scholarly journals Rod-genesis driven by mafba in an nrl knockout zebrafish model with altered photoreceptor compositions and progressive retinal degeneration

2021 ◽  
Author(s):  
Fei Liu ◽  
Yayun Qin ◽  
Yuwen Huang ◽  
Pan Gao ◽  
Jingzhen Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Developmental Process ◽  
Essential Gene ◽  
Expression Profiles ◽  
Embryonic Stage ◽  
Retinal Cell ◽  
Suitable Model ◽  
Double Knockout ◽  
Zebrafish Model

The neural retina leucine zipper (NRL) is an essential gene for the fate determination and differentiation of rod photoreceptors in mammals. Mutations in NRL have been associated with autosomal recessive enhanced S-cone syndrome and autosomal dominant retinitis pigmentosa. However, the exact role of Nrl in regulating the development and maintenance of photoreceptors in zebrafish, a popular animal model used for retinal degeneration and regeneration studies, has not been fully determined. In this study, we generated an nrl knockout zebrafish model by CRISPR-Cas9 technology and observed a surprising phenotype characterized by the reduction but not total elimination of rods and the over-grown of green-cones. By tracing the developmental process of rods, we discovered two waves of rod genesis in zebrafish, emerging at the embryonic stage with an nrl-dependent pattern and the post-embryonic stage with an nrl-independent pattern, respectively. Through bulk and single-cell RNA sequencing, we constructed the gene expression profiles for the whole retinal tissues and each of the retinal cell types in WT and nrl knockout zebrafish. We detected the rod/green-cone intermediate photoreceptors in nrl knockout zebrafish, suggesting that there may be a kind of rod/green-cone bipotent precursors and its fate choice between rod and green-cone is controlled by nrl. Besides, we identified the mafba gene as a novel regulator for nrl-independent rods, based on the cell-type-specific expression pattern and the retinal phenotype of nrl/mafba double knockout zebrafish. Furthermore, the altered photoreceptor compositions and abnormal gene expression caused progressive retinal degeneration and subsequent regeneration in nrl knockout zebrafish. Our work revealed a novel function of mafba gene in rod development and established a more suitable model for the developmental processes and regulatory mechanisms of rod and green-cone photoreceptors in zebrafish.

252 DIFFERENCES IN GENE EXPRESSION PROFILES IN MOUSE FERTILIZED BLASTOCYSTS AND DIPLOID BLASTOCYST STAGE PARTHENOTES

2006 ◽  
Vol 18 (2) ◽  
pp. 233
Author(s):  
N.-H. Kim ◽  
S.-K. Cho ◽  
X.-Y. Li ◽  
X.-H. Shen ◽  
X.-S. Cui
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Developmental Process ◽  
Expression Profiles ◽  
Polar Body ◽  
Gene Expression Profiles ◽  
Blastocyst Stage ◽  
Calcium Signal ◽  
Ionophore A23187 ◽  
Parthenogenetic Activation

Following parthenogenetic activation, in the absence of a male contribution, oocytes progress into early gestation. To gain insight into the role of the paternal genome during pre-implantation development, we used microarray to compare gene expression profiles in pre-implantation embryos following fertilization and parthenogenetic activation. Fertilized embryos and oocytes were collected from superovulated C57BL/6J female mice. The oocytes were activated with 50 �M calcium ionophore A23187 for 5 min. After 5 h of culture in M16 medium with 7.5 �g/mL cytochalasin B, oocytes with one polar body and two pronuclei were used in this experiment. The activated oocytes and zygotes were cultured in M16 to the blatocyst stage. Messenger RNA from 50 blastocysts was extracted by means of the Dynabeads mRNA Direct Kit (Dynal, Oslo, Norway), and then linearly amplified for two rounds using the RiboAmp HS RNA Amplification Kit (Arcturus Bioscience, Inc., Mountain View, CA, USA). A set of cRNA targets from the embryos was assembled into a hybridization reaction on the Applied Biosystems 1700 chemiluminescent microarray analyzer (Jung Hwa Scientific Co., Ltd., Seoul, Korea). Each set was repeated three times. All of the correlation coefficients were above 0.9 for experiment replications. Differences in microarray intensities were normalized and grouped by using the Avadis Prophetic 3.3 version, and categories are based on the PANTHER classification system. According to the cDNA microarray data, we additionally categorized genes into transcription- and developmental process-related genes and compared them in both fertilized and parthenogenetically activated blastocysts. Five transcription-related genes (Goosecoid, transcription factor 1, LIM domain, Spi-C transcription factor, and hypoxia inducible factor 3) and seven developmental process related genes (metaxin 1, serine/threonine kinase 22, stromal antigen, butyrophilin, anti-Mullerian hormone type 2 receptor, prolactin-like protein C2, and otoconin 90) were identified in the fertilized blastocysts compared to the blastocyst-stage parthenotes. In contrast, seven transcription- (Amnionless, EHOX-like, calcium signal transducer 2, nuclear receptor 0B, transcription factor CP2, Iroquois related homeobox 3, and zinc finger protein 3) and eight developmental process-related genes (prion protein dublet, X-linked lymphocyte-regulated 3a, muscleblind-like 3, stathmin-like 2, SRY-box-containing gene 7, ephrin B1, muscleblind-like 3, and Iroquois-related homeobox 3) were expressed at a higher level in parthenotes than in fertilized blastocysts. These genes were selected, and their expression levels confirmed, by real-time quantitative RT-PCR. The results indicate that diploid parthenotes at the blastocyst stage may lack or over express genes related to transcription and development processes which possibly result in fetal lethality. Further studies are required to determine whether aberrant gene expression in parthenotes is due to lack of paternal contribution. This work was funded by a grant from the National Research Laboratory Program in Korea.

EFFECTIVE MODELS FOR GENE NETWORKS AND THEIR APPLICATIONS

2012 ◽  
Vol 07 (01n02) ◽  
pp. 41-70 ◽  
Author(s):  
JASON SHULMAN ◽  
LARS SEEMANN ◽  
GREGG W. ROMAN ◽  
GEMUNU H. GUNARATNE
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
Gene Network ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Stationary Solutions ◽  
The State ◽  
Effective Model ◽  
Knockout Mutant ◽  
Double Knockout

Networks are used to abstract large, highly-coupled sets of objects. Their analyses have included network classification into a few broad classes and selection of small substructures that perform simple yet common tasks. One issue that has received little attention is how the state of a network can be moved according to a pre-specified set of guidelines. In this paper, we address this question in the context of gene networks. In general, neither the full membership of the gene network associated with a biological process nor the precise form of interactions between nodes is known. What is available, through microarrays or sequencing, are gene expression profiles of an organism or its viable mutants. Our approach relies only on these expression profiles, and not on the availability of an accurate model for the network. The first step is to select a small set of core- or master- nodes, such as transcription factors or microRNAs, that can be used to alter the levels of many of the remaining genes in the network. We ask how the state — or solution — of the gene network changes as the levels of these master nodes are altered externally. The object of our study is, not the network, but the surface of these solutions. We argue that it can be approximated using gene expression profiles of the organism and single manipulation of master node activity. This is done through an "effective model." The effective model as well as error estimates for its predictions can be derived from experimental data. The method is validated using synthetic gene networks that have stationary solutions and those that are periodically driven, e.g., circadian networks. An effective model for the oxygen-deprivation network of E.coli is constructed using previously published gene expression profiles, and used to predict the expression levels in a double knockout mutant. Less that 30% of the predictions lie outside the 5% confidence level. We propose the use of the effective model methodology to compute how Drosophila melanogaster in the normal state can be genetically altered into a pre-defined sleep deprived-like state.

scholarly journals Effect of Huanglian Jiedu Decoction on Thoracic Aorta Gene Expression in Spontaneous Hypertensive Rats

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Gui-Hua Yue ◽  
Shao-Yuan Zhuo ◽  
Meng Xia ◽  
Zhuo Zhang ◽  
Yi-Wen Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Thoracic Aorta ◽  
Group Treatment ◽  
Developmental Process ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Smooth Muscle Contraction ◽  
Control Group ◽  
Hypertensive Rats ◽  
Altered Expression

Objective. Hypertension is one of the most common cardiovascular disorders with high mortality. Here we explored the antihypertension effects of Huanglian Jiedu Decoction (HJD) on thoracic aorta gene expression in spontaneous hypertensive rats.Methods. A rat model of spontaneous hypertension was used. The gene change profile of thoracic aorta after JHD treatment was assessed by GeneChip(GC) analysis using the Agilent Whole Rat Genome Oligo Microarray.Results. Hypertension induced 441 genes upregulated and 417 genes downregulated compared with the normal control group. Treatment of HJD resulted in 76 genes downregulated and 20 genes upregulated. GC data analysis showed that the majority of change genes were involved in immune system process, developmental process, and cell death.Conclusion. Hypertension altered expression of many genes that regulate various biological functions. HJD significantly reduced hypertension and altered the gene expression profiles of SHR rats. These changing genes were involved in many cellular functions such as regulating smooth muscle contraction, Ca(2+) homeostasis, and NO pathway. This study provides the potential novel insights into hypertension and antihypertension effects of HJD.

scholarly journals Gene expression profiling reveals a regulatory role for RORα and RORγ in phase I and phase II metabolism

2007 ◽  
Vol 31 (2) ◽  
pp. 281-294 ◽  
Author(s):  
Hong Soon Kang ◽  
Martin Angers ◽  
Ju Youn Beak ◽  
Xiying Wu ◽  
Jeffrey M. Gimble ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phase I ◽  
Phase Ii ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Functional Redundancy ◽  
Cytochrome P450 Enzymes ◽  
Double Knockout ◽  
Physiological Functions ◽  
Oscillatory Pattern

Retinoid-related orphan receptors alpha (RORα) and gamma (RORγ) are both expressed in liver; however, their physiological functions in this tissue have not yet been clearly defined. The RORα1 and RORγ1 isoforms, but not RORα4, show an oscillatory pattern of expression during circadian rhythm. To obtain insight into the physiological functions of ROR receptors in liver, we analyzed the gene expression profiles of livers from WT, RORα-deficient staggerer (sg) mice ( RORα sg/sg), RORγ−/−, and RORα sg/sg RORγ−/− double knockout (DKO) mice by microarray analysis. DKO mice were generated to study functional redundancy between RORα and RORγ. These analyses demonstrated that RORα and RORγ affect the expression of a number of genes. RORα and RORγ are particularly important in the regulation of genes encoding several phase I and phase II metabolic enzymes, including several 3β-hydroxysteroid dehydrogenases, cytochrome P450 enzymes, and sulfotransferases. In addition, our results indicate that RORα and RORγ each affect the expression of a specific set of genes but also exhibit functional redundancy. Our study shows that RORα and RORγ receptors influence the regulation of several metabolic pathways, including those involved in the metabolism of steroids, bile acids, and xenobiotics, suggesting that RORs are important in the control of metabolic homeostasis.

scholarly journals Canine transmissible venereal tumour established in immunodeficient mice reprograms the gene expression profiles associated with a favourable tumour microenvironment to enable cancer malignancy

2022 ◽  
Vol 18 (1) ◽  
Author(s):  
Chiao-Hsu Ke ◽  
Hirotaka Tomiyasu ◽  
Yu-Ling Lin ◽  
Wei-Hsiang Huang ◽  
Hsiao-Hsuan Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Inflammation ◽  
Extracellular Space ◽  
Tumour Progression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Host Immunity ◽  
Suitable Model ◽  
Beagle Dogs ◽  
Immunodeficient Mice

Abstract Background Canine transmissible venereal tumours (CTVTs) can cross the major histocompatibility complex barrier to spread among dogs. In addition to the transmissibility within canids, CTVTs are also known as a suitable model for investigating the tumour–host immunity interaction because dogs live with humans and experience the same environmental risk factors for tumourigenesis. Moreover, outbred dogs are more appropriate than inbred mice models for simulating the diversity of human cancer development. This study built a new model of CTVTs, known as MCTVTs, to further probe the shaping effects of immune stress on tumour development. For xenotransplantation, CTVTs were first injected and developed in immunodeficient mice (NOD.CB17-Prkdcscid/NcrCrl), defined as XCTVTs. The XCTVTs harvested from NOD/SCID mice were then inoculated and grown in beagles and named mouse xenotransplantation of CTVTs (MCTVTs). Results After the inoculation of CTVTs and MCTVTs into immune-competent beagle dogs separately, MCTVTs grew faster and metastasized more frequently than CTVTs did. Gene expression profiles in CTVTs and MCTVTs were analysed by cDNA microarray to reveal that MCTVTs expressed many tumour-promoting genes involved in chronic inflammation, chemotaxis, extracellular space modification, NF-kappa B pathways, and focal adhesion. Furthermore, several well-known tumour-associated biomarkers which could predict tumour progression were overexpressed in MCTVTs. Conclusions This study demonstrated that defective host immunity can result in gene instability and enable transcriptome reprogramming within tumour cells. Fast tumour growth in beagle dogs and overexpression of tumour-associated biomarkers were found in a CTVT strain previously established in immunodeficient mice. In addition, dysregulated interaction of chronic inflammation, chemotaxis, and extracellular space modification were revealed to imply the possibly exacerbating mechanisms in the microenvironments of these tumours. In summary, this study offers a potential method to facilitate tumour progression and provide a niche for discovering tumour-associated biomarkers in cancer research.

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.

Comparison of gene expression profiling during postnatal development of mouse dentate gyrus and cerebellum

2002 ◽  
Vol 8 (2) ◽  
pp. 131-137 ◽  
Author(s):  
Sakae Saito ◽  
Ryo Matoba ◽  
Noriko Ueno ◽  
Kenichi Matsubara ◽  
Kikuya Kato
Keyword(s):  
Gene Expression ◽  
Dentate Gyrus ◽  
Postnatal Development ◽  
Granule Cells ◽  
Developmental Process ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Competitive Pcr ◽  
Elevated Expression

Both the dentate gyrus of the hippocampus and the cerebellar cortex consist mainly of granule cells and develop postnatally. The granule cells in both tissues are presumed to be similar. Changes in gene expression were analyzed during the postnatal development of the dentate gyrus. Altogether, expression patterns of 1,937 genes were determined by adaptor-tagged competitive PCR. More than 90% of the genes belong to groups characterized by elevated expression either at earlier or later stages of development. A majority of the genes expressed showed marked changes during the developmental process, but there was little correlation between gene function and expression, unlike that observed during mouse postnatal cerebellar development. Despite anatomical and physiological similarities between these two processes, the gene expression profiles are completely different.

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.

Sign in / Sign up

Export Citation Format

Share Document