The matrix attachment regions (MARs) binding proteins could finely orchestrate temporal and spatial gene expression during development. InArabidopsis,transposable elements (TEs) and TE-like repeat sequences are transcriptionally repressed or attenuated by the coordination of many key players including DNA methyltransferases, histone deacetylases, histone methyltransferases and the siRNA pathway, which help to protect genomic integrity and control multiple developmental processes such as flowering. We have recently reported that an AT-hook nuclear matrix binding protein, TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK), participates in a histone deacetylation (HDAC) complex to silence TEs and genes containing TE-like sequence, includingAtMu1, FWAandFLOWERING LOCUS C (FLC)inLerbackground. We have shown thatTEKknockdown causes increased histone acetylation, reduced H3K9me2 and moderate reduction of DNA methylation in the target loci, leading to the derepression ofFLCandFWA,as well as TE reactivation. Here we discuss the role ofTEKas a putative MAR binding protein which functions in the maintenance of genome integrity and in flowering control by silencing TEs and repeatcontaining genes.