Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions

Copyright and License

© 2023 Elsevier.

Acknowledgement

Z.L. is a CPRIT Scholar in Cancer Research. This work was supported by funds from CPRIT RR160017 to Z.L., V Foundation V2016-017 to Z.L., V Foundation DVP2019-018 to Z.L., Voelcker Fund Young Investigator Award to Z.L., UT Rising STARs Award to Z.L., Susan G. Komen CCR Award CCR17483391 to Z.L., NCI U54 CA217297/PRJ001 to Z.L., the Mary Kay Foundation Cancer Research Grant to Z.L.‬, Voelcker Fund Young Investigator Award to L.C., NIA R01AG070214 to L.C., NIA R01AG071591 to L.C., Pew-Stewart Scholar Award to S.C., Searle Scholar Award to S.C., the Shurl and Kay Curci Foundation Research Grant to S.C., Merkin Innovation Seed Grant for S.C., and the National Science Foundation Graduate Research Fellowship grant no. DGE-1745301 to S.R.Y. Research reported in this publication was also supported by the NIGMS of the NIH under award number R01GM137009 to Z.L. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. S.C. is also supported by the NIH/NCI under award number P30CA016042. We would like to thank all the members of Liu and Chen labs for technical assistance and helpful discussion, especially Dr. Meina Wang for her help with western blots associated with droplet sedimentation assays, Dr. Mingjun Bi for his technical support on ATAC-seq and ChIP-seq, and Dr. Jian Gao for his help with imaging and 1,6-HD treatment work. We also thank Dr. Luke Lavis for providing the fluorescent Halo ligand PA-JF646 for SPT and the Caltech Biological Imaging Facility for providing access to confocal fluorescence microscopes.

Contributions

Z.L., L.C., and S.C. conceived the work and designed the study. L.C., Z.L., Q.H., B.K.M., L.R., and E.Z. performed experiments and data analyses with assistance from R.A., S.-H.K., X.L., S.R.Y., P.X., and E.S. Z.Z. performed the computational analyses for all next-generation sequencing assays. Z.L. and L.C. supervised the research and oversaw the project. L.C. and Z.L. wrote the manuscript with input from all authors. S.C., Z.Z., K.X., Q.W., and T.H.-M.H. provided comments and reviewed the manuscript.

Data Availability

All ChIP-seq, ATAC-seq, and GRO-seq data were visualized in Integrative Genomics Viewer (IGV).76 For GRO-seq, the reads were separated by strand and extended to a length of 100 nt in the 5′-to-3′ direction; for ChIP-seq and ATAC-seq, the reads were extended to 200 nt in the 5′-to-3′ direction. All data were normalized to 10 million uniquely mapped reads per experiment. A customized R script was used to generate heatmap and line plots for ChIP-seq, ATAC-seq, and GRO-seq data.

The GEO accession number for all deep sequencing data reported in this paper is GSE215163, which includes the ChIP-seq data set (GSE215161), ATAC-seq data set (GSE215160), and GRO-seq data set (GSE215162).

We also used some published ChIP-seq data from the Gene Expression Omnibus database for AR and H3K27ac under accession number GSE8386039 and GSE5162140 respectively.

Conflict of Interest

The authors declare no competing interests.

Additional Information

We support inclusive, diverse, and equitable conduct of research.