1. The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening.
- Author
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Patrick, R, Naval-Sanchez, M, Deshpande, N, Huang, Y, Zhang, J, Chen, X, Yang, Y, Tiwari, K, Esmaeili, M, Tran, M, Mohamed, AR, Wang, B, Xia, D, Ma, J, Bayliss, J, Wong, K, Hun, ML, Sun, X, Cao, B, Cottle, DL, Catterall, T, Barzilai-Tutsch, H, Troskie, R-L, Chen, Z, Wise, AF, Saini, S, Soe, YM, Kumari, S, Sweet, MJ, Thomas, HE, Smyth, IM, Fletcher, AL, Knoblich, K, Watt, MJ, Alhomrani, M, Alsanie, W, Quinn, KM, Merson, TD, Chidgey, AP, Ricardo, SD, Yu, D, Jardé, T, Cheetham, SW, Marcelle, C, Nilsson, SK, Nguyen, Q, White, MD, Nefzger, CM, Patrick, R, Naval-Sanchez, M, Deshpande, N, Huang, Y, Zhang, J, Chen, X, Yang, Y, Tiwari, K, Esmaeili, M, Tran, M, Mohamed, AR, Wang, B, Xia, D, Ma, J, Bayliss, J, Wong, K, Hun, ML, Sun, X, Cao, B, Cottle, DL, Catterall, T, Barzilai-Tutsch, H, Troskie, R-L, Chen, Z, Wise, AF, Saini, S, Soe, YM, Kumari, S, Sweet, MJ, Thomas, HE, Smyth, IM, Fletcher, AL, Knoblich, K, Watt, MJ, Alhomrani, M, Alsanie, W, Quinn, KM, Merson, TD, Chidgey, AP, Ricardo, SD, Yu, D, Jardé, T, Cheetham, SW, Marcelle, C, Nilsson, SK, Nguyen, Q, White, MD, and Nefzger, CM
- Abstract
A mechanistic connection between aging and development is largely unexplored. Through profiling age-related chromatin and transcriptional changes across 22 murine cell types, analyzed alongside previous mouse and human organismal maturation datasets, we uncovered a transcription factor binding site (TFBS) signature common to both processes. Early-life candidate cis-regulatory elements (cCREs), progressively losing accessibility during maturation and aging, are enriched for cell-type identity TFBSs. Conversely, cCREs gaining accessibility throughout life have a lower abundance of cell identity TFBSs but elevated activator protein 1 (AP-1) levels. We implicate TF redistribution toward these AP-1 TFBS-rich cCREs, in synergy with mild downregulation of cell identity TFs, as driving early-life cCRE accessibility loss and altering developmental and metabolic gene expression. Such remodeling can be triggered by elevating AP-1 or depleting repressive H3K27me3. We propose that AP-1-linked chromatin opening drives organismal maturation by disrupting cell identity TFBS-rich cCREs, thereby reprogramming transcriptome and cell function, a mechanism hijacked in aging through ongoing chromatin opening.
- Published
- 2024