FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs

Abstract

Focal adhesion kinase (FAK) localizes to focal adhesions and is overexpressed in many cancers. FAK can also translocate to the nucleus, where it binds to, and regulates, several transcription factors, including MBD2, p53 and IL-33, to control gene expression by unknown mechanisms. We have used ATAC-seq to reveal that FAK controls chromatin accessibility at a subset of regulated genes. Integration of ATAC-seq and RNA-seq data showed that FAK-dependent chromatin accessibility is linked to differential gene expression, including of the FAK-regulated cytokine and transcriptional regulator interleukin-33 (Il33), which controls anti-tumor immunity. Analysis of the accessibility peaks on the Il33 gene promoter/enhancer regions revealed sequences for several transcription factors, including ETS and AP-1 motifs, and we show that c-Jun, a component of AP-1, regulates Il33 gene expression by binding to its enhancer in a FAK kinase-dependent manner. This work provides the first demonstration that FAK controls transcription via chromatin accessibility, identifying a novel mechanism by which nuclear FAK regulates biologically important gene expression.

Characterisation of a nucleo-adhesome

“…For example, zyxin, paxillin, α-actinin, TRIP6 and focal adhesion kinase (FAK) have been reported to localise to the nucleus under conditions associated with cellular stress (reviewed in refs 4, 18-21). For FAK, we, and others, have demonstrated nuclear localisation and molecular and biological functions [22][23][24][25][26][27][28] . In some cases, these can be related to oncogenic stress; for example, FAK is not detectable in nuclear fractions of normal keratinocytes, but it accumulates in the nucleus of their malignant squamous cell carcinoma (SCC) counterparts 25 .…”

“…To interrogate the nuclear localisation of adhesion proteins, we purified nuclei from SCC cells that we used previously to decipher nuclear functions for FAK [25][26][27][28] for biochemical analysis. As organelles contiguous with or adjacent to the nuclear membrane, such as the endoplasmic reticulum (ER), often contaminate nuclear preparations 35 , we developed a method that optimised removal of perinuclear cellular components.…”

“…Given the now well-documented and important nuclear functions of the adhesion protein FAK [23][24][25][26][27][28] , which is a component of the core nucleo-adhesome network we describe here (Fig. 3b), we examined whether there was a role for FAK in specifying the nucleo-adhesome and, more broadly, the nuclear proteome.…”

“…In some cases, these can be related to oncogenic stress; for example, FAK is not detectable in nuclear fractions of normal keratinocytes, but it accumulates in the nucleus of their malignant squamous cell carcinoma (SCC) counterparts 25 . Nuclear FAK is important, since we have shown that it drives tumour immune evasion and the growth of tumours in vivo by building molecular transcription complexes in the nucleus that regulate the expression of cytokines, such as IL- 33 and Ccl5 (refs 25,27,28). However, in contrast to all that we know for FAK, very little is known about the true extent of nuclear localisation and functions of adhesion proteins.…”

Molecular Regulation of Paused Pluripotency in Early Mammalian Embryos and Stem Cells

“…Indeed, several genomic profiling studies comparing diapause and active blastocysts documented altered expression of cellular adhesion genes (Hamatani et al, 2004;Fu et al, 2014;van der Weijden et al, 2019). Adhesion pathways and the cytoskeleton are not merely structural components of the cell, but also affect transcriptional networks, as they are additionally involved in signaling pathways and chromatin regulation (Klages-Mundt et al, 2018;Griffith et al, 2021). Thus, altered adhesion properties may have an impact on the diapause blastocyst at multiple levels, e.g., by altering implantation capacity of the TE and polarity of the epiblast, by maintaining the blastocoel and adjusting the blastocyst in its new elongated form, and by altering transcriptional networks to adapt cellular states.…”