Combinatorial expression motifs in signaling pathways
Summary: In animal cells, molecular pathways often comprise families of variant components, such as ligands or receptors. These pathway components are differentially expressed by different cell types, potentially tailoring pathway function to cell context. However, it has remained unclear how pathwa...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-01-01
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| Series: | Cell Genomics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666979X23003075 |
| _version_ | 1797356890550697984 |
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| author | Alejandro A. Granados Nivedita Kanrar Michael B. Elowitz |
| author_facet | Alejandro A. Granados Nivedita Kanrar Michael B. Elowitz |
| author_sort | Alejandro A. Granados |
| collection | DOAJ |
| description | Summary: In animal cells, molecular pathways often comprise families of variant components, such as ligands or receptors. These pathway components are differentially expressed by different cell types, potentially tailoring pathway function to cell context. However, it has remained unclear how pathway expression profiles are distributed across cell types and whether similar profiles can occur in dissimilar cell types. Here, using single-cell gene expression datasets, we identified pathway expression motifs, defined as recurrent expression profiles that are broadly distributed across diverse cell types. Motifs appeared in core pathways, including TGF-β, Notch, Wnt, and the SRSF splice factors, and involved combinatorial co-expression of multiple components. Motif usage was weakly correlated between pathways in adult cell types and during dynamic developmental transitions. Together, these results suggest a mosaic view of cell type organization, in which different cell types operate many of the same pathways in distinct modes. |
| first_indexed | 2024-03-08T14:35:27Z |
| format | Article |
| id | doaj.art-9eec8271a7a34aefb49fabbbb083935f |
| institution | Directory Open Access Journal |
| issn | 2666-979X |
| language | English |
| last_indexed | 2024-03-08T14:35:27Z |
| publishDate | 2024-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Genomics |
| spelling | doaj.art-9eec8271a7a34aefb49fabbbb083935f2024-01-12T04:57:44ZengElsevierCell Genomics2666-979X2024-01-0141100463Combinatorial expression motifs in signaling pathwaysAlejandro A. Granados0Nivedita Kanrar1Michael B. Elowitz2Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USADivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USADivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA; Corresponding authorSummary: In animal cells, molecular pathways often comprise families of variant components, such as ligands or receptors. These pathway components are differentially expressed by different cell types, potentially tailoring pathway function to cell context. However, it has remained unclear how pathway expression profiles are distributed across cell types and whether similar profiles can occur in dissimilar cell types. Here, using single-cell gene expression datasets, we identified pathway expression motifs, defined as recurrent expression profiles that are broadly distributed across diverse cell types. Motifs appeared in core pathways, including TGF-β, Notch, Wnt, and the SRSF splice factors, and involved combinatorial co-expression of multiple components. Motif usage was weakly correlated between pathways in adult cell types and during dynamic developmental transitions. Together, these results suggest a mosaic view of cell type organization, in which different cell types operate many of the same pathways in distinct modes.http://www.sciencedirect.com/science/article/pii/S2666979X23003075single celltranscriptional profilessignaling pathwaysmotifsintegrated datatranscriptome |
| spellingShingle | Alejandro A. Granados Nivedita Kanrar Michael B. Elowitz Combinatorial expression motifs in signaling pathways Cell Genomics single cell transcriptional profiles signaling pathways motifs integrated data transcriptome |
| title | Combinatorial expression motifs in signaling pathways |
| title_full | Combinatorial expression motifs in signaling pathways |
| title_fullStr | Combinatorial expression motifs in signaling pathways |
| title_full_unstemmed | Combinatorial expression motifs in signaling pathways |
| title_short | Combinatorial expression motifs in signaling pathways |
| title_sort | combinatorial expression motifs in signaling pathways |
| topic | single cell transcriptional profiles signaling pathways motifs integrated data transcriptome |
| url | http://www.sciencedirect.com/science/article/pii/S2666979X23003075 |
| work_keys_str_mv | AT alejandroagranados combinatorialexpressionmotifsinsignalingpathways AT niveditakanrar combinatorialexpressionmotifsinsignalingpathways AT michaelbelowitz combinatorialexpressionmotifsinsignalingpathways |