Epigenetic regulation of plastin 3 expression by the macrosatellite DXZ4 and the transcriptional regulator CHD4

Eike A Strathmann; Irmgard Hölker; Nikolai Tschernoster; Seyyedmohsen Hosseinibarkooie; Julien Come; Cecile Martinat; Janine Altmüller; Brunhilde Wirth

doi:10.1016/j.ajhg.2023.02.004

Epigenetic regulation of plastin 3 expression by the macrosatellite DXZ4 and the transcriptional regulator CHD4

Am J Hum Genet. 2023 Mar 2;110(3):442-459. doi: 10.1016/j.ajhg.2023.02.004. Epub 2023 Feb 21.

Authors

Eike A Strathmann¹, Irmgard Hölker¹, Nikolai Tschernoster², Seyyedmohsen Hosseinibarkooie¹, Julien Come³, Cecile Martinat³, Janine Altmüller⁴, Brunhilde Wirth⁵

Affiliations

¹ Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany.
² Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Cologne Center for Genomics and West German Genome Center, University of Cologne, 50931 Cologne, Germany.
³ INSERM/ UEVE UMR 861, Université Paris Saclay, I-STEM, 91100 Corbeil-Essonnes, France.
⁴ Cologne Center for Genomics and West German Genome Center, University of Cologne, 50931 Cologne, Germany.
⁵ Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Center for Rare Diseases, University Hospital of Cologne, 50931 Cologne, Germany. Electronic address: brunhilde.wirth@uk-koeln.de.

Abstract

Dysregulated Plastin 3 (PLS3) levels associate with a wide range of skeletal and neuromuscular disorders and the most common types of solid and hematopoietic cancer. Most importantly, PLS3 overexpression protects against spinal muscular atrophy. Despite its crucial role in F-actin dynamics in healthy cells and its involvement in many diseases, the mechanisms that regulate PLS3 expression are unknown. Interestingly, PLS3 is an X-linked gene and all asymptomatic SMN1-deleted individuals in SMA-discordant families who exhibit PLS3 upregulation are female, suggesting that PLS3 may escape X chromosome inactivation. To elucidate mechanisms contributing to PLS3 regulation, we performed a multi-omics analysis in two SMA-discordant families using lymphoblastoid cell lines and iPSC-derived spinal motor neurons originated from fibroblasts. We show that PLS3 tissue-specifically escapes X-inactivation. PLS3 is located ∼500 kb proximal to the DXZ4 macrosatellite, which is essential for X chromosome inactivation. By applying molecular combing in a total of 25 lymphoblastoid cell lines (asymptomatic individuals, individuals with SMA, control subjects) with variable PLS3 expression, we found a significant correlation between the copy number of DXZ4 monomers and PLS3 levels. Additionally, we identified chromodomain helicase DNA binding protein 4 (CHD4) as an epigenetic transcriptional regulator of PLS3 and validated co-regulation of the two genes by siRNA-mediated knock-down and overexpression of CHD4. We show that CHD4 binds the PLS3 promoter by performing chromatin immunoprecipitation and that CHD4/NuRD activates the transcription of PLS3 by dual-luciferase promoter assays. Thus, we provide evidence for a multilevel epigenetic regulation of PLS3 that may help to understand the protective or disease-associated PLS3 dysregulation.

Keywords: CHD4; DXZ4; PLS3; Plastin 3; SMN1; SMN2; X chromosome inactivation; cancer; osteoporosis; spinal muscular atrophy.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Epigenesis, Genetic*
Female
Humans
Male
Mi-2 Nucleosome Remodeling and Deacetylase Complex / genetics
Mi-2 Nucleosome Remodeling and Deacetylase Complex / metabolism
Microfilament Proteins / genetics
Motor Neurons / metabolism
Muscular Atrophy, Spinal* / genetics

Substances

CHD4 protein, human
Mi-2 Nucleosome Remodeling and Deacetylase Complex
Microfilament Proteins
plastin