Intestinal differentiation involves cleavage of histone H3 N-terminal tails by multiple proteases.

Karin Johanna Ferrari,Cecilia Toscani,Simona Amato,Pasquale Conforti,Daniel Fernández-Pérez,Diego Pasini,Simone Tamburri,Marika Zanotti,Roberta Noberini,Alessandra Rossi,Tiziana Bonaldi

doi:10.1093/nar/gkaa1228

Karin Johanna Ferrari, Cecilia Toscani + Show 9 more

Open Access

https://doi.org/10.1093/nar/gkaa1228

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Abstract

The proteolytic cleavage of histone tails, also termed histone clipping, has been described as a mechanism for permanent removal of post-translational modifications (PTMs) from histone proteins. Such activity has been ascribed to ensure regulatory function in key cellular processes such as differentiation, senescence and transcriptional control, for which different histone-specific proteases have been described. However, all these studies were exclusively performed using cell lines cultured in vitro and no clear evidence that histone clipping is regulated in vivo has been reported. Here we show that histone H3 N-terminal tails undergo extensive cleavage in the differentiated cells of the villi in mouse intestinal epithelium. Combining biochemical methods, 3D organoid cultures and in vivo approaches, we demonstrate that intestinal H3 clipping is the result of multiple proteolytic activities. We identified Trypsins and Cathepsin L as specific H3 tail proteases active in small intestinal differentiated cells and showed that their proteolytic activity is differentially affected by the PTM pattern of histone H3 tails. Together, our findings provide in vivo evidence of H3 tail proteolysis in mammalian tissues, directly linking H3 clipping to cell differentiation.

Highlights

Histones are the principal protein components of chromatin
We identified Trypsins and Cathepsin L as specific H3 tail proteases active in small intestinal differentiated cells and showed that their proteolytic activity is differentially affected by the post-translational modifications (PTMs) pattern of histone H3 tails
Our findings provide in vivo evidence of H3 tail proteolysis in mammalian tissues, directly linking H3 clipping to cell differentiation

Summary

INTRODUCTION

Histones are the principal protein components of chromatin. Their N-terminal regions protrude from the globular core of nucleosomes, are rich in lysine and arginine residues and serve as substrate for a complex pattern of regulatory post-translational modifications (PTMs) central to most biological processes [1], including a variety of human diseases like cancer, metabolic and neurological disorders, as well as inflammation [2]. Several studies reported that proteolytic cleavage of histones N-terminal tails is mediated by the activity of nuclear peptidases This was termed clipping and is conserved across species from ciliates to mammalian cells. H3 clipping has been described in different mammalian cell types such as embryonic stem cells (ESCs) [8,9], senescent fibroblasts and melanocytes [10], peripheral blood mononuclear cells (PBMCs) [11], Raji cells [12] and hepatocytes [13] All these studies were aimed to identify the enzymes, the cleavage sites or the cellular processes involved. We report for the first time that the N-terminal tail of histone H3 undergoes extensive proteolytic cleavage in the differentiated compartment (villi) of the mouse small intestinal tract. Our findings uncover a mechanism for in vivo H3 clipping in mammalian adult tissue and suggest the involvement of the enzymatic removal of histone tails in the homeostasis of adult tissues

MATERIALS AND METHODS

RESULTS AND DISCUSSION

H3K4me1

F Nuclear Lysates