Abnormal gene expression during early placental development has been associated with adverse pregnancy
outcomes. However, the transcriptional regulatory networks underlying normal placental development, includ-
ing the transcription factors, the enhancers they bind to, and the genes they regulate, are unknown. Until this fundamental gap is filled, the variants in genomic DNA that cause aberrant gene expression and lead to preg-
nancy complications cannot be understood. The applicant’s long-term goal is to identify global mechanisms by
which transcription factors and enhancers work together to regulate placental development. The overall objec-
tive of this application is to define and characterize transcriptional regulatory networks for processes that occur
during three critical time points of mouse placental development (embryonic days 7.5, 8.5, and 9.5), prior to the
formation of the mature placenta. The central hypothesis, based on published and preliminary data, is that time
point-specific transcriptional regulatory networks regulate distinct processes during early placental develop-
ment, and that disruption of transcription factors or enhancers central to these networks leads to abnormal
trophoblast gene expression. The rationale for the proposed research is that understanding the regulatory net-
works underlying early placental development will enable early detection and treatment of placental disorders.
The central hypothesis will be tested using three specific aims: (1) to define process-specific transcriptional
regulatory networks during early placental development;; (2) to determine the mechanisms by which key TF-
enhancer pairs regulate gene expression in mouse trophoblast subtypes;; and (3) to determine the relationship
between cis-regulation in mouse and human trophoblasts. To execute these aims, we will use an integrated
approach, combining experimental genomics (RNA-Seq, ChIP-Seq, and ATAC-Seq), computational analysis
(e.g. co-expression analysis, enhancer module analysis, and binding site predictions), and functional assays
(e.g. ChIP, reporter assays, and siRNA knockdown). Each aim is supported by a strong scientific premise and
preliminary data, and each method has been established either in the applicant’s lab or in the lab of a member
of the research team. Completion of this project will result in a global understanding of the transcriptional net-
works regulating early placental development, and in an understanding of the mechanisms by which key TF-
enhancer pairs regulate gene expression in mouse and human trophoblast cells. The research proposed in this
application is innovative, in the applicant’s opinion, because it represents a new and substantive departure
from the status quo by shifting focus to genome-scale identification and characterization of TF-enhancer net-
works that regulate specific processes during placental development. This contribution is significant because it
will provide a new understanding of normal placental development, ultimately leading to the development of
novel therapeutic interventions for placenta-associated disorders.