TFIIIC binding to alu elements controls gene expression via chromatin looping and histone acetylation

Ferrari, Roberto; De Llobet, Lara Isabel; Di Vona, Chiara, 1981-; Le Dily, François; Vidal Ocabo, Enrique; Lloutas, Antonios; Quilez Oliete, Javier; Jochem, Laura; Cuts, Erin; Dieci, Giorgio; Vannini, Alessandro; Teichmann, Martin; de la Luna, Susana; Beato, Miguel

doi:http://dx.doi.org/10.1016/j.molcel.2019.10.020

TFIIIC binding to alu elements controls gene expression via chromatin looping and histone acetylation

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Ferrari R, de Llobet Cucalon LI, Di Vona C, Le Dilly F, Vidal E, Lioutas A et al. TFIIIC binding to alu elements controls gene expression via chromatin looping and histone acetylation. Mol Cell. 2020 Feb 6; 77(3): 475-487.e11. DOI: 10.1016/j.molcel.2019.10.020

Abstract

How repetitive elements, epigenetic modifications, and architectural proteins interact ensuring proper genome expression remains poorly understood. Here, we report regulatory mechanisms unveiling a central role of Alu elements (AEs) and RNA polymerase III transcription factor C (TFIIIC) in structurally and functionally modulating the genome via chromatin looping and histone acetylation. Upon serum deprivation, a subset of AEs pre-marked by the activity-dependent neuroprotector homeobox Protein (ADNP) and located near cell-cycle genes recruits TFIIIC, which alters their chromatin accessibility by direct acetylation of histone H3 lysine-18 (H3K18). This facilitates the contacts of AEs with distant CTCF sites near promoter of other cell-cycle genes, which also become hyperacetylated at H3K18. These changes ensure basal transcription of cell-cycle genes and are critical for their re-activation upon serum re-exposure. Our study reveals how direct manipulation of the epigenetic state of AEs by a general transcription factor regulates 3D genome folding and expression.