A cell's history determines its fate and physiology, but it has been technically challenging to follow cellular history at a large scale and over extended periods. It has therefore been difficult to answer many important questions in biology and medicine: how are the cells in an organism related through their lineage? When was a cell exposed to a signal? Which neurons were active during a particular behavioral state? Answering these questions is fundamental for understanding the dynamics of multicellular systems. The premise of this proposal is that just as evolutionary history is recorded in genome sequence changes, a cell's history can be recorded by the introduction of changes in the genome. Recent genome editing studies have resulted in the development of a technology called GESTALT that uses the combinatorial and cumulative editing of a genomic barcode to permanently mark cells and through sequencing uncovers their lineage relationships. This and complementary studies have demonstrated the remarkable potential for DNA-mediated recording. The proposed project aims to optimize DNA-mediated recording and combine it with other nascent technologies to (1) record the lineage trees that generate the juvenile brain; (2) record the cellular history of Notch and TGF signaling pathway activation; and (3) record the history of neuronal activity during day/wake and night/sleep. Zebrafish will be used as a model system because of the powerful application of genomic, genetic and imaging approaches and its relevance to other vertebrates, including humans.

Public Health Relevance

The fate and physiology of a cell is a result of its history, but it has been technically challenging to follow cellular history at a large scale and over extended periods. This project aims to use DNA editing to record cellular history during development and behavior.

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
NIH Director’s Pioneer Award (NDPA) (DP1)
Project #
1DP1HD094764-01
Application #
9343374
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Henken, Deborah B
Project Start
2017-09-30
Project End
2022-06-30
Budget Start
2017-09-30
Budget End
2018-06-30
Support Year
1
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Harvard University
Department
Microbiology/Immun/Virology
Type
Schools of Arts and Sciences
DUNS #
082359691
City
Cambridge
State
MA
Country
United States
Zip Code
02138
Farrell, Jeffrey A; Wang, Yiqun; Riesenfeld, Samantha J et al. (2018) Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 360:
Raj, Bushra; Wagner, Daniel E; McKenna, Aaron et al. (2018) Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat Biotechnol 36:442-450
Pandey, Shristi; Shekhar, Karthik; Regev, Aviv et al. (2018) Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq. Curr Biol 28:1052-1065.e7
Raj, Bushra; Gagnon, James A; Schier, Alexander F (2018) Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT. Nat Protoc 13:2685-2713
Haesemeyer, Martin; Robson, Drew N; Li, Jennifer M et al. (2018) A Brain-wide Circuit Model of Heat-Evoked Swimming Behavior in Larval Zebrafish. Neuron 98:817-831.e6