TM6, a Novel Nuclear Matrix Attachment Region, Enhances Its Flanking Gene Expression through Influencing Their Chromatin Structure

Abstract

Nuclear matrix attachment regions (MARs) regulate the higher-order organization of chromatin and affect the expression of their flanking genes. In this study, a tobacco MAR, TM6, was isolated and demonstrated to remarkably increase the expression of four different promoters that drive gusA gene and adjacent nptII gene. In turn, this expression enhanced the transformation frequency of transgenic tobacco. Deletion analysis of topoisomerase II-binding site, AT-rich element, and MAR recognition signature (MRS) showed that MRS has the highest contribution (61.7%) to the TM6 sequence-mediated transcription activation. Micrococcal nuclease (MNase) accessibility assay showed that 35S and NOS promoter regions with TM6 are more sensitive than those without TM6. The analysis also revealed that TM6 reduces promoter DNA methylation which can affect the gusA expression. In addition, two tobacco chromatin-associated proteins, NtMBP1 and NtHMGB, isolated using a yeast one-hybrid system, specifically bound to the TM6II-1 region (761 bp to 870 bp) and to the MRS element in the TM6II-2 (934 bp to 1,021 bp) region, respectively. We thus suggested that TM6 mediated its chromatin opening and chromatin accessibility of its flanking promoters with consequent enhancement of transcription.

Sequence Exchange between Homologous NB-LRR Genes Converts Virus Resistance into Nematode Resistance, and Vice Versa

“…S4) also points to the coordinated expression of Rx1 and Gpa2. MARs are widespread sequence elements in eukaryotic genomes that bind to the nuclear matrix to regulate the higher order organization of chromatin and affect the transcriptional activity of their flanking genes to orchestrate the spatial and temporal expression of genes during development (Iarovaia et al, 2005;Ji et al, 2013;Xu et al, 2013). This implies that similar regulatory mechanisms may be involved in the coordinated expression and transcriptional dynamics of R genes at complex loci like Rx1/ Gpa2.…”

Matrix attachment regions as a tool to influence plant transgene expression

“…Similar results were obtained with another tobacco MAR, TM2, which was discovered later (Zhang et al 2009). However, a novel MAR, TM6, enhanced transcription activation in transgenic tobacco independent of the promoters 35S, DREB, PNZIP or mini35S (Ji et al 2013). Therefore, it is possible that MARs are a heterogeneous group of elements that share only the capacity of binding to the nuclear matrix (Holmes-Davis and Luca 1998), and their influence on transgene expression depends on both the promoter and their sequence.…”

“…SM11 is the only known MAR that is able to increase transgene expression in non-mutant Arabidopsis. Although novel MARs are continuously being discovered (Wang et al 2007;Festa et al 2013), researchers in recent years have been increasingly adhering to verified MARs, such as RB7, while conducting their investigations (Ji et al 2013;Diamos and Mason 2018).…”

The Actin-Related Protein BAF53 Is Essential for Chromosomal Subdomain Integrity

“…A fractal globule is characterized by a hierarchy of crumples that are formed spontaneously by polymer collapse. Polymer collapse in interphase chromatin fibers could be provided by nuclear matrix attachment regions and DNA-binding condensing/linking proteins like cohesin and CTCF ( Ji et al, 2013 ; Rao et al, 2014 ). Therefore, chromosomal subdomains can be conceived as predominant crumples with sizes of approximately 1 Mb.…”