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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...

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Autores principales: Yuan, Meng, Yang, Xujiang, Lin, Jinghua, Cao, Xiaolong, Chen, Feng, Zhang, Xiaoyu, Li, Zizhang, Zheng, Guifeng, Wang, Xueqin, Chen, Xiaoshu, Yang, Jian-Rong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2020
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.
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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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