High-throughput sequencing revealed the expression profile and potential key molecules of the circular RNAs involved in the process of hypoxic adaptation in Tibetan chickens
The Tibetan chicken ( Gallus gallus ) provides high quality protein and iron for humans, which shows many phenotypic adaptations to the low oxygen. Study of the genetic mechanisms of circular RNAs (circRNAs) in hypoxia adaptation has not been reported. Four embryonic heart tissue samples from Tibeta...
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| Veröffentlicht in: | Biológia 2021-11, Vol.76 (11), p.3439-3447 |
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| creator | Zhang, Zengrong Qiu, Mohan Du, Huarui Li, Qingyun Gan, Wu Xiong, Xia Yu, Chunlin Peng, Han Xia, Bo Song, Xiaoyan Yang, Li Hu, Chenming Chen, Jialei Jiang, Xiaosong Yang, Chaowu |
| description | The Tibetan chicken (
Gallus gallus
) provides high quality protein and iron for humans, which shows many phenotypic adaptations to the low oxygen. Study of the genetic mechanisms of circular RNAs (circRNAs) in hypoxia adaptation has not been reported. Four embryonic heart tissue samples from Tibetan chickens and Daheng broilers were collected. Differentially expressed circRNAs (DEcircRNAs) were identified via high-throughput sequencing. Bioinformatic analysis was used to indicate the functions and pathways of the DEcircRNAs. A total of 29 DEcircRNAs were identified between 4 Tibetan chickens and 4 Daheng broilers, including 15 upregulated and 14 downregulated DEcircRNAs in Tibetan chickens. GO analysis revealed that the DEcircRNAs were mainly involved in lung development or oxygen metabolism, such as ubiqunegative regulation of mesenchymal cell proliferation involved in lung development, oxidoreductase activity, and peroxisome. Pathway analysis showed that DEcircRNAs were mainly enriched in oxidative phosphorylation, tight junction, VEGF/MAPK/PPAR/Ras/PI3K-Akt signaling pathway. We also constructed a circRNA-miRNA-mRNA-pathway network to visualize the regulatory relationship associated with hypoxia adaptation of the tight junction pathways. The circRNA expression profile was obtained to complement the current Tibetan chicken circRNA database and provides new information for future studies into biological adaptation to hypoxic stress in the Tibetan chicken. |
| doi_str_mv | 10.1007/s11756-021-00848-0 |
| format | Article |
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Gallus gallus
) provides high quality protein and iron for humans, which shows many phenotypic adaptations to the low oxygen. Study of the genetic mechanisms of circular RNAs (circRNAs) in hypoxia adaptation has not been reported. Four embryonic heart tissue samples from Tibetan chickens and Daheng broilers were collected. Differentially expressed circRNAs (DEcircRNAs) were identified via high-throughput sequencing. Bioinformatic analysis was used to indicate the functions and pathways of the DEcircRNAs. A total of 29 DEcircRNAs were identified between 4 Tibetan chickens and 4 Daheng broilers, including 15 upregulated and 14 downregulated DEcircRNAs in Tibetan chickens. GO analysis revealed that the DEcircRNAs were mainly involved in lung development or oxygen metabolism, such as ubiqunegative regulation of mesenchymal cell proliferation involved in lung development, oxidoreductase activity, and peroxisome. Pathway analysis showed that DEcircRNAs were mainly enriched in oxidative phosphorylation, tight junction, VEGF/MAPK/PPAR/Ras/PI3K-Akt signaling pathway. We also constructed a circRNA-miRNA-mRNA-pathway network to visualize the regulatory relationship associated with hypoxia adaptation of the tight junction pathways. The circRNA expression profile was obtained to complement the current Tibetan chicken circRNA database and provides new information for future studies into biological adaptation to hypoxic stress in the Tibetan chicken.</description><identifier>ISSN: 0006-3088</identifier><identifier>EISSN: 1336-9563</identifier><identifier>DOI: 10.1007/s11756-021-00848-0</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>1-Phosphatidylinositol 3-kinase ; Adaptation ; AKT protein ; Biomedical and Life Sciences ; Cell Biology ; Cell proliferation ; Chickens ; Embryos ; Hypoxia ; Life Sciences ; Lungs ; MAP kinase ; Mesenchyme ; Microbiology ; miRNA ; mRNA ; Next-generation sequencing ; Original Article ; Oxidative phosphorylation ; Oxidoreductase ; Oxygen ; Oxygen metabolism ; Peroxisome proliferator-activated receptors ; Phosphorylation ; Plant Sciences ; Poultry ; Signal transduction ; Vascular endothelial growth factor ; Zoology</subject><ispartof>Biológia, 2021-11, Vol.76 (11), p.3439-3447</ispartof><rights>Institute of Molecular Biology, Slovak Academy of Sciences 2021</rights><rights>Institute of Molecular Biology, Slovak Academy of Sciences 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c270t-6fa7e670647120a2d9ebf95496c2bd98f7e3803247fcf1775355771373e1968a3</cites><orcidid>0000-0002-7114-869X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11756-021-00848-0$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11756-021-00848-0$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27922,27923,41486,42555,51317</link.rule.ids></links><search><creatorcontrib>Zhang, Zengrong</creatorcontrib><creatorcontrib>Qiu, Mohan</creatorcontrib><creatorcontrib>Du, Huarui</creatorcontrib><creatorcontrib>Li, Qingyun</creatorcontrib><creatorcontrib>Gan, Wu</creatorcontrib><creatorcontrib>Xiong, Xia</creatorcontrib><creatorcontrib>Yu, Chunlin</creatorcontrib><creatorcontrib>Peng, Han</creatorcontrib><creatorcontrib>Xia, Bo</creatorcontrib><creatorcontrib>Song, Xiaoyan</creatorcontrib><creatorcontrib>Yang, Li</creatorcontrib><creatorcontrib>Hu, Chenming</creatorcontrib><creatorcontrib>Chen, Jialei</creatorcontrib><creatorcontrib>Jiang, Xiaosong</creatorcontrib><creatorcontrib>Yang, Chaowu</creatorcontrib><title>High-throughput sequencing revealed the expression profile and potential key molecules of the circular RNAs involved in the process of hypoxic adaptation in Tibetan chickens</title><title>Biológia</title><addtitle>Biologia</addtitle><description>The Tibetan chicken (
Gallus gallus
) provides high quality protein and iron for humans, which shows many phenotypic adaptations to the low oxygen. Study of the genetic mechanisms of circular RNAs (circRNAs) in hypoxia adaptation has not been reported. Four embryonic heart tissue samples from Tibetan chickens and Daheng broilers were collected. Differentially expressed circRNAs (DEcircRNAs) were identified via high-throughput sequencing. Bioinformatic analysis was used to indicate the functions and pathways of the DEcircRNAs. A total of 29 DEcircRNAs were identified between 4 Tibetan chickens and 4 Daheng broilers, including 15 upregulated and 14 downregulated DEcircRNAs in Tibetan chickens. GO analysis revealed that the DEcircRNAs were mainly involved in lung development or oxygen metabolism, such as ubiqunegative regulation of mesenchymal cell proliferation involved in lung development, oxidoreductase activity, and peroxisome. Pathway analysis showed that DEcircRNAs were mainly enriched in oxidative phosphorylation, tight junction, VEGF/MAPK/PPAR/Ras/PI3K-Akt signaling pathway. We also constructed a circRNA-miRNA-mRNA-pathway network to visualize the regulatory relationship associated with hypoxia adaptation of the tight junction pathways. The circRNA expression profile was obtained to complement the current Tibetan chicken circRNA database and provides new information for future studies into biological adaptation to hypoxic stress in the Tibetan chicken.</description><subject>1-Phosphatidylinositol 3-kinase</subject><subject>Adaptation</subject><subject>AKT protein</subject><subject>Biomedical and Life Sciences</subject><subject>Cell Biology</subject><subject>Cell proliferation</subject><subject>Chickens</subject><subject>Embryos</subject><subject>Hypoxia</subject><subject>Life Sciences</subject><subject>Lungs</subject><subject>MAP kinase</subject><subject>Mesenchyme</subject><subject>Microbiology</subject><subject>miRNA</subject><subject>mRNA</subject><subject>Next-generation sequencing</subject><subject>Original Article</subject><subject>Oxidative phosphorylation</subject><subject>Oxidoreductase</subject><subject>Oxygen</subject><subject>Oxygen metabolism</subject><subject>Peroxisome proliferator-activated receptors</subject><subject>Phosphorylation</subject><subject>Plant Sciences</subject><subject>Poultry</subject><subject>Signal transduction</subject><subject>Vascular endothelial growth factor</subject><subject>Zoology</subject><issn>0006-3088</issn><issn>1336-9563</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp9kdFuFCEUhonRxLX6Al6ReD16gBmYuWwatSaNTZp6TVjmsEM7hRGYTfeh-o6yuybeeUUI3_-dE35CPjL4zADUl8yY6mQDnDUAfds38IpsmBCyGTopXpMNAMhGQN-_Je9yfgBoVQdsQ16u_W5qypTiupuWtdCMv1cM1ocdTbhHM-NIy4QUn5eEOfsY6JKi8zNSE0a6xIKheDPTRzzQpzijXWfMNLpTyvpU7ybRu5-Xmfqwj_O-Cn04vVaRrc4jPB2W-OwtNaNZiinHMRW691ssJlA7efuIIb8nb5yZM374e16QX9--3l9dNze3339cXd40lisojXRGoVQgW8U4GD4OuHVD1w7S8u049E6h6EHwVjnrmFKd6DqlmFAC2SB7Iy7Ip7O3bli_Ixf9ENcU6kjNu0FILhlnleJnyqaYc0Knl-SfTDpoBvpYiz7Xomst-lSLhhoS51CucNhh-qf-T-oPJGyTWA</recordid><startdate>20211101</startdate><enddate>20211101</enddate><creator>Zhang, Zengrong</creator><creator>Qiu, Mohan</creator><creator>Du, Huarui</creator><creator>Li, Qingyun</creator><creator>Gan, Wu</creator><creator>Xiong, Xia</creator><creator>Yu, Chunlin</creator><creator>Peng, Han</creator><creator>Xia, Bo</creator><creator>Song, Xiaoyan</creator><creator>Yang, Li</creator><creator>Hu, Chenming</creator><creator>Chen, Jialei</creator><creator>Jiang, Xiaosong</creator><creator>Yang, Chaowu</creator><general>Springer International Publishing</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><orcidid>https://orcid.org/0000-0002-7114-869X</orcidid></search><sort><creationdate>20211101</creationdate><title>High-throughput sequencing revealed the expression profile and potential key molecules of the circular RNAs involved in the process of hypoxic adaptation in Tibetan chickens</title><author>Zhang, Zengrong ; Qiu, Mohan ; Du, Huarui ; Li, Qingyun ; Gan, Wu ; Xiong, Xia ; Yu, Chunlin ; Peng, Han ; Xia, Bo ; Song, Xiaoyan ; Yang, Li ; Hu, Chenming ; Chen, Jialei ; Jiang, Xiaosong ; Yang, Chaowu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c270t-6fa7e670647120a2d9ebf95496c2bd98f7e3803247fcf1775355771373e1968a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>1-Phosphatidylinositol 3-kinase</topic><topic>Adaptation</topic><topic>AKT protein</topic><topic>Biomedical and Life Sciences</topic><topic>Cell Biology</topic><topic>Cell proliferation</topic><topic>Chickens</topic><topic>Embryos</topic><topic>Hypoxia</topic><topic>Life Sciences</topic><topic>Lungs</topic><topic>MAP kinase</topic><topic>Mesenchyme</topic><topic>Microbiology</topic><topic>miRNA</topic><topic>mRNA</topic><topic>Next-generation sequencing</topic><topic>Original Article</topic><topic>Oxidative phosphorylation</topic><topic>Oxidoreductase</topic><topic>Oxygen</topic><topic>Oxygen metabolism</topic><topic>Peroxisome proliferator-activated receptors</topic><topic>Phosphorylation</topic><topic>Plant Sciences</topic><topic>Poultry</topic><topic>Signal transduction</topic><topic>Vascular endothelial growth factor</topic><topic>Zoology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Zengrong</creatorcontrib><creatorcontrib>Qiu, Mohan</creatorcontrib><creatorcontrib>Du, Huarui</creatorcontrib><creatorcontrib>Li, Qingyun</creatorcontrib><creatorcontrib>Gan, Wu</creatorcontrib><creatorcontrib>Xiong, Xia</creatorcontrib><creatorcontrib>Yu, Chunlin</creatorcontrib><creatorcontrib>Peng, Han</creatorcontrib><creatorcontrib>Xia, Bo</creatorcontrib><creatorcontrib>Song, Xiaoyan</creatorcontrib><creatorcontrib>Yang, Li</creatorcontrib><creatorcontrib>Hu, Chenming</creatorcontrib><creatorcontrib>Chen, Jialei</creatorcontrib><creatorcontrib>Jiang, Xiaosong</creatorcontrib><creatorcontrib>Yang, Chaowu</creatorcontrib><collection>CrossRef</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Biológia</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Zengrong</au><au>Qiu, Mohan</au><au>Du, Huarui</au><au>Li, Qingyun</au><au>Gan, Wu</au><au>Xiong, Xia</au><au>Yu, Chunlin</au><au>Peng, Han</au><au>Xia, Bo</au><au>Song, Xiaoyan</au><au>Yang, Li</au><au>Hu, Chenming</au><au>Chen, Jialei</au><au>Jiang, Xiaosong</au><au>Yang, Chaowu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>High-throughput sequencing revealed the expression profile and potential key molecules of the circular RNAs involved in the process of hypoxic adaptation in Tibetan chickens</atitle><jtitle>Biológia</jtitle><stitle>Biologia</stitle><date>2021-11-01</date><risdate>2021</risdate><volume>76</volume><issue>11</issue><spage>3439</spage><epage>3447</epage><pages>3439-3447</pages><issn>0006-3088</issn><eissn>1336-9563</eissn><abstract>The Tibetan chicken (
Gallus gallus
) provides high quality protein and iron for humans, which shows many phenotypic adaptations to the low oxygen. Study of the genetic mechanisms of circular RNAs (circRNAs) in hypoxia adaptation has not been reported. Four embryonic heart tissue samples from Tibetan chickens and Daheng broilers were collected. Differentially expressed circRNAs (DEcircRNAs) were identified via high-throughput sequencing. Bioinformatic analysis was used to indicate the functions and pathways of the DEcircRNAs. A total of 29 DEcircRNAs were identified between 4 Tibetan chickens and 4 Daheng broilers, including 15 upregulated and 14 downregulated DEcircRNAs in Tibetan chickens. GO analysis revealed that the DEcircRNAs were mainly involved in lung development or oxygen metabolism, such as ubiqunegative regulation of mesenchymal cell proliferation involved in lung development, oxidoreductase activity, and peroxisome. Pathway analysis showed that DEcircRNAs were mainly enriched in oxidative phosphorylation, tight junction, VEGF/MAPK/PPAR/Ras/PI3K-Akt signaling pathway. We also constructed a circRNA-miRNA-mRNA-pathway network to visualize the regulatory relationship associated with hypoxia adaptation of the tight junction pathways. The circRNA expression profile was obtained to complement the current Tibetan chicken circRNA database and provides new information for future studies into biological adaptation to hypoxic stress in the Tibetan chicken.</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><doi>10.1007/s11756-021-00848-0</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-7114-869X</orcidid></addata></record> |
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| subjects | 1-Phosphatidylinositol 3-kinase Adaptation AKT protein Biomedical and Life Sciences Cell Biology Cell proliferation Chickens Embryos Hypoxia Life Sciences Lungs MAP kinase Mesenchyme Microbiology miRNA mRNA Next-generation sequencing Original Article Oxidative phosphorylation Oxidoreductase Oxygen Oxygen metabolism Peroxisome proliferator-activated receptors Phosphorylation Plant Sciences Poultry Signal transduction Vascular endothelial growth factor Zoology |
| title | High-throughput sequencing revealed the expression profile and potential key molecules of the circular RNAs involved in the process of hypoxic adaptation in Tibetan chickens |
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