Sequencing an inserted concatemer in Caenorhabditis elegans strain hlh-29::gfp

Author

Simon T. Anderson, James Madison UniversityFollow

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 4.0 International License.

Date of Graduation

12-17-2022

ORCID

https://orcid.org/0000-0002-1624-5542

Publish

yes

Document Type

Thesis

Degree Name

Bachelor of Science (BS)

Department

Department of Biology

Advisor(s)

Casonya M. Johnson

Karen B. Barnard-Kubow

Timothy A. Bloss

Abstract

Hairy/Enhancer of Split (HES) proteins and their homologs play vital roles in the development of animals, and in the regulation of cancer and other diseases. HLH-29 is an REF-1 family protein and a Caenorhabditis elegans homolog of human HES proteins. A transgenic animal model has been developed to facilitate analyses of this protein, containing an inserted concatemer of the green fluorescent protein reporter gene, regulated by the hlh-29 promoter, and a mutant rol-6 allele. Though the strain has been used previously, the location and structure of the insertion has been unknown. Sequencing of the whole hlh-29::gfp genome with high-molecular weight Nanopore sequencing on the MinION platform has elucidated the structure. The concatemer was found to have been inserted into Chromosome III of Bristol N2 oocytes, deleting two genes with no immediately observable phenotypic abnormalities. The insertion was found to be at least 188.5 kb long, containing 26 copies of hlh-29::gfp and 11 copies of rol-6. While the hlh-29::gfp strain was confirmed to be a good tool for investigating expression of HLH-29, the insertion could not be assembled in its entirety and is likely much longer than 188 kb. Future use of this strain may seek to model dysregulation of HLH-29 in response to oxidative stress, which has implications for the alleviation of health disparities regarding various types of breast cancer.

Recommended Citation

Anderson, Simon T., "Sequencing an inserted concatemer in Caenorhabditis elegans strain hlh-29::gfp" (2022). Senior Honors Projects, 2020-current. 135.
https://commons.lib.jmu.edu/honors202029/135