Genome-wide mapping of binding sites of the transposase-derived SETMAR protein in the human genome.

Márton Miskei,Lóránt Székvölgyi,Zoltán Ivics,Csaba Miskey,Adrienn Horváth,Éva Nagy,Lívia Viola,Laura Varga,Jason Roszik,Orsolya Feró,Zsolt Karányi

doi:10.1016/j.csbj.2021.07.010

Abstract

Throughout evolution, DNA transposons provide a recurrent supply of genetic information to give rise to novel gene functions by fusion of their transposase domain to various domains of host-encoded proteins. One of these "domesticated", transposase-derived factors is SETMAR/Metnase which is a naturally occurring fusion protein that consists of a histone-lysine methyltransferase domain and an HsMar1 transposase. To elucidate the biological role of SETMAR, it is crucial to identify genomic targets to which SETMAR specifically binds and link these sites to the regulation of gene expression. Herein, we mapped the genomic landscape of SETMAR binding in a near-haploid human leukemia cell line (HAP1) in order to identify on-target and off-target binding sites at high resolution and to elucidate their role in terms of gene expression. Our analysis revealed a perfect correlation between SETMAR and inverted terminal repeats (ITRs) of HsMar1 transposon remnants, which are considered as natural target sites for SETMAR binding. However, we did not detect any untargeted events at non-ITR sequences, calling into question previously proposed off-target binding sites. We identified sequence fidelity of the ITR motif as a key factor for determining the binding affinity of SETMAR for chromosomes, as higher conservation of ITR sequences resulted in increased affinity for chromatin and stronger repression of SETMAR-bound gene loci. These associations highlight how SETMAR's chromatin binding fine-tune gene regulatory networks in human tumour cells.

Highlights

Transposons of the mariner family are present in a wide variety of eukaryotic genomes, including humans [1,2,3]
To map the chromatin binding sites of SETMAR with high spatial resolution, we set up an experimental system in the nearly haploid HAP1 lymphoblastoid leukaemia cell line [33] in which the endogenous SETMAR locus was knocked out by CRISPR/Cas9 technology followed by complementation by a doxycycline-inducible isoform of SETMAR carrying an N-terminal hemagglutinin tag
Western blot analysis shows that the kinetics of SETMAR-HA induction linearly scaled with the dose of dox concentration, while the tagged protein was not expressed in the absence of drug treatment (Fig. 2B) or in wild-type HAP1 cells (Supplementary Fig. S3A)

Summary

Introduction

Transposons of the mariner family are present in a wide variety of eukaryotic genomes, including humans [1,2,3]. These transposons contain a single gene encoding the transposase, flanked by short,

Methods

Results

Conclusion