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

Abstract

Focal adhesion kinase (FAK) localises 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-tumour 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 22–28 . 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 .…”

“…As mentioned, FAK has been reported extensively to generate nuclear molecular complexes that regulate gene expression 25–28 . To determine whether FAK also associates with other adhesion proteins that locate to the nucleus to regulate gene expression, we examined the FAK-proximal nuclear interactome using the proximity-dependent biotinylation technique BioID 59 .…”

“…To interrogate the nuclear localisation of adhesion proteins, we purified nuclei from SCC cells that we used previously to decipher nuclear functions for FAK 25–28 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 23–28 , 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.…”

“…These data indicate that nuclear FAK regulates the nuclear abundance of a subset of cell-surface or cytoskeletal adhesion proteins, and this is largely at the level of gene expression rather than nuclear translocation per se. Although we do not investigate the mechanisms by which FAK regulates transcription of these genes here, we have already reported previously that FAK associates with transcriptional complexes in the nucleus to influence gene expression in the case of Ccl5 and Il33 , including via chromatin accessibility 25,27,28 .…”