NSF Postdoctoral Fellowship in Biology FY 2021: Deciphering grammatical rules of notochord enhancers and their role in notochord development in Ciona intestinalis

Tellez, Krissie, San Diego CA

Investigators

Abstract

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2021, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. Early developmental stage cells differentiate into all of the cell types present in an organism’s adult body. These transitions are the result of changes in gene expression and the subsequent changes in RNA and protein products. Enhancers are genetic elements that encode instructions for the location and timing of gene expression, which ensures that tissues are created at the right time and place during development; variations in enhancer sequences are associated with outcomes that impact organisms in many ways. However, the millions of enhancer sequence variations have made it difficult to determine causal links between enhancer genotype and its expression (phenotype). The Fellow will investigate how control of gene expression is encoded within enhancers and the links between enhancers and these organismal traits. Research findings will be communicated by the Fellow to diverse audiences through mentorship of undergraduate student researchers and public science outreach programs. This research will examine tissue-specific enhancers in the notochord, an embryonic tissue that provides structural support and developmental patterning signals to adjacent tissues. To study how notochord activity is encoded within notochord-specific enhancers, the Fellow will create synthetic notochord enhancer variant reporter DNA constructs, which will be introduced into fertilized eggs of the sea squirt, Ciona intestinalis (Ciona). Ciona embryos will be screened for enhancer activity by measuring fluorescent reporter activity with microscopy and unique DNA barcode expression with RNA sequencing. The Fellow will use data generated from enhancer activity screens to identify common features of notochord enhancers. These notochord enhancer features will then be used to inform an existing computational pipeline to identify potential notochord enhancers within the Ciona genome. Additionally, the Fellow will use targeted gene editing in fertilized Ciona eggs to examine how genetic variations within notochord-specific enhancers impact gene expression (of genes controlled by selected enhancers) and notochord development (phenotype). Data generated from this research will be incorporated into interactive guest lectures for undergraduates; the Fellow will also gain training and experience in university-level teaching and mentorship, computational methods to analyze large data sets, and scientific communication. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.