Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep
Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mechanism of FecB impact on reproduction is unclear. In this study,...
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| Veröffentlicht in: | Genes 2023-01, Vol.14 (1), p.203 |
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| creator | Xie, Lingli Miao, Xiangyang Luo, Qingmiao Zhao, Huijing Qin, Xiaoyu |
| description | Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mechanism of FecB impact on reproduction is unclear.
In this study, adult Han ewes with homozygous FecB(B)/FecB(B) mutations (Han BB group) and ewes with FecB(+)/FecB(+) wildtype (Han ++ group) were selected. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to identify differences in methylated genes in ovary tissue.
We examined differences in DNA methylation patterns between HanBB and Han ++ sheep. In both sheep, methylated reads were mainly distributed at the gene body regions, CpG islands and introns. The differentially methylated genes were enriched in neurotrophy in signaling pathway, Gonadotropin Releasing Hormone (GnRH) signaling pathway, Wnt signaling pathway, oocyte meiosis, vascular endothelial growth factor (VEGF) signaling pathway, etc. Differentially-methylated genes were co-analyzed with differentially-expressed mRNAs. Several genes which could be associated with female reproduction were identified, such as FOXP3 (forkhead box P3), TMEFF2 (Transmembrane Protein with EGF Like and Two Follistatin Like Domains 2) and ADAT2 (Adenosine Deaminase TRNA Specific 2).
We constructed a MeDIP-seq based methylomic study to investigate the ovarian DNA methylation differences between Small-Tail Han sheep with homozygous FecB mutant and wildtype, and successfully identified FecB gene-associated differentially-methylated genes. This study has provided information with which to understand the mechanisms of FecB gene-induced hyperprolificacy in sheep. |
| doi_str_mv | 10.3390/genes14010203 |
| format | Article |
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In this study, adult Han ewes with homozygous FecB(B)/FecB(B) mutations (Han BB group) and ewes with FecB(+)/FecB(+) wildtype (Han ++ group) were selected. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to identify differences in methylated genes in ovary tissue.
We examined differences in DNA methylation patterns between HanBB and Han ++ sheep. In both sheep, methylated reads were mainly distributed at the gene body regions, CpG islands and introns. The differentially methylated genes were enriched in neurotrophy in signaling pathway, Gonadotropin Releasing Hormone (GnRH) signaling pathway, Wnt signaling pathway, oocyte meiosis, vascular endothelial growth factor (VEGF) signaling pathway, etc. Differentially-methylated genes were co-analyzed with differentially-expressed mRNAs. Several genes which could be associated with female reproduction were identified, such as FOXP3 (forkhead box P3), TMEFF2 (Transmembrane Protein with EGF Like and Two Follistatin Like Domains 2) and ADAT2 (Adenosine Deaminase TRNA Specific 2).
We constructed a MeDIP-seq based methylomic study to investigate the ovarian DNA methylation differences between Small-Tail Han sheep with homozygous FecB mutant and wildtype, and successfully identified FecB gene-associated differentially-methylated genes. This study has provided information with which to understand the mechanisms of FecB gene-induced hyperprolificacy in sheep.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes14010203</identifier><identifier>PMID: 36672944</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Adenosine deaminase ; Animals ; CpG islands ; Data analysis ; DNA methylation ; DNA sequencing ; Epigenetics ; Epigenome ; FecB gene ; Fecundity ; Female ; Fertility - genetics ; Follistatin ; Forkhead protein ; Foxp3 protein ; Gene expression ; Genomes ; Genomics ; Genotype ; Genotype & phenotype ; Gonadotropin-releasing hormone ; Gonadotropins ; Immunoprecipitation ; Introns ; Meiosis ; Mutants ; Mutation ; Next-generation sequencing ; Ovaries ; Ovary - metabolism ; Ovulation ; Pituitary (anterior) ; Proteins ; RNA polymerase ; Sheep ; Sheep - genetics ; Signal transduction ; Statistical analysis ; Tail ; tRNA ; Vascular endothelial growth factor ; Vascular Endothelial Growth Factor A - genetics ; Wnt protein</subject><ispartof>Genes, 2023-01, Vol.14 (1), p.203</ispartof><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 by the authors. 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c415t-48c1edbb313457737f4464b38dc153c2126bfa66e48a814566aafdbedf5a5c6a3</citedby><cites>FETCH-LOGICAL-c415t-48c1edbb313457737f4464b38dc153c2126bfa66e48a814566aafdbedf5a5c6a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9859159/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9859159/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36672944$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Xie, Lingli</creatorcontrib><creatorcontrib>Miao, Xiangyang</creatorcontrib><creatorcontrib>Luo, Qingmiao</creatorcontrib><creatorcontrib>Zhao, Huijing</creatorcontrib><creatorcontrib>Qin, Xiaoyu</creatorcontrib><title>Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mechanism of FecB impact on reproduction is unclear.
In this study, adult Han ewes with homozygous FecB(B)/FecB(B) mutations (Han BB group) and ewes with FecB(+)/FecB(+) wildtype (Han ++ group) were selected. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to identify differences in methylated genes in ovary tissue.
We examined differences in DNA methylation patterns between HanBB and Han ++ sheep. In both sheep, methylated reads were mainly distributed at the gene body regions, CpG islands and introns. The differentially methylated genes were enriched in neurotrophy in signaling pathway, Gonadotropin Releasing Hormone (GnRH) signaling pathway, Wnt signaling pathway, oocyte meiosis, vascular endothelial growth factor (VEGF) signaling pathway, etc. Differentially-methylated genes were co-analyzed with differentially-expressed mRNAs. Several genes which could be associated with female reproduction were identified, such as FOXP3 (forkhead box P3), TMEFF2 (Transmembrane Protein with EGF Like and Two Follistatin Like Domains 2) and ADAT2 (Adenosine Deaminase TRNA Specific 2).
We constructed a MeDIP-seq based methylomic study to investigate the ovarian DNA methylation differences between Small-Tail Han sheep with homozygous FecB mutant and wildtype, and successfully identified FecB gene-associated differentially-methylated genes. This study has provided information with which to understand the mechanisms of FecB gene-induced hyperprolificacy in sheep.</description><subject>Adenosine deaminase</subject><subject>Animals</subject><subject>CpG islands</subject><subject>Data analysis</subject><subject>DNA methylation</subject><subject>DNA sequencing</subject><subject>Epigenetics</subject><subject>Epigenome</subject><subject>FecB gene</subject><subject>Fecundity</subject><subject>Female</subject><subject>Fertility - genetics</subject><subject>Follistatin</subject><subject>Forkhead protein</subject><subject>Foxp3 protein</subject><subject>Gene expression</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Genotype & phenotype</subject><subject>Gonadotropin-releasing hormone</subject><subject>Gonadotropins</subject><subject>Immunoprecipitation</subject><subject>Introns</subject><subject>Meiosis</subject><subject>Mutants</subject><subject>Mutation</subject><subject>Next-generation sequencing</subject><subject>Ovaries</subject><subject>Ovary - metabolism</subject><subject>Ovulation</subject><subject>Pituitary (anterior)</subject><subject>Proteins</subject><subject>RNA polymerase</subject><subject>Sheep</subject><subject>Sheep - genetics</subject><subject>Signal transduction</subject><subject>Statistical analysis</subject><subject>Tail</subject><subject>tRNA</subject><subject>Vascular endothelial growth factor</subject><subject>Vascular Endothelial Growth Factor A - genetics</subject><subject>Wnt protein</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpdkUlLxEAQhRtRVEaPXqXBi5do70kugo7LDLgc1HNT6VScSJIe04ngv7d1VNSioArq4_GKR8geZ0dS5uz4CTsMXDHOBJNrZFuwVCZKCb3-a98iuyE8s1gqYkxvki1pTCpypbbJbN4uwQ3UV_QS3Rm9GQcYat_R2Hev0NfQ0fPbU3qDw-Kt8S3SuqP3LTRN8gB1Q2fxfr9AXO6QjQqagLtfc0IeLy8eprPk-u5qPj29TpziekhU5jiWRSG5VDpNZVopZVQhs9JxLZ3gwhQVGIMqg4wrbQxAVRZYVhq0MyAn5GSluxyLFkuH3dBDY5d93UL_Zj3U9u-lqxf2yb_aPNM513kUOPwS6P3LiGGwbR0cNg106MdgRWoyITIdHU7IwT_02Y99F9_7oNJoVn8KJivK9T6EHqsfM5zZj5jsn5giv__7gx_6OxT5Duz1jKc</recordid><startdate>20230112</startdate><enddate>20230112</enddate><creator>Xie, Lingli</creator><creator>Miao, Xiangyang</creator><creator>Luo, Qingmiao</creator><creator>Zhao, Huijing</creator><creator>Qin, Xiaoyu</creator><general>MDPI AG</general><general>MDPI</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>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</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></search><sort><creationdate>20230112</creationdate><title>Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep</title><author>Xie, Lingli ; Miao, Xiangyang ; Luo, Qingmiao ; Zhao, Huijing ; Qin, Xiaoyu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c415t-48c1edbb313457737f4464b38dc153c2126bfa66e48a814566aafdbedf5a5c6a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Adenosine deaminase</topic><topic>Animals</topic><topic>CpG islands</topic><topic>Data analysis</topic><topic>DNA methylation</topic><topic>DNA sequencing</topic><topic>Epigenetics</topic><topic>Epigenome</topic><topic>FecB gene</topic><topic>Fecundity</topic><topic>Female</topic><topic>Fertility - genetics</topic><topic>Follistatin</topic><topic>Forkhead protein</topic><topic>Foxp3 protein</topic><topic>Gene expression</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Genotype</topic><topic>Genotype & phenotype</topic><topic>Gonadotropin-releasing hormone</topic><topic>Gonadotropins</topic><topic>Immunoprecipitation</topic><topic>Introns</topic><topic>Meiosis</topic><topic>Mutants</topic><topic>Mutation</topic><topic>Next-generation sequencing</topic><topic>Ovaries</topic><topic>Ovary - metabolism</topic><topic>Ovulation</topic><topic>Pituitary (anterior)</topic><topic>Proteins</topic><topic>RNA polymerase</topic><topic>Sheep</topic><topic>Sheep - genetics</topic><topic>Signal transduction</topic><topic>Statistical analysis</topic><topic>Tail</topic><topic>tRNA</topic><topic>Vascular endothelial growth factor</topic><topic>Vascular Endothelial Growth Factor A - genetics</topic><topic>Wnt protein</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Xie, Lingli</creatorcontrib><creatorcontrib>Miao, Xiangyang</creatorcontrib><creatorcontrib>Luo, Qingmiao</creatorcontrib><creatorcontrib>Zhao, Huijing</creatorcontrib><creatorcontrib>Qin, Xiaoyu</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection (ProQuest)</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</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><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xie, Lingli</au><au>Miao, Xiangyang</au><au>Luo, Qingmiao</au><au>Zhao, Huijing</au><au>Qin, Xiaoyu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2023-01-12</date><risdate>2023</risdate><volume>14</volume><issue>1</issue><spage>203</spage><pages>203-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mechanism of FecB impact on reproduction is unclear.
In this study, adult Han ewes with homozygous FecB(B)/FecB(B) mutations (Han BB group) and ewes with FecB(+)/FecB(+) wildtype (Han ++ group) were selected. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to identify differences in methylated genes in ovary tissue.
We examined differences in DNA methylation patterns between HanBB and Han ++ sheep. In both sheep, methylated reads were mainly distributed at the gene body regions, CpG islands and introns. The differentially methylated genes were enriched in neurotrophy in signaling pathway, Gonadotropin Releasing Hormone (GnRH) signaling pathway, Wnt signaling pathway, oocyte meiosis, vascular endothelial growth factor (VEGF) signaling pathway, etc. Differentially-methylated genes were co-analyzed with differentially-expressed mRNAs. Several genes which could be associated with female reproduction were identified, such as FOXP3 (forkhead box P3), TMEFF2 (Transmembrane Protein with EGF Like and Two Follistatin Like Domains 2) and ADAT2 (Adenosine Deaminase TRNA Specific 2).
We constructed a MeDIP-seq based methylomic study to investigate the ovarian DNA methylation differences between Small-Tail Han sheep with homozygous FecB mutant and wildtype, and successfully identified FecB gene-associated differentially-methylated genes. This study has provided information with which to understand the mechanisms of FecB gene-induced hyperprolificacy in sheep.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>36672944</pmid><doi>10.3390/genes14010203</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Adenosine deaminase Animals CpG islands Data analysis DNA methylation DNA sequencing Epigenetics Epigenome FecB gene Fecundity Female Fertility - genetics Follistatin Forkhead protein Foxp3 protein Gene expression Genomes Genomics Genotype Genotype & phenotype Gonadotropin-releasing hormone Gonadotropins Immunoprecipitation Introns Meiosis Mutants Mutation Next-generation sequencing Ovaries Ovary - metabolism Ovulation Pituitary (anterior) Proteins RNA polymerase Sheep Sheep - genetics Signal transduction Statistical analysis Tail tRNA Vascular endothelial growth factor Vascular Endothelial Growth Factor A - genetics Wnt protein |
| title | Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep |
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