The molecular basis of the cellular taxonomy of the human body

Breschi, A., Davis, C., Djebali, S., Gillis, J., Pervouchine, D. D., Vlasova, A., Dobin, A., Zaleski, C., Drenkow, J., Danyko, C., Scavelli, A., Munoz, M., Garrido, D., Reverter, F., Gingeras, T. R., Guigo, R. (March 2018) The molecular basis of the cellular taxonomy of the human body. Human Genomics, 12 (Supple). Meeting Abstract A107. ISSN 1473-9542

DOI: 10.1186/s40246-018-0138-6


The collection of RNA sequencing experiments produced by the ENCODE project from many cell lines and bulk tissues constitutes a comprehensive catalogue of the expression programs utilized by human cells. However, the relationship between the transcriptomes of tissues and the transcriptomes of the constituent primary cells, and how these impact tissue phenotypes has not been well established. Here we have produced RNA sequencing data for a number of primary cells from multiple human body locations. The analysis of this data, together with additional epigenetic data also produced by the ENCODE project for a total of 146 primary cells, indicate that most cells in the human body belong to five major cell types: epithelial, endothelial, mesenchymal, neural and blood cells. These redefine, based on gene expression, the basic histological types in which tissues are usually classified. We identified genes specific to these cell types, including a core set of transcription factors (TFs). Cell type specific genes, particularly when lying in open chromatin domains, are enriched for motifs for these cell type specific TFs, suggesting that they are potential candidates to drive cell type specificity. We estimated the relative proportion in tissues of the different cell types based on the transcriptional profiles obtained from bulk tissue sections. This inferred cellular composition is a characteristic signature of tissues and reflects.

Item Type: Paper
Additional Information: Meeting Abstract
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > RNA expression
Publication Type > Meeting Abstract
Investigative techniques and equipment > assays > RNA-seq
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Gillis Lab
CSHL labs > Gingeras lab
CSHL labs > Dobin Lab
Depositing User: Matt Covey
Date: 9 March 2018
Date Deposited: 23 Apr 2018 19:10
Last Modified: 08 Jul 2020 18:17

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