TY - JOUR
T1 - Synthetic and genomic regulatory elements reveal aspects of Cis-regulatory grammar in mouse embryonic stem cells
AU - King, Dana M.
AU - Hong, Clarice Kit Yee
AU - Shepherdson, James L.
AU - Granas, David M.
AU - Maricque, Brett B.
AU - Cohen, Barak A.
N1 - Funding Information:
We thank members of the Cohen Lab for critical reading and feedback, particularly Michael White, Max Staller and Hemangi Chaudhari for helpful discussion over the course of the project, Jessica Hoisington-Lopez from the DNA Sequencing Innovation Lab for assistance with high-throughput sequencing, and Karl Kumbier for modeling discussions. This work is supported by a grant from the National Institutes of Health, R01 GM092910 to B.A.C.
Publisher Copyright:
© 2020, eLife Sciences Publications Ltd. All rights reserved.
PY - 2020/2
Y1 - 2020/2
N2 - 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 cis-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 cis-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 affinity 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.
AB - 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 cis-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 cis-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 affinity 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.
UR - http://www.scopus.com/inward/record.url?scp=85082095662&partnerID=8YFLogxK
U2 - 10.7554/eLife.41279
DO - 10.7554/eLife.41279
M3 - Article
C2 - 32043966
AN - SCOPUS:85082095662
SN - 2050-084X
VL - 9
JO - eLife
JF - eLife
M1 - e41279
ER -