Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38

ABSTRACT

DNA methylation on CpGs regulates transcription in mammals, both by decreasing the binding of methylation-repelled factors and by increasing the binding of methylation-attracted factors. Among the latter, zinc finger proteins have the potential to bind methylated CpGs in a sequence-specific context. The protein ZBTB38 is unique in that it has two independent sets of zinc fingers, which recognize two different methylated consensus sequences in vitro. Here, we identify the binding sites of ZBTB38 in a human cell line, and show that they contain the two methylated consensus sequences identified in vitro. In addition, we show that the distribution of ZBTB38 sites is highly unusual: while 10% of the ZBTB38 sites are also bound by CTCF, the other 90% of sites reside in closed chromatin and are not bound by any of the other factors mapped in our model cell line. Finally, a third of ZBTB38 sites are found upstream of long and active CpG islands. Our work therefore validates ZBTB38 as a methyl-DNA binder in vivo and identifies its unique distribution in the genome.

KEYWORDS:

• DNA methylation
• zinc finger protein ZBTB38
• E2F factor
• Alu repeats
• cell cycle

Acknowledgments

We would like to thank Dr Jorg Tost, Dr Aurélie Bousard, and the sequencing facility at ‘Centre National de Génotypage’ (CEA, France) for handling the sequencing procedure. We thank Dr Slimane Ait-Si-Ali and Dr Laurianne Fritsch (UMR7216, Paris, France) for their help in establishing the cell line. We thank Alexey Ruzov (University of Nottingham, United Kingdom), Didier Trouche (Centre de Biologie Intégrative, Toulouse, France), and colleagues at UMR7216 ‘Epigenetics and Cell Fate’ and at Institut Cochin (INSERM U1016) for helpful comments and suggestions during the conduct of this study. C.M. was the recipient of a MESNT PhD fellowship and a Fondation pour la Recherche Médicale fellowship (FDT20150532354).

Disclosure statement

No potential conflict of interest was reported by the author(s).

Grant support

Laboratories of B.M. and P.A.D. are partners of Labex ‘Who am I?’ (ANR-11-LABX-0071 and ANR-11-IDEX-005-02). This work was supported by Electricité de France (RB2018-14), by Ligue contre le cancer Comité de Paris (RS11/75-8; RS12/75/95-21; RS13/75-59), by a FP7 Marie Curie action grant (PIRG07-GA-2010-268,448), and by Association pour la Recherche sur les Tumeurs de Prostate (ARTP, RAK22004KKA). Work of B.M. is supported by Fondation pour la Recherche Médicale (AJE20151234749), INCa-Plan Cancer (ASC15018KSA), and INSERM. Work of P.A.D. is supported by Agence Nationale de la Recherche (PRCI INTEGER ANR-19-CE12-0030-01), LabEx ‘Who Am I?’ (ANR-11-LABX-0071), Université de Paris IdEx (ANR-18-IDEX-0001) funded by the French Government through its ‘Investments for the Future’ program, Fondation pour la Recherche Médicale, and Fondation ARC (Programme Labellisé PGA1/RF20180206807).

Author contributions

B.M. and P.A.D. designed the experiments. C.M. and B.M. performed the experiments and analyzed the data. B.M., C.M., and P.-A.D. wrote the manuscript.

Data availability statement

ChIP-sequencing data are available on NCBI GEO with accession number GSE108618. Software and pipelines used for analysis are listed in Materials and Methods section, and references are cited accordingly. Homemade analysis are available on https://github.com/ClaireMarchal.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/15592294.2022.2111135

Additional information

Funding

This work was supported by the Fondation ARC pour la Recherche sur le Cancer [PGA1/RF20180206807]; Fondation pour la Recherche Médicale [FDT20150532354]; Ligue contre le cancer Comité de Paris [RS11/75-8; RS12/75/95-21; RS13/75-59]; Association pour la Recherche sur les Tumeurs de Prostate [RAK22004KKA]; Labex ‘Who am I?’ [ANR-11-LABX-0071 and ANR-11-IDEX-005-02]; Agence Nationale de la Recherche [PRCI INTEGER ANR-19-CE12-0030-01]; Electricité de France [RB2018-14]; FP7 Marie Curie action grant [PIRG07-GA-2010-268448].