Synthetic and genomic regulatory elements reveal aspects of cis -regulatory grammar in mouse embryonic stem cells

• Published in: eLife Vol. 9
• Main Authors: King, Dana M, Hong, Clarice Kit Yee, Shepherdson, James L, Granas, David M, Maricque, Brett B, Cohen, Barak A
• Format: Journal Article
• Language: English
• Published: England eLife Science Publications, Ltd 11.02.2020; eLife Sciences Publications Ltd; eLife Sciences Publications, Ltd
• Subjects: Analysis; Animal genetics; Animals; Billboards; Binding sites; Computational and Systems Biology; Deoxyribonucleic acid; Design; DNA; DNA binding proteins; Embryo cells; Embryonic stem cells; Embryonic Stem Cells - metabolism; Gene expression; Genes; Genetic research; Genomes; Genomics; Grammar; Identity; Journalists; KLF4 protein; Language; Libraries; Mice; Multiprocessing; Occupancy; Oct-4 protein; Pluripotency; Proteins; Regulatory Elements, Transcriptional; Regulatory sequences; Stem cell transplantation; Stem cells; systems biology; Transcription (Genetics); Transcription factors; Transcription Factors - metabolism; computational biology; systems biology; mouse; pluripotency; transcription factors; gene expression
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.41279

In embryonic stem cells (ESCs), a core transcription factor (TF) network establishes the gene expression program necessary for pluripotency. To address how interactions between four key TFs contribute to regulation in mouse ESCs, we assayed two massively parallel reporter assay (MPRA) libraries composed of binding sites for SOX2, POU5F1 (OCT4), KLF4, and ESRRB. Comparisons between synthetic -regulatory elements and genomic sequences with comparable binding site configurations revealed some aspects of a regulatory grammar. The expression of synthetic elements is influenced by both the number and arrangement of binding sites. This grammar plays only a small role for genomic sequences, as the relative activities of genomic sequences are best explained by the predicted occupancy of binding sites, regardless of binding site identity and positioning. Our results suggest that the effects of transcription factor binding sites (TFBS) are influenced by the order and orientation of sites, but that in the genome the overall occupancy of TFs is the primary determinant of activity.