Type
Text
Type
Dissertation
Advisor
Gergen, J. Peter | Sirotkin, Howard | Martin, Benjamin | Gingeras, Thomas | Rushlow, Christine.
Date
2015-12-01
Keywords
Genetics | blastoderm, cis-regulatory module, enhancer-promoter interaction, transcription, wingless
Department
Department of Genetics.
Language
en_US
Source
This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree.
Identifier
http://hdl.handle.net/11401/77620
Publisher
The Graduate School, Stony Brook University: Stony Brook, NY.
Format
application/pdf
Abstract
The Drosophila anterior/posterior segmentation pathway is a robust system for investigating transcription regulation in an in vivo setting. Runt, the founding member of the Runx family of transcription factors, is a master regulator of gene expression during development. Distinct combinations of Runt and other pair-rule factors act at two recently identified cis-regulatory modules (CRMs) DESE and PESE, to generate the initial 14-stripe sloppy paired 1 (slp1) pattern (Swantek & Gergen, 2004; Prazak et al, 2010). Each CRM alone drives a subset of the slp1 pattern, but their combined action recapitulates early expression of slp1 in a manner not expected from simple addition of their respective patterns. Runt is key in mediating these “non-additive†interactions, and its presence determines which enhancer regulates activity of the promoter in a particular cell context. I investigated if Runt mediates non-additive interactions for the segment polarity gene, wingless (wg). Experiments utilizing reporter constructs containing two putative pair-rule regulated CRMs for wg and double in situ hybridization confirm that the two CRMs are active at the blastoderm stage and moreover, respond to pair-rule regulation. Each CRM drives expression of all 14 wg stripes, however wg2946 also drives ectopic expression posterior to the odd-numbered stripes, and the even-numbered stripes are weak. A composite wg3911/2946 reporter recapitulates the endogenous wg pattern. Pair-rule loss and gain of function experiments reveal both similarities and differences to slp1 regulation. This detailed functional analysis was complemented by efforts to investigate the physical basis of CRM/promoter interactions in different genetic backgrounds. 4C-seq and ChIP experiments can confirm if Runt mediates physical interactions and influences modENCODE identified enhancer signatures. Overall, these experiments provide a second example of the Runt-dependent regulation of enhancer promoter interaction and further suggest that the non-additive integration of inputs from different CRMs is a widespread aspect of regulating transcription in animal systems. | 108 pages
Recommended Citation
Bell, Kimberly, "Regulation of wingless transcription in the Drosophila blastoderm embryo" (2015). Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions). 3415.
https://commons.library.stonybrook.edu/stony-brook-theses-and-dissertations-collection/3415