Single‐nucleus transcriptomics and chromatin accessibility analysis of musk gland development in Chinese forest musk deer (Moschus berezovskii)
Musk secreted by male forest musk deer (Moschus berezovskii) musk glands is an invaluable component of medicine and perfume. Musk secretion depends on musk gland maturation; however, the mechanism of its development remains elusive. Herein, using single cell multiome ATAC + gene expression coupled w...
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| Veröffentlicht in: | Integrative zoology 2024-09, Vol.19 (5), p.955-974 |
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| creator | LIU, Chenmiao HONG, Tingting ZHAO, Chengcheng XUE, Tao WANG, Shuhui REN, Zhanjun |
| description | Musk secreted by male forest musk deer (Moschus berezovskii) musk glands is an invaluable component of medicine and perfume. Musk secretion depends on musk gland maturation; however, the mechanism of its development remains elusive. Herein, using single cell multiome ATAC + gene expression coupled with several bioinformatic analyses, a dynamic transcriptional cell atlas of musk gland development was revealed, and key genes and transcription factors affecting its development were determined. Twelve cell types, including two different types of acinar cells (Clusters 0 and 10) were identified. Single‐nucleus RNA and single‐nucleus ATAC sequencing analyses revealed that seven core target genes associated with musk secretion (Hsd17b2, Acacb, Lss, Vapa, Aldh16a1, Aldh7a1, and Sqle) were regulated by 12 core transcription factors (FOXO1, CUX2, RORA, RUNX1, KLF6, MGA, NFIC, FOXO3, ETV5, NR3C1, HSF4, and MITF) during the development of Cluster 0 acinar cells. Kyoto Encyclopedia of Genes and Genomes enrichment showed significant changes in the pathways associated with musk secretion during acinar cell development. Gene set variation analysis also revealed that certain pathways associated with musk secretion were enriched in 6‐year‐old acinar cells. A gene co‐expression network was constructed during acinar cell development to provide a precise understanding of the connections between transcription factors, genes, and pathways. Finally, intercellular communication analysis showed that intercellular communication is involved in musk gland development. This study provides crucial insights into the changes and key factors underlying musk gland development, which serve as valuable resources for studying musk secretion mechanisms and promoting the protection of this endangered species.
Herein, using single cell multiome ATAC + gene expression coupled with several bioinformatic analyses, a dynamic transcriptional cell atlas of musk gland development was revealed, and key genes and transcription factors affecting its development were determined. |
| doi_str_mv | 10.1111/1749-4877.12823 |
| format | Article |
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Herein, using single cell multiome ATAC + gene expression coupled with several bioinformatic analyses, a dynamic transcriptional cell atlas of musk gland development was revealed, and key genes and transcription factors affecting its development were determined.</description><identifier>ISSN: 1749-4877</identifier><identifier>ISSN: 1749-4869</identifier><identifier>EISSN: 1749-4877</identifier><identifier>DOI: 10.1111/1749-4877.12823</identifier><identifier>PMID: 38644525</identifier><language>eng</language><publisher>Australia: Wiley Subscription Services, Inc</publisher><subject>Acinar cells ; Animals ; Cell interactions ; Chinese forest musk deer ; Chromatin ; Chromatin - metabolism ; Deer ; Deer - genetics ; Encyclopaedias ; Endangered species ; Fatty Acids, Monounsaturated - metabolism ; FOXO1 protein ; FOXO3 protein ; Gene expression ; Genes ; Genomes ; Glands ; Male ; Moschus berezovskii ; musk gland development ; Nucleus ; Rare species ; Runx1 protein ; Secretion ; single cell multiome ATAC + gene expression ; Transcription factors ; Transcriptome ; Transcriptomics</subject><ispartof>Integrative zoology, 2024-09, Vol.19 (5), p.955-974</ispartof><rights>2024 The Authors. published by International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.</rights><rights>2024 The Authors. Integrative Zoology published by International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.</rights><rights>2024. This article is published under http://creativecommons.org/licenses/by-nc-nd/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c3673-f9dd6a13211b81ee68f3debe97c40b85bda83c10e03823f9b988ab3e8f146f5a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2F1749-4877.12823$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1749-4877.12823$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>314,776,780,1411,27903,27904,45553,45554</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38644525$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>LIU, Chenmiao</creatorcontrib><creatorcontrib>HONG, Tingting</creatorcontrib><creatorcontrib>ZHAO, Chengcheng</creatorcontrib><creatorcontrib>XUE, Tao</creatorcontrib><creatorcontrib>WANG, Shuhui</creatorcontrib><creatorcontrib>REN, Zhanjun</creatorcontrib><title>Single‐nucleus transcriptomics and chromatin accessibility analysis of musk gland development in Chinese forest musk deer (Moschus berezovskii)</title><title>Integrative zoology</title><addtitle>Integr Zool</addtitle><description>Musk secreted by male forest musk deer (Moschus berezovskii) musk glands is an invaluable component of medicine and perfume. Musk secretion depends on musk gland maturation; however, the mechanism of its development remains elusive. Herein, using single cell multiome ATAC + gene expression coupled with several bioinformatic analyses, a dynamic transcriptional cell atlas of musk gland development was revealed, and key genes and transcription factors affecting its development were determined. Twelve cell types, including two different types of acinar cells (Clusters 0 and 10) were identified. Single‐nucleus RNA and single‐nucleus ATAC sequencing analyses revealed that seven core target genes associated with musk secretion (Hsd17b2, Acacb, Lss, Vapa, Aldh16a1, Aldh7a1, and Sqle) were regulated by 12 core transcription factors (FOXO1, CUX2, RORA, RUNX1, KLF6, MGA, NFIC, FOXO3, ETV5, NR3C1, HSF4, and MITF) during the development of Cluster 0 acinar cells. Kyoto Encyclopedia of Genes and Genomes enrichment showed significant changes in the pathways associated with musk secretion during acinar cell development. Gene set variation analysis also revealed that certain pathways associated with musk secretion were enriched in 6‐year‐old acinar cells. A gene co‐expression network was constructed during acinar cell development to provide a precise understanding of the connections between transcription factors, genes, and pathways. Finally, intercellular communication analysis showed that intercellular communication is involved in musk gland development. This study provides crucial insights into the changes and key factors underlying musk gland development, which serve as valuable resources for studying musk secretion mechanisms and promoting the protection of this endangered species.
Herein, using single cell multiome ATAC + gene expression coupled with several bioinformatic analyses, a dynamic transcriptional cell atlas of musk gland development was revealed, and key genes and transcription factors affecting its development were determined.</description><subject>Acinar cells</subject><subject>Animals</subject><subject>Cell interactions</subject><subject>Chinese forest musk deer</subject><subject>Chromatin</subject><subject>Chromatin - metabolism</subject><subject>Deer</subject><subject>Deer - genetics</subject><subject>Encyclopaedias</subject><subject>Endangered species</subject><subject>Fatty Acids, Monounsaturated - metabolism</subject><subject>FOXO1 protein</subject><subject>FOXO3 protein</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genomes</subject><subject>Glands</subject><subject>Male</subject><subject>Moschus berezovskii</subject><subject>musk gland development</subject><subject>Nucleus</subject><subject>Rare species</subject><subject>Runx1 protein</subject><subject>Secretion</subject><subject>single cell multiome ATAC + gene expression</subject><subject>Transcription factors</subject><subject>Transcriptome</subject><subject>Transcriptomics</subject><issn>1749-4877</issn><issn>1749-4869</issn><issn>1749-4877</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><recordid>eNqFkb9u1TAUhyMEoqUwsyFLLGW4rR07iTOiK_5UKmUAFhbLdo573TrxxScpukw8An3FPgkOaSvEghdb9nd-9vFXFM8ZPWJ5HLNGtCshm-aIlbLkD4r9-52Hf633iieIF5TWtKqrx8Uel7UQVVntF9ef_HAe4Obnr2GyASYkY9ID2uS3Y-y9RaKHjthNir0e_UC0tYDojQ9-3OUzHXbokURH-gkvyXmY8Q6uIMRtD8NIcs164wdAIC4mwHEBO4BEDj9EtJt8p4EEP-IVXnr_6mnxyOmA8Ox2Pii-vH3zef1-dfrx3cn69enK8rrhK9d2Xa0ZLxkzkgHU0vEODLSNFdTIynRacssoUJ4_xrWmlVIbDtIxUbtK84PicMndpvhtyg9TvUcLIXcAcULFqeCNpJWsM_ryH_QiTin3PlNtw1shOMvU8ULZFBETOLVNvtdppxhVsy01-1CzD_XHVq54cZs7mR66e_5OTwbqBfjuA-z-l6dOzr6WS_Jvx06jRQ</recordid><startdate>202409</startdate><enddate>202409</enddate><creator>LIU, Chenmiao</creator><creator>HONG, Tingting</creator><creator>ZHAO, Chengcheng</creator><creator>XUE, Tao</creator><creator>WANG, Shuhui</creator><creator>REN, Zhanjun</creator><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>WIN</scope><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>7SS</scope><scope>7TN</scope><scope>8FD</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>H99</scope><scope>L.F</scope><scope>L.G</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>202409</creationdate><title>Single‐nucleus transcriptomics and chromatin accessibility analysis of musk gland development in Chinese forest musk deer (Moschus berezovskii)</title><author>LIU, Chenmiao ; 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Musk secretion depends on musk gland maturation; however, the mechanism of its development remains elusive. Herein, using single cell multiome ATAC + gene expression coupled with several bioinformatic analyses, a dynamic transcriptional cell atlas of musk gland development was revealed, and key genes and transcription factors affecting its development were determined. Twelve cell types, including two different types of acinar cells (Clusters 0 and 10) were identified. Single‐nucleus RNA and single‐nucleus ATAC sequencing analyses revealed that seven core target genes associated with musk secretion (Hsd17b2, Acacb, Lss, Vapa, Aldh16a1, Aldh7a1, and Sqle) were regulated by 12 core transcription factors (FOXO1, CUX2, RORA, RUNX1, KLF6, MGA, NFIC, FOXO3, ETV5, NR3C1, HSF4, and MITF) during the development of Cluster 0 acinar cells. Kyoto Encyclopedia of Genes and Genomes enrichment showed significant changes in the pathways associated with musk secretion during acinar cell development. Gene set variation analysis also revealed that certain pathways associated with musk secretion were enriched in 6‐year‐old acinar cells. A gene co‐expression network was constructed during acinar cell development to provide a precise understanding of the connections between transcription factors, genes, and pathways. Finally, intercellular communication analysis showed that intercellular communication is involved in musk gland development. This study provides crucial insights into the changes and key factors underlying musk gland development, which serve as valuable resources for studying musk secretion mechanisms and promoting the protection of this endangered species.
Herein, using single cell multiome ATAC + gene expression coupled with several bioinformatic analyses, a dynamic transcriptional cell atlas of musk gland development was revealed, and key genes and transcription factors affecting its development were determined.</abstract><cop>Australia</cop><pub>Wiley Subscription Services, Inc</pub><pmid>38644525</pmid><doi>10.1111/1749-4877.12823</doi><tpages>20</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Acinar cells Animals Cell interactions Chinese forest musk deer Chromatin Chromatin - metabolism Deer Deer - genetics Encyclopaedias Endangered species Fatty Acids, Monounsaturated - metabolism FOXO1 protein FOXO3 protein Gene expression Genes Genomes Glands Male Moschus berezovskii musk gland development Nucleus Rare species Runx1 protein Secretion single cell multiome ATAC + gene expression Transcription factors Transcriptome Transcriptomics |
| title | Single‐nucleus transcriptomics and chromatin accessibility analysis of musk gland development in Chinese forest musk deer (Moschus berezovskii) |
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