A genome scale transcriptional regulatory model of the human placenta.
Publication Title
Sci Adv
Document Type
Article
Publication Date
6-28-2024
Keywords
washington; isb; genomics; Humans; Placenta; Female; Pregnancy; Gene Regulatory Networks; Transcription Factors; Genome, Human; Transcriptome; Gene Expression Regulation; Gene Expression Profiling
Abstract
Gene regulation is essential to placental function and fetal development. We built a genome-scale transcriptional regulatory network (TRN) of the human placenta using digital genomic footprinting and transcriptomic data. We integrated 475 transcriptomes and 12 DNase hypersensitivity datasets from placental samples to globally and quantitatively map transcription factor (TF)-target gene interactions. In an independent dataset, the TRN model predicted target gene expression with an out-of-sample R2 greater than 0.25 for 73% of target genes. We performed siRNA knockdowns of four TFs and achieved concordance between the predicted gene targets in our TRN and differences in expression of knockdowns with an accuracy of >0.7 for three of the four TFs. Our final model contained 113,158 interactions across 391 TFs and 7712 target genes and is publicly available. We identified 29 TFs which were significantly enriched as regulators for genes previously associated with preterm birth, and eight of these TFs were decreased in preterm placentas.
Area of Special Interest
Women & Children
Specialty/Research Institute
Oncology
Specialty/Research Institute
Institute for Systems Biology
DOI
10.1126/sciadv.adf3411
