Animal development requires exquisite coordination of developmental transitions. These transitions include moving from pluripotent to differentiated cell states, proliferation via the cell cycle, and changes in gene expression. When these transitions go awry in humans, developmental defects or diseases such as cancer can result. Many embryos undergo a major developmental transition when maternally deposited mRNAs are cleared and embryonic (zygotic) genes are activated, a process called the Maternal- to-Zygotic Transition (MZT). In many vertebrate species, the timing of the MZT depends on changes in the DNA-to-cytoplasmic ratio and a titration mechanism: As the DNA content increases exponentially with each round of cell division (in an embryo of constant size), the inhibitory factor(s) is titrated away, allowing gene activation. This gene expression is accompanied by changes in cellular properties such as the slowing of cell division, and the start of cell migration. The titratable inhibitory factor(s) was demonstrated by the sponsors' labs to be histones--proteins that bind to DNA to form nucleosomes. It is unknown, however, how this mechanism regulates gene expression at the MZT. Using the Xenopus (frog) embryo system, a powerful model organism for cell fate studies, I propose to test the histone titration hypothesis i vivo, and determine whether a causal relationship exists between nucleosome occupancy and the start of embryonic transcription. I will use biochemical methods and high-throughput sequencing to define temporal dynamics of new zygotic transcription at the MBT (Aim1), identify nucleosome-rich and nucleosome-depleted loci (Aim2), and analyze these data in embryos with wild-type or manipulated histone levels (Aim3). I will also test the hypothesis that specific earl expressed zygotic genes provide feedback to sharpen MBT events and further promote zygotic transcription. The results of this proposal will provide insight global gene regulation, developmental reprogramming, and cell fate transitions. Many processes that occur during early Xenopus development also occur in human development, so this study will also provide insight into human birth defects and cancer.
The precise timing of when genes turn ON and OFF is critical for human development, physiology, and disease. We use the frog embryo to study how genes turn on because frogs are vertebrates and share many developmental features with humans. Insights from these experiments will help understand how an embryo develops, and also provide knowledge that relates to cancer, cell reprogramming, and regenerative medicine.
| Bell, Jason C; Jukam, David; Teran, Nicole A et al. (2018) Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts. Elife 7: |
| Jukam, David; Shariati, S Ali M; Skotheim, Jan M (2017) Zygotic Genome Activation in Vertebrates. Dev Cell 42:316-332 |
| Amodeo, Amanda A; Jukam, David; Straight, Aaron F et al. (2015) Histone titration against the genome sets the DNA-to-cytoplasm threshold for the Xenopus midblastula transition. Proc Natl Acad Sci U S A 112:E1086-95 |
