BORDER proteins protect expression of neighboring genes by promoting 3′ Pol II pausing in plants

• Published in: Nature communications Vol. 10; no. 1; pp. 4359 - 15
• Main Authors: Yu, Xuhong, Martin, Pascal G. P., Michaels, Scott D.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.09.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/91; 45; 45/15; 631/208/191; 631/208/199; 631/208/200; 631/208/2491; 631/337/572; Arabidopsis - genetics; Arabidopsis - growth & development; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; DNA-directed RNA polymerase; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene regulation; Genes; Homology; Humanities and Social Sciences; Interference; Life Sciences; multidisciplinary; Mutation; Plant Roots - genetics; Plant Roots - growth & development; Plant Roots - metabolism; Protein Isoforms - genetics; Protein Isoforms - metabolism; Proteins; Ribonucleic acid; RNA; RNA polymerase; RNA polymerase II; RNA Polymerase II - genetics; RNA Polymerase II - metabolism; RNA-mediated interference; Science; Science (multidisciplinary); Seedlings - genetics; Seedlings - growth & development; Seedlings - metabolism; Transcription; Transcriptional Elongation Factors - genetics; Transcriptional Elongation Factors - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-12328-w

Ensuring that one gene’s transcription does not inappropriately affect the expression of its neighbors is a fundamental challenge to gene regulation in a genomic context. In plants, which lack homologs of animal insulator proteins, the mechanisms that prevent transcriptional interference are not well understood. Here we show that BORDER proteins are enriched in intergenic regions and prevent interference between closely spaced genes on the same strand by promoting the 3′ pausing of RNA polymerase II at the upstream gene. In the absence of BORDER proteins, 3′ pausing associated with the upstream gene is reduced and shifts into the promoter region of the downstream gene. This is consistent with a model in which BORDER proteins inhibit transcriptional interference by preventing RNA polymerase from intruding into the promoters of downstream genes. In plants, 3′ Pol II pausing helps prevent transcriptional interference. Here the authors provide evidence that BORDER proteins are enriched in intergenic regions and inhibit transcriptional interference between closely spaced genes by preventing RNA polymerase from intruding into the promoters of nearby downstream genes.