Tatjana Piotrowski Ph.D.

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Cross-Species Epigenetics

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Cross-Species Epigenetics
Tatjana Piotrowski, Ph.D. (chair), Stowers Institute for Medical Research
Alain Dabdoub, Ph.D., Sunnybrook Research Institute
Andy Groves, Ph.D., Baylor College of Medicine
Stefan Heller, Ph.D., Stanford University
The Lab of Neil Segil, Ph.D., University of Southern California
Litao Tao, Ph.D., Creighton University

This group will complete the collection of transcriptomic and epigenetic data from systems that regenerate (neonatal mouse, zebrafish, chick) and those that do not (mature mouse and human). In addition, they will begin to perform cross-species comparisons of the behavior of a shared set of hair cell loci across species. Collection of chick data is spearheaded by the Heller lab; the Groves, Segil, and Tao labs are responsible for mouse data; the Piotrowski lab leads work on zebrafish; and the Dabdoub lab will add data from humans. High-quality single-cell RNA-seq, ATAC-seq, and SHARE-seq data from multiple timepoints and conditions will be generated by all member labs.

Fish Epigenomics and Enhancer Screening

Fish epigenomics and enhancer screening
Tatjana Piotrowski, Ph.D. Stowers Institute for Medical Research

As explained in Project #2, many genes are turned off by chemical modifications (epigenetic marks) that silence genes and prevent their activation. This inactivation often occurs at enhancers, which are regions of DNA that control the activation of genes. In this project, Piotrowski will use the ATAC-seq and H3K27ac ChIP-seq methods, which were successful for the mouse inner ear, to find enhancers that are active during hair cell regeneration in the fish. Identification of regeneration enhancers will enable the HRP to examine epigenetic marks comparatively—to determine whether regenerating species, such as the zebrafish and chick, utilize different enhancers than non-regenerating species like the mouse, or whether these enhancers are inactive in mammals.

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Transcriptomics-based Analysis of Hair Cell Regeneration in Non-Mammals

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Transcriptomics-based analysis of hair cell regeneration in non-mammals
Stefan Heller, Ph.D. Stanford University
Tatjana Piotrowski, Ph.D. Stowers Institute for Medical Research
Jennifer Stone, Ph.D. University of Washington
Mark Warchol, Ph.D. Washington University in St. Louis
Michael Lovett, Ph.D. Imperial College London

In this third-year project, we will disrupt hair cells, then analyze how gene expression changes in single cells from species that show robust hair cell regeneration. Heller’s lab will examine the consequences of aminoglycoside damage at the single-cell level in the chick utricle, while the Piotrowski lab will examine fish lateral-line cells. In another component, the project will add two time points to the chick cochlea and utricle bulk RNA-seq datasets that were generated by Lovett and Warchol and which are extremely valuable datasets for the HRP consortium.

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Single-cell RNA-seq Expression Analysis of Homeostatic Zebrafish Neuromasts

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Single-cell RNA-seq expression analysis of homeostatic zebrafish neuromasts
Stefan Heller, Ph.D. Stanford University School of Medicine
Tatjana Piotrowski, Ph.D. Stowers Institute for Medical Research

The zebrafish is one of the primary models of the HRP, as hair cells in its lateral line organ show robust regeneration. Because of its superficial location in the skin, we can watch the regeneration process at the single-cell level using microscopy. We discovered that even within a regenerating cell population, individual cells are not synchronized in their behavior and gene expression. Therefore, conventional
gene expression analyses of the entire cell population provide only averages of gene expression, masking the cell heterogeneity.This project will use single-cell expression analysis techniques to determine how many supporting cell types exist and in future experiments how they respond to damage with high precision.

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Single Cell RT-PCR-based Expression Analysis of Homeostatic and Regenerating Zebrafish Neuromasts

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Single cell RT-PCR-based expression analysis of homeostatic and regenerating zebrafish neuromasts
Tatjana Piotrowski, Ph.D. Stowers Institute for Medical Research
Stefan Heller, Ph.D. Stanford University School of Medicine

The zebrafish is one of the primary models of the HRP; hair cells in its lateral line organ show robust regeneration, the accessibility of this organ means that we can watch the whole process take place using microscopy. However, the lack of complete synchronization of this process means that when we are looking at molecular changes, they are smeared out in time. This project will use single-cell transcript analysis techniques to order supporting cell responses to damage and determine the order of expression of transcripts with high precision.

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