Synthetic and Genomic Regulatory Elements Reveal Aspects of -regulatory Grammar in Mouse Embryonic Stem Cells

Overview

Journal Elife

Specialty Biology

Date 2020 Feb 12

PMID 32043966

Citations 41

Authors

Dana M King

Clarice Kit Yee Hong

James L Shepherdson

David M Granas

Brett B Maricque

Barak A Cohen

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Antagonizing regulatory elements of a conserved flowering gene mediate developmental robustness.

Lanctot A, Hendelman A, Udilovich P, Robitaille G, Lippman Z Proc Natl Acad Sci U S A. 2025; 122(8):e2421990122.

PMID: 39964724 PMC: 11874208. DOI: 10.1073/pnas.2421990122.

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.

Pampari A, Shcherbina A, Kvon E, Kosicki M, Nair S, Kundu S bioRxiv. 2025; .

PMID: 39829783 PMC: 11741299. DOI: 10.1101/2024.12.25.630221.

Active learning of enhancers and silencers in the developing neural retina.

Friedman R, Ramu A, Lichtarge S, Wu Y, Tripp L, Lyon D Cell Syst. 2025; 16(1):101163.

PMID: 39778579 PMC: 11827711. DOI: 10.1016/j.cels.2024.12.004.

A suboptimal OCT4-SOX2 binding site facilitates the naïve-state specific function of a Klf4 enhancer.

Waite J, Boytz R, Traeger A, Lind T, Lumbao-Conradson K, Torigoe S PLoS One. 2024; 19(9):e0311120.

PMID: 39348365 PMC: 11441684. DOI: 10.1371/journal.pone.0311120.

Identification of transcription factor co-binding patterns with non-negative matrix factorization.

Rauluseviciute I, Launay T, Barzaghi G, Nikumbh S, Lenhard B, Krebs A Nucleic Acids Res. 2024; 52(18):e85.

PMID: 39217462 PMC: 11472169. DOI: 10.1093/nar/gkae743.

References

Williams Jr D, Cai M, Clore G . Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex. J Biol Chem. 2003; 279(2):1449-57. DOI: 10.1074/jbc.M309790200. View

White M, Kwasnieski J, Myers C, Shen S, Corbo J, Cohen B . A Simple Grammar Defines Activating and Repressing cis-Regulatory Elements in Photoreceptors. Cell Rep. 2016; 17(5):1247-1254. PMC: 5123866. DOI: 10.1016/j.celrep.2016.09.066. View

Chen X, Vega V, Ng H . Transcriptional regulatory networks in embryonic stem cells. Cold Spring Harb Symp Quant Biol. 2008; 73:203-9. DOI: 10.1101/sqb.2008.73.026. View

Zhang X, Zhang J, Wang T, Esteban M, Pei D . Esrrb activates Oct4 transcription and sustains self-renewal and pluripotency in embryonic stem cells. J Biol Chem. 2008; 283(51):35825-33. DOI: 10.1074/jbc.M803481200. View

Spitz F, Furlong E . Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012; 13(9):613-26. DOI: 10.1038/nrg3207. View

Chen X, Xu H, Yuan P, Fang F, Huss M, Vega V . Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008; 133(6):1106-17. DOI: 10.1016/j.cell.2008.04.043. View

Visel A, Blow M, Li Z, Zhang T, Akiyama J, Holt A . ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009; 457(7231):854-8. PMC: 2745234. DOI: 10.1038/nature07730. View

Jauch R, Ng C, Saikatendu K, Stevens R, Kolatkar P . Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog. J Mol Biol. 2008; 376(3):758-70. DOI: 10.1016/j.jmb.2007.11.091. View

Wu J, Huang B, Chen H, Yin Q, Liu Y, Xiang Y . The landscape of accessible chromatin in mammalian preimplantation embryos. Nature. 2016; 534(7609):652-7. DOI: 10.1038/nature18606. View

10.

Hare E, Peterson B, Eisen M . A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids. PLoS Genet. 2008; 4(11):e1000268. PMC: 2582681. DOI: 10.1371/journal.pgen.1000268. View

11.

Sandelin A, Alkema W, Engstrom P, Wasserman W, Lenhard B . JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2003; 32(Database issue):D91-4. PMC: 308747. DOI: 10.1093/nar/gkh012. View

12.

Ulirsch J, Nandakumar S, Wang L, Giani F, Zhang X, Rogov P . Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits. Cell. 2016; 165(6):1530-1545. PMC: 4893171. DOI: 10.1016/j.cell.2016.04.048. View

13.

Wang J, Zhuang J, Iyer S, Lin X, Whitfield T, Greven M . Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012; 22(9):1798-812. PMC: 3431495. DOI: 10.1101/gr.139105.112. View

14.

Mulas C, Chia G, Jones K, Hodgson A, Stirparo G, Nichols J . Oct4 regulates the embryonic axis and coordinates exit from pluripotency and germ layer specification in the mouse embryo. Development. 2018; 145(12). PMC: 6031404. DOI: 10.1242/dev.159103. View

15.

Grant C, Bailey T, Noble W . FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011; 27(7):1017-8. PMC: 3065696. DOI: 10.1093/bioinformatics/btr064. View

16.

Kuhn R, Haussler D, Kent W . The UCSC genome browser and associated tools. Brief Bioinform. 2012; 14(2):144-61. PMC: 3603215. DOI: 10.1093/bib/bbs038. View

17.

Dunn S, Martello G, Yordanov B, Emmott S, Smith A . Defining an essential transcription factor program for naïve pluripotency. Science. 2014; 344(6188):1156-1160. PMC: 4257066. DOI: 10.1126/science.1248882. View

18.

Ludwig M, Bergman C, Patel N, Kreitman M . Evidence for stabilizing selection in a eukaryotic enhancer element. Nature. 2000; 403(6769):564-7. DOI: 10.1038/35000615. View

19.

Panne D . The enhanceosome. Curr Opin Struct Biol. 2008; 18(2):236-42. DOI: 10.1016/j.sbi.2007.12.002. View

20.

Chambers I, Tomlinson S . The transcriptional foundation of pluripotency. Development. 2009; 136(14):2311-22. PMC: 2729344. DOI: 10.1242/dev.024398. View