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Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types
A full understanding of the developmental process requires fine-scale characterization of cell divisions and cell types, which are naturally organized as the developmental cell lineage tree (CLT). Technological breakthroughs facilitated determination of more CLTs, but complete comprehension of the d...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7327887/ https://www.ncbi.nlm.nih.gov/pubmed/32599560 http://dx.doi.org/10.1016/j.isci.2020.101273 |
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author | Yuan, Meng Yang, Xujiang Lin, Jinghua Cao, Xiaolong Chen, Feng Zhang, Xiaoyu Li, Zizhang Zheng, Guifeng Wang, Xueqin Chen, Xiaoshu Yang, Jian-Rong |
author_facet | Yuan, Meng Yang, Xujiang Lin, Jinghua Cao, Xiaolong Chen, Feng Zhang, Xiaoyu Li, Zizhang Zheng, Guifeng Wang, Xueqin Chen, Xiaoshu Yang, Jian-Rong |
author_sort | Yuan, Meng |
collection | PubMed |
description | A full understanding of the developmental process requires fine-scale characterization of cell divisions and cell types, which are naturally organized as the developmental cell lineage tree (CLT). Technological breakthroughs facilitated determination of more CLTs, but complete comprehension of the data remains difficult without quantitative comparison among CLTs. We hereby quantified phenotypic similarity between CLTs using a novel computational method that exhaustively searches for optimal correspondence between individual cells meanwhile retaining their topological relationships. The revealed CLT similarities allowed us to infer functional similarity at the transcriptome level, identify cell fate transformations, predict functional relationships between mutants, and find evolutionary correspondence between cell types of different species. By allowing quantitative comparison between CLTs, our work is expected to greatly enhance the interpretability of relevant data and help answer the myriad of questions surrounding the developmental process. |
format | Online Article Text |
id | pubmed-7327887 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-73278872020-07-06 Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types Yuan, Meng Yang, Xujiang Lin, Jinghua Cao, Xiaolong Chen, Feng Zhang, Xiaoyu Li, Zizhang Zheng, Guifeng Wang, Xueqin Chen, Xiaoshu Yang, Jian-Rong iScience Article A full understanding of the developmental process requires fine-scale characterization of cell divisions and cell types, which are naturally organized as the developmental cell lineage tree (CLT). Technological breakthroughs facilitated determination of more CLTs, but complete comprehension of the data remains difficult without quantitative comparison among CLTs. We hereby quantified phenotypic similarity between CLTs using a novel computational method that exhaustively searches for optimal correspondence between individual cells meanwhile retaining their topological relationships. The revealed CLT similarities allowed us to infer functional similarity at the transcriptome level, identify cell fate transformations, predict functional relationships between mutants, and find evolutionary correspondence between cell types of different species. By allowing quantitative comparison between CLTs, our work is expected to greatly enhance the interpretability of relevant data and help answer the myriad of questions surrounding the developmental process. Elsevier 2020-06-16 /pmc/articles/PMC7327887/ /pubmed/32599560 http://dx.doi.org/10.1016/j.isci.2020.101273 Text en © 2020 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Article Yuan, Meng Yang, Xujiang Lin, Jinghua Cao, Xiaolong Chen, Feng Zhang, Xiaoyu Li, Zizhang Zheng, Guifeng Wang, Xueqin Chen, Xiaoshu Yang, Jian-Rong Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types |
title | Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types |
title_full | Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types |
title_fullStr | Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types |
title_full_unstemmed | Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types |
title_short | Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types |
title_sort | alignment of cell lineage trees elucidates genetic programs for the development and evolution of cell types |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7327887/ https://www.ncbi.nlm.nih.gov/pubmed/32599560 http://dx.doi.org/10.1016/j.isci.2020.101273 |
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