food deprivation, peaked at 12 h, and returned to the basal level by 24 h of refeeding. The induction was also found in skeletal muscle of mice with glucocorticoid treatment. Moreover, we found that the levels of PDK4 (pyruvate dehydrogenase kinase 4) gene expression were up-regulated through the direct binding of FKHR to the promoter region of the gene in C2C12 cells. These results suggest that FKHR has an important role in the regulation of energy metabolism, at least in part, through the up-regulation of PDK4 gene expression in skeletal muscle during starvation.

scholarly journals A temporal switch in the insulin-signalling pathway that regulates hepatic IGF-binding protein-1 gene expression

2006 ◽  
Vol 37 (2) ◽  
pp. 227-237 ◽  
Author(s):  
David Finlay ◽  
Antonio J Ruiz-Alcaraz ◽  
Christopher Lipina ◽  
Stephane Perrier ◽  
Calum Sutherland
Keyword(s):  
Gene Expression ◽  
Insulin Signalling ◽  
Binding Protein ◽  
Regulation Of Gene Expression ◽  
Mammalian Target Of Rapamycin ◽  
Temporal Analysis ◽  
Insulin Regulation ◽  
Insulin Signalling Pathway ◽  
Igf Binding ◽  
Igf Binding Protein

Insulin regulation of hepatic gene transcription is a vital component of glucose homeostasis. Understanding the molecular regulationof thisprocess aids the searchfor the defect(s) that promotesinsulin-resistant states, such asdiabetesmellitus. We havepreviously shownthat the insulin regulationof hepatic IGF-binding protein-1 (IGFBP1) expression requiresthe signalling proteins phosphatidylinositol 3-kinase (PI 3-kinase) and mammalian target of rapamycin (mTOR). In this report, we demonstrate that activation of the mTOR pathway, without activation of its upstream regulator PI 3-kinase, reduces IGFBP1 expression. Therefore, mTOR activation is sufficient to mimic insulin regulation of this gene. However, longer exposure (>3 h) of cells to insulin reduces the importance of this pathway in insulin regulation of the gene, suggesting a temporal switch in signalling mechanisms linking insulin action to the IGFBP1 gene promoter. In contrast, the activation of PI 3-kinase is required for insulin regulation of IGFBP1 under all conditions tested. Therefore, an mTOR-independent, PI 3-kinase-dependent pathway becomes more important in IGFBP1 regulation after long exposure to insulin. This is a novel concept in insulin regulation of gene expression and demonstrates the importance of temporal analysis of signalling processes.

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