An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver
Summary: An effective combination of multi-omic datasets can enhance our understanding of complex biological phenomena. To build a context-dependent network with multiple omic layers, i.e., a trans-omic network, we perform phosphoproteomics, transcriptomics, proteomics, and metabolomics of murine li...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-08-01
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| Series: | Cell Reports |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124721010032 |
| _version_ | 1818572822470983680 |
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| author | Fumiko Matsuzaki Shinsuke Uda Yukiyo Yamauchi Masaki Matsumoto Tomoyoshi Soga Kazumitsu Maehara Yasuyuki Ohkawa Keiichi I. Nakayama Shinya Kuroda Hiroyuki Kubota |
| author_facet | Fumiko Matsuzaki Shinsuke Uda Yukiyo Yamauchi Masaki Matsumoto Tomoyoshi Soga Kazumitsu Maehara Yasuyuki Ohkawa Keiichi I. Nakayama Shinya Kuroda Hiroyuki Kubota |
| author_sort | Fumiko Matsuzaki |
| collection | DOAJ |
| description | Summary: An effective combination of multi-omic datasets can enhance our understanding of complex biological phenomena. To build a context-dependent network with multiple omic layers, i.e., a trans-omic network, we perform phosphoproteomics, transcriptomics, proteomics, and metabolomics of murine liver for 4 h after insulin administration and integrate the resulting time series. Structural characteristics and dynamic nature of the network are analyzed to elucidate the impact of insulin. Early and prominent changes in protein phosphorylation and persistent and asynchronous changes in mRNA and protein levels through non-transcriptional mechanisms indicate enhanced crosstalk between phosphorylation-mediated signaling and protein expression regulation. Metabolic response shows different temporal regulation with transient increases at early time points across categories and enhanced response in the amino acid and nucleotide categories at later time points as a result of process convergence. This extensive and dynamic view of the trans-omic network elucidates prominent regulatory mechanisms that drive insulin responses through intricate interlayer coordination. |
| first_indexed | 2024-12-15T00:02:47Z |
| format | Article |
| id | doaj.art-bda0cb6d08e645f0b537c16d4a675d84 |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-12-15T00:02:47Z |
| publishDate | 2021-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-bda0cb6d08e645f0b537c16d4a675d842022-12-21T22:42:51ZengElsevierCell Reports2211-12472021-08-01368109569An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liverFumiko Matsuzaki0Shinsuke Uda1Yukiyo Yamauchi2Masaki Matsumoto3Tomoyoshi Soga4Kazumitsu Maehara5Yasuyuki Ohkawa6Keiichi I. Nakayama7Shinya Kuroda8Hiroyuki Kubota9Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, JapanResearch Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, JapanResearch Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, JapanDepartment of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata 951-8510, JapanInstitute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, JapanResearch Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, JapanResearch Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, JapanDepartment of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, JapanDepartment of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, JapanResearch Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan; Corresponding authorSummary: An effective combination of multi-omic datasets can enhance our understanding of complex biological phenomena. To build a context-dependent network with multiple omic layers, i.e., a trans-omic network, we perform phosphoproteomics, transcriptomics, proteomics, and metabolomics of murine liver for 4 h after insulin administration and integrate the resulting time series. Structural characteristics and dynamic nature of the network are analyzed to elucidate the impact of insulin. Early and prominent changes in protein phosphorylation and persistent and asynchronous changes in mRNA and protein levels through non-transcriptional mechanisms indicate enhanced crosstalk between phosphorylation-mediated signaling and protein expression regulation. Metabolic response shows different temporal regulation with transient increases at early time points across categories and enhanced response in the amino acid and nucleotide categories at later time points as a result of process convergence. This extensive and dynamic view of the trans-omic network elucidates prominent regulatory mechanisms that drive insulin responses through intricate interlayer coordination.http://www.sciencedirect.com/science/article/pii/S2211124721010032trans-omicsmulti-omicstrans-omic networknetwork dynamicsinsulin |
| spellingShingle | Fumiko Matsuzaki Shinsuke Uda Yukiyo Yamauchi Masaki Matsumoto Tomoyoshi Soga Kazumitsu Maehara Yasuyuki Ohkawa Keiichi I. Nakayama Shinya Kuroda Hiroyuki Kubota An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver Cell Reports trans-omics multi-omics trans-omic network network dynamics insulin |
| title | An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver |
| title_full | An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver |
| title_fullStr | An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver |
| title_full_unstemmed | An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver |
| title_short | An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver |
| title_sort | extensive and dynamic trans omic network illustrating prominent regulatory mechanisms in response to insulin in the liver |
| topic | trans-omics multi-omics trans-omic network network dynamics insulin |
| url | http://www.sciencedirect.com/science/article/pii/S2211124721010032 |
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