Loading…
RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio
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, a...
Saved in:
| Published in: | BMC genomics 2020-02, Vol.21 (1), p.132-132, Article 132 |
|---|---|
| Main Authors: | , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that this one cites Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-c594t-513e5b681d5f8a454332352b1abcaea68b75f07325beb4a206fa52ac7b62fb3b3 |
|---|---|
| cites | cdi_FETCH-LOGICAL-c594t-513e5b681d5f8a454332352b1abcaea68b75f07325beb4a206fa52ac7b62fb3b3 |
| container_end_page | 132 |
| container_issue | 1 |
| container_start_page | 132 |
| container_title | BMC genomics |
| container_volume | 21 |
| creator | Saddala, Madhu Sudhana Lennikov, Anton Bouras, Adam Huang, Hu |
| description | 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 log fold change (logFC) (±4) and p-values (p |
| doi_str_mv | 10.1186/s12864-020-6550-z |
| format | article |
| fullrecord | <record><control><sourceid>gale_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_484a6814d19c478b911a452e9dbdb678</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A616422867</galeid><doaj_id>oai_doaj_org_article_484a6814d19c478b911a452e9dbdb678</doaj_id><sourcerecordid>A616422867</sourcerecordid><originalsourceid>FETCH-LOGICAL-c594t-513e5b681d5f8a454332352b1abcaea68b75f07325beb4a206fa52ac7b62fb3b3</originalsourceid><addsrcrecordid>eNptkk1v1DAQhiMEoqXwA7igSFzgkGI7tpNckFbla6UKUAtnyx-TxVXW3trJqvRX8JOZdEvpIuSD7fEzrz3jtyieU3JMaSvfZMpaySvCSCWFINX1g-KQ8oZWjEr-8N76oHiS8wUhtGmZeFwc1IzUtWDdYfHr7POiOofLMsEW9JBL5_seEoTR66GEq02CnH0M5SbF3g-QSx1c2U_BjhhFRIcQRz1vytiXKwiI-LCNwxYcLlB39DPnYD5LOxLjXx1IW66nUYexfKeDj4gmH58Wj3p8Bzy7nY-K7x_efzv5VJ1--bg8WZxWVnR8rAStQRjZUif6VnPB65phRYZqYzVo2ZpG9KSpmTBguGZE9lowbRsjWW9qUx8Vy52ui_pCbZJf6_RTRe3VTSCmldJp9HYAxVuOgpQ72lnetKajFG9k0DnjjGxa1Hq709pMZg3OYveSHvZE90-C_6FWcasaQmTddSjw6lYgxcsJ8qjWPlsYBh0gTlnNpUlJSUsQffkPehGnhB2-oRpOW8LEX2qlsQAf-oj32llULSQagqFxGqSO_0PhcLD2NgaYf3w_4fVeAjIjXI0rPeWsludn-yzdsTbFnBP0d_2gRM32VTv7KrSvmu2rrjHnxf1G3mX88Wv9G3ro64M</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2357418025</pqid></control><display><type>article</type><title>RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio</title><source>Publicly Available Content Database</source><source>PubMed Central</source><creator>Saddala, Madhu Sudhana ; Lennikov, Anton ; Bouras, Adam ; Huang, Hu</creator><creatorcontrib>Saddala, Madhu Sudhana ; Lennikov, Anton ; Bouras, Adam ; Huang, Hu</creatorcontrib><description>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 log fold change (logFC) (±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 3527 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 down-regulated, while fewer were up-regulated in the retina of pde6c mutant zebrafish.
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.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/s12864-020-6550-z</identifier><identifier>PMID: 32033529</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Abnormalities ; Adapters ; Adaptor proteins ; Animals ; Annotations ; Apoptosis ; Biochemistry ; Biological activity ; Biosynthesis ; Calcium ; Cardiomyocytes ; Citric acid ; Criminal investigation ; Cyclic Nucleotide Phosphodiesterases, Type 6 - genetics ; Danio rerio ; Degeneration ; Degenerative diseases ; Diseases ; Disruption ; Encyclopedias ; Epithelium ; FastQC ; Gene expression ; Gene Ontology ; Gene Regulatory Networks ; Genes ; Genetic aspects ; Genetic research ; Genomes ; Genomics ; Gluconeogenesis ; Glycolysis ; Health aspects ; Heart cells ; Immunology ; Insulin ; KEGG ; Light Signal Transduction - genetics ; Messenger RNA ; Mutants ; Mutation ; Neurodegeneration ; Oxidative phosphorylation ; Pathogenesis ; Pde6c ; Peptidase ; Phosphodiesterase ; Phosphorylation ; Photoreceptors ; Phototransduction ; Proteins ; Retina ; Retina - metabolism ; Retinal degeneration ; Retinal Degeneration - genetics ; Retinal pigment epithelium ; Rhodopsin ; Ribonucleic acid ; RNA ; RNA sequencing ; RNA transport ; RNA-Seq ; Signal transduction ; Signaling ; Systems development ; Tricarboxylic acid cycle ; Trinity ; Zebrafish ; Zebrafish - genetics ; Zebrafish Proteins - genetics</subject><ispartof>BMC genomics, 2020-02, Vol.21 (1), p.132-132, Article 132</ispartof><rights>COPYRIGHT 2020 BioMed Central Ltd.</rights><rights>2020. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s). 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c594t-513e5b681d5f8a454332352b1abcaea68b75f07325beb4a206fa52ac7b62fb3b3</citedby><cites>FETCH-LOGICAL-c594t-513e5b681d5f8a454332352b1abcaea68b75f07325beb4a206fa52ac7b62fb3b3</cites><orcidid>0000-0003-2843-0320</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7006399/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2357418025?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,882,25734,27905,27906,36993,36994,44571,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32033529$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Saddala, Madhu Sudhana</creatorcontrib><creatorcontrib>Lennikov, Anton</creatorcontrib><creatorcontrib>Bouras, Adam</creatorcontrib><creatorcontrib>Huang, Hu</creatorcontrib><title>RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>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 log fold change (logFC) (±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 3527 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 down-regulated, while fewer were up-regulated in the retina of pde6c mutant zebrafish.
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.</description><subject>Abnormalities</subject><subject>Adapters</subject><subject>Adaptor proteins</subject><subject>Animals</subject><subject>Annotations</subject><subject>Apoptosis</subject><subject>Biochemistry</subject><subject>Biological activity</subject><subject>Biosynthesis</subject><subject>Calcium</subject><subject>Cardiomyocytes</subject><subject>Citric acid</subject><subject>Criminal investigation</subject><subject>Cyclic Nucleotide Phosphodiesterases, Type 6 - genetics</subject><subject>Danio rerio</subject><subject>Degeneration</subject><subject>Degenerative diseases</subject><subject>Diseases</subject><subject>Disruption</subject><subject>Encyclopedias</subject><subject>Epithelium</subject><subject>FastQC</subject><subject>Gene expression</subject><subject>Gene Ontology</subject><subject>Gene Regulatory Networks</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic research</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Gluconeogenesis</subject><subject>Glycolysis</subject><subject>Health aspects</subject><subject>Heart cells</subject><subject>Immunology</subject><subject>Insulin</subject><subject>KEGG</subject><subject>Light Signal Transduction - genetics</subject><subject>Messenger RNA</subject><subject>Mutants</subject><subject>Mutation</subject><subject>Neurodegeneration</subject><subject>Oxidative phosphorylation</subject><subject>Pathogenesis</subject><subject>Pde6c</subject><subject>Peptidase</subject><subject>Phosphodiesterase</subject><subject>Phosphorylation</subject><subject>Photoreceptors</subject><subject>Phototransduction</subject><subject>Proteins</subject><subject>Retina</subject><subject>Retina - metabolism</subject><subject>Retinal degeneration</subject><subject>Retinal Degeneration - genetics</subject><subject>Retinal pigment epithelium</subject><subject>Rhodopsin</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>RNA transport</subject><subject>RNA-Seq</subject><subject>Signal transduction</subject><subject>Signaling</subject><subject>Systems development</subject><subject>Tricarboxylic acid cycle</subject><subject>Trinity</subject><subject>Zebrafish</subject><subject>Zebrafish - genetics</subject><subject>Zebrafish Proteins - genetics</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptkk1v1DAQhiMEoqXwA7igSFzgkGI7tpNckFbla6UKUAtnyx-TxVXW3trJqvRX8JOZdEvpIuSD7fEzrz3jtyieU3JMaSvfZMpaySvCSCWFINX1g-KQ8oZWjEr-8N76oHiS8wUhtGmZeFwc1IzUtWDdYfHr7POiOofLMsEW9JBL5_seEoTR66GEq02CnH0M5SbF3g-QSx1c2U_BjhhFRIcQRz1vytiXKwiI-LCNwxYcLlB39DPnYD5LOxLjXx1IW66nUYexfKeDj4gmH58Wj3p8Bzy7nY-K7x_efzv5VJ1--bg8WZxWVnR8rAStQRjZUif6VnPB65phRYZqYzVo2ZpG9KSpmTBguGZE9lowbRsjWW9qUx8Vy52ui_pCbZJf6_RTRe3VTSCmldJp9HYAxVuOgpQ72lnetKajFG9k0DnjjGxa1Hq709pMZg3OYveSHvZE90-C_6FWcasaQmTddSjw6lYgxcsJ8qjWPlsYBh0gTlnNpUlJSUsQffkPehGnhB2-oRpOW8LEX2qlsQAf-oj32llULSQagqFxGqSO_0PhcLD2NgaYf3w_4fVeAjIjXI0rPeWsludn-yzdsTbFnBP0d_2gRM32VTv7KrSvmu2rrjHnxf1G3mX88Wv9G3ro64M</recordid><startdate>20200207</startdate><enddate>20200207</enddate><creator>Saddala, Madhu Sudhana</creator><creator>Lennikov, Anton</creator><creator>Bouras, Adam</creator><creator>Huang, Hu</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><general>BMC</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0003-2843-0320</orcidid></search><sort><creationdate>20200207</creationdate><title>RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio</title><author>Saddala, Madhu Sudhana ; Lennikov, Anton ; Bouras, Adam ; Huang, Hu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c594t-513e5b681d5f8a454332352b1abcaea68b75f07325beb4a206fa52ac7b62fb3b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Abnormalities</topic><topic>Adapters</topic><topic>Adaptor proteins</topic><topic>Animals</topic><topic>Annotations</topic><topic>Apoptosis</topic><topic>Biochemistry</topic><topic>Biological activity</topic><topic>Biosynthesis</topic><topic>Calcium</topic><topic>Cardiomyocytes</topic><topic>Citric acid</topic><topic>Criminal investigation</topic><topic>Cyclic Nucleotide Phosphodiesterases, Type 6 - genetics</topic><topic>Danio rerio</topic><topic>Degeneration</topic><topic>Degenerative diseases</topic><topic>Diseases</topic><topic>Disruption</topic><topic>Encyclopedias</topic><topic>Epithelium</topic><topic>FastQC</topic><topic>Gene expression</topic><topic>Gene Ontology</topic><topic>Gene Regulatory Networks</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic research</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Gluconeogenesis</topic><topic>Glycolysis</topic><topic>Health aspects</topic><topic>Heart cells</topic><topic>Immunology</topic><topic>Insulin</topic><topic>KEGG</topic><topic>Light Signal Transduction - genetics</topic><topic>Messenger RNA</topic><topic>Mutants</topic><topic>Mutation</topic><topic>Neurodegeneration</topic><topic>Oxidative phosphorylation</topic><topic>Pathogenesis</topic><topic>Pde6c</topic><topic>Peptidase</topic><topic>Phosphodiesterase</topic><topic>Phosphorylation</topic><topic>Photoreceptors</topic><topic>Phototransduction</topic><topic>Proteins</topic><topic>Retina</topic><topic>Retina - metabolism</topic><topic>Retinal degeneration</topic><topic>Retinal Degeneration - genetics</topic><topic>Retinal pigment epithelium</topic><topic>Rhodopsin</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA sequencing</topic><topic>RNA transport</topic><topic>RNA-Seq</topic><topic>Signal transduction</topic><topic>Signaling</topic><topic>Systems development</topic><topic>Tricarboxylic acid cycle</topic><topic>Trinity</topic><topic>Zebrafish</topic><topic>Zebrafish - genetics</topic><topic>Zebrafish Proteins - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Saddala, Madhu Sudhana</creatorcontrib><creatorcontrib>Lennikov, Anton</creatorcontrib><creatorcontrib>Bouras, Adam</creatorcontrib><creatorcontrib>Huang, Hu</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Science In Context</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Saddala, Madhu Sudhana</au><au>Lennikov, Anton</au><au>Bouras, Adam</au><au>Huang, Hu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2020-02-07</date><risdate>2020</risdate><volume>21</volume><issue>1</issue><spage>132</spage><epage>132</epage><pages>132-132</pages><artnum>132</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><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 log fold change (logFC) (±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 3527 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 down-regulated, while fewer were up-regulated in the retina of pde6c mutant zebrafish.
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.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>32033529</pmid><doi>10.1186/s12864-020-6550-z</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0003-2843-0320</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1471-2164 |
| ispartof | BMC genomics, 2020-02, Vol.21 (1), p.132-132, Article 132 |
| issn | 1471-2164 1471-2164 |
| language | eng |
| recordid | cdi_doaj_primary_oai_doaj_org_article_484a6814d19c478b911a452e9dbdb678 |
| source | Publicly Available Content Database; PubMed Central |
| subjects | Abnormalities Adapters Adaptor proteins Animals Annotations Apoptosis Biochemistry Biological activity Biosynthesis Calcium Cardiomyocytes Citric acid Criminal investigation Cyclic Nucleotide Phosphodiesterases, Type 6 - genetics Danio rerio Degeneration Degenerative diseases Diseases Disruption Encyclopedias Epithelium FastQC Gene expression Gene Ontology Gene Regulatory Networks Genes Genetic aspects Genetic research Genomes Genomics Gluconeogenesis Glycolysis Health aspects Heart cells Immunology Insulin KEGG Light Signal Transduction - genetics Messenger RNA Mutants Mutation Neurodegeneration Oxidative phosphorylation Pathogenesis Pde6c Peptidase Phosphodiesterase Phosphorylation Photoreceptors Phototransduction Proteins Retina Retina - metabolism Retinal degeneration Retinal Degeneration - genetics Retinal pigment epithelium Rhodopsin Ribonucleic acid RNA RNA sequencing RNA transport RNA-Seq Signal transduction Signaling Systems development Tricarboxylic acid cycle Trinity Zebrafish Zebrafish - genetics Zebrafish Proteins - genetics |
| title | RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-18T23%3A03%3A22IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=RNA-Seq%20reveals%20differential%20expression%20profiles%20and%20functional%20annotation%20of%20genes%20involved%20in%20retinal%20degeneration%20in%20Pde6c%20mutant%20Danio%20rerio&rft.jtitle=BMC%20genomics&rft.au=Saddala,%20Madhu%20Sudhana&rft.date=2020-02-07&rft.volume=21&rft.issue=1&rft.spage=132&rft.epage=132&rft.pages=132-132&rft.artnum=132&rft.issn=1471-2164&rft.eissn=1471-2164&rft_id=info:doi/10.1186/s12864-020-6550-z&rft_dat=%3Cgale_doaj_%3EA616422867%3C/gale_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c594t-513e5b681d5f8a454332352b1abcaea68b75f07325beb4a206fa52ac7b62fb3b3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2357418025&rft_id=info:pmid/32033529&rft_galeid=A616422867&rfr_iscdi=true |