Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis

Citation

Xiao, J., Jin, R., Yu, X., Shen, M., Wagner, J.D., Pai, A., Song, C., Zhuang, M., Klasfeld, S., He, C., Santos, A.M., Helliwell, C., Pruneda-Paz, J.L., Kay, S.A., Lin, X., Cui, S., Garcia, M.F., Clarenz, O., Goodrich, J., Zhang, X., Austin, R.S., Bonasio, R., Wagner, D. (2017). Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nature Genetics, [online] 49(10), 1546-1552. http://dx.doi.org/10.1038/ng.3937

Plain language summary

Molecular machinery known as Polycomb repressive complex 2 (PRC2) is known to be responsible for silencing the expression of different genes by modifying the genome to shut down gene expression. Here the authors demonstrate for the first time, that the recruitment of PRC2 to such regions that are silenced is performed through the action of patterns in DNA sequence around the genes that are turned off. They identify regions throughout the genome silenced by PRC2, use algorithmic predictions to identify distinct DNA patterns in these regions, and then show the sufficiency of identified sequences for silencing by PRC2 by inserting the identified patterns into the genome and showing that they recruit PRC2 and silence the synthetic marker gene introduced. This discovery opens new lines of research and potential for manipulating gene expression in plants through subtle modifications to the DNA surrounding genes in order to influence expression without introducing transgenic material from other species or making extensive genomic changes.

Abstract

Disruption of gene silencing by Polycomb protein complexes leads to homeotic transformations and altered developmental-phase identity in plants1-5. Here we define short genomic fragments, known as Polycomb response elements (PREs), that direct Polycomb repressive complex 2 (PRC2) placement at developmental genes regulated by silencing in Arabidopsis thaliana. We identify transcription factor families that bind to these PREs, colocalize with PRC2 on chromatin, physically interact with and recruit PRC2, and are required for PRC2-mediated gene silencing in vivo. Two of the cis sequence motifs enriched in the PREs are cognate binding sites for the identified transcription factors and are necessary and sufficient for PRE activity. Thus PRC2 recruitment in Arabidopsis relies in large part on binding of trans-acting factors to cis-localized DNA sequence motifs.

Publication date

2017-10-01

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