While the cohesin complex is a key player in genome architecture, how it localizes to specific chromatin sites is not understood. Recently, we and others have proposed that direct interactions with transcription factors lead to the localization of the cohesin-loader complex (NIPBL/MAU2) within enhancers. Here, we identify two clusters of LxxLL motifs within the NIPBL sequence that regulate NIPBL dynamics, interactome, and NIPBL-dependent transcriptional programs. One of these clusters interacts with MAU2 and is necessary for the maintenance of the NIPBL-MAU2 heterodimer. The second cluster binds specifically to the ligand-binding domains of steroid receptors. For the glucocorticoid receptor (GR), we examine in detail its interaction surfaces with NIPBL and MAU2. Using AlphaFold2 and molecular docking algorithms, we uncover a GR-NIPBL-MAU2 ternary complex and describe its importance in GR-dependent gene regulation. Finally, we show that multiple transcription factors interact with NIPBL-MAU2, likely using interfaces other than those characterized for GR.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Fettweis, Grégory ; Université de Liège - ULiège > Département des sciences de la vie
Wagh, Kaustubh ; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
Stavreva, Diana A; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
Jiménez-Panizo, Alba; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States ; Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
Kim, Sohyoung; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
Lion, Michelle ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et biologie moléculaires animales
Alegre-Martí, Andrea; Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona (UB), 08028 Barcelona, Spain ; Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain
Rinaldi, Lorenzo; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
Johnson, Thomas A; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
Gilson, Elise ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et biologie moléculaires animales
Krishnamurthy, Manan; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
Wang, Li; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
Ball, David A; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
Karpova, Tatiana S; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
Upadhyaya, Arpita; Department of Physics, University of Maryland, College Park, MD 20742, United States ; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, United States
Vertommen, Didier ; de Duve Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
Recio, Juan Fernández; Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, 26007 Logroño, Spain
Estébanez-Perpiñá, Eva ; Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona (UB), 08028 Barcelona, Spain ; Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain
Dequiedt, Franck ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et biologie moléculaires animales
Hager, Gordon L ; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-5055, United States
NIH - National Institutes of Health NCI - National Cancer Institute MINECO - Gobierno de Espana. Ministerio de Economia y Competitividad NIGMS - National Institute of General Medical Sciences NSF - National Science Foundation
Funding text :
We would like to thank the Viral Vector Platform of the GIGA, ULi\u00E8ge for the production of lentiviral particles used for the NIPBL-KD, the GIGA Flow Cytometry Core for cell sorting, Luke Lavis (Janelia Research Campus) for the Halo-JF dyes, Razi Raziuddin and Le Hoang (NIH) for assistance with experiments, and Supriya V. Vartak (NIH) for constructive feedback on the manuscript. This work was supported (in part) by the Intramural Research Program of the National Institutes of Health, National Cancer Institute, Center for Cancer Research. E.E.-P. thanks the G.E. Carretero Fund. The research was also supported by Spanish Ministry of Science (MINECO) [PID2022-141399-OB-100 to E.E.-P., JDC2022-048702-I to A.J.-P., and JDC2023-051138-I to A.M.-M]. A.U. acknowledges support from awards NIGMS 145313 and NSF 2132922. J.F.-R. thanks the Spanish Ministry of Science (MINECO) PID2019-110167RBI00/AEI/10.13039/501100011033. Funding to pay the Open Access publication charges for this article was provided by Intramural Research Program of the NIH.This work was supported (in part) by the Intramural Research Program of the National Institutes of Health, National Cancer Institute, Center for Cancer Research. E.E.-P. thanks the G.E. Carretero Fund. The research was also supported by Spanish Ministry of Science (MINECO) [PID2022-141399-OB-100 to E.E.-P., JDC2022-048702-I to A.J.-P., and JDC2023-051138-I to A.M.-M]. A.U. acknowledges support from awards NIGMS 145313 and NSF 2132922. J.F.-R. thanks the Spanish Ministry of Science (MINECO) PID2019-110167RB-I00/AEI/10.13039/501100011033. Funding to pay the Open Access publication charges for this article was provided by Intramural Research Program of the NIH.
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