Understanding the molecular regulation of early mammalian development is of fundamental importance and may inform new therapeutic avenues in Reproductive Health and Regenerative Medicine. Our knowledge of early development is very limited and largely derived from studies of single copy protein-coding genes. However, single copy protein-coding genes comprise only a minor fraction (~2%) of our genome. About half of the mouse and human genomes is derived from Transposable Elements (TEs), which are sequences repeated throughout the chromosomes and in some cases capable of moving to different locations in the genome. Despite being generally silenced in differentiated cell types, certain classes of TEs are highly expressed in mouse and human pre-implantation embryos and pluripotent stem cells. The role of TEs in early mammalian development remains essentially unknown. Our preliminary data in mouse embryonic stem cells and embryos support a new model in which the alternative transcriptional programs of totipotency and pluripotency are regulated by distinct classes of TEs. We will test the hypothesis that RNA derived from one family of TEs acts in cis as a long non-coding RNA to bind specific sites in the chromatin and promote pluripotency in part by repressing another family of TEs. Elements of this second family of TEs, in turn, act as promoters for genes that drive expression of the totipotency program.
In Aim 1, we will dissect the antagonistic role of specific TEs in mouse embryonic stem cells;
in Aim 2, we will use cutting-edge technology to dissect the molecular mechanism of action of a critical family of TEs in embryonic stem cells;
in Aim 3, we will define the molecular role of this TE in early mouse development. This proposal is anticipated to cast pre-implantation development in an entirely new light, uncovering specific TEs as key mediators of the totipotency-to-pluripotency transition and deciphering their mechanism of action. This knowledge is expected to have important implications for understanding and treating infertility, and for using pluripotent stem cells as a platform for studying and treating degenerative diseases.

Public Health Relevance

The proposed research aims to understand the molecular regulation of developmental progression in the early mammalian embryo. Such fundamental knowledge is relevant to the mission of the NIH because it may contribute to a better understanding and treatment of infertility, and to harnessing the potential of pluripotent stem cells in Regenerative Medicine.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Development - 2 Study Section (DEV2)
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Gibbs, Kenneth D
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University of California San Francisco
Obstetrics & Gynecology
Schools of Medicine
San Francisco
United States
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Percharde, Michelle; Lin, Chih-Jen; Yin, Yafei et al. (2018) A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity. Cell 174:391-405.e19
Bulut-Karslioglu, Aydan; Macrae, Trisha A; Oses-Prieto, Juan A et al. (2018) The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output. Cell Stem Cell 22:369-383.e8