Poster abstracts
Poster number 32 submitted by Ben Oakes
RNA polymerase IV defines heritable regulatory patterns
Benjamin P. Oakes (Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210), Natalie C. Deans (Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210; Centers for RNA Biology and Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210), Jay B. Hollick (Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210; Centers for RNA Biology and Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210)
Abstract:
Paramutation is a behavior in which one parental allele facilitates a meiotically heritable regulatory change at the other1. This behavior occurs at specific alleles of multiple maize loci - including purple plant1 (pl1) - encoding transcriptional activators of flavonoid biosynthesis2. The Pl1-Rhoades (Pl1-Rh) allele can exist in a highly expressed reference state (Pl-Rh) or a repressed paramutant state (denoted Pl′ )3. Pl′ states often revert to Pl-Rh in rmr6-1 mutants4 deficient for the RNA polymerase (RNAP) IV largest subunit5 indicating that RNAP IV maintains the heritable information specifying Pl1-Rh paramutation. Because RNAP IV both sources 24-nucleotide (24nt) RNAs5 and conditions the heritable regulatory status of Pl1-Rh4,6, we hypothesize that RNAP IV, and potentially small RNAs (sRNAs), define the heritable regulatory status of other genes. To test this idea, seedling RNA-seq and corresponding sRNA-seq profiles of heterozygous BC5 progeny from sibling rmr6-1 mutant and Rmr6-B73 / rmr6-1 fathers were compared to identify heritable RNAP IV-dependent effects. We found the absence of paternal RNAP IV significantly altered the RNA abundances of 144 genes. Additionally, normalized read abundances of 711 24nt sRNA clusters were significantly distinct. We discovered that a significant number of genes with increased messenger RNA (mRNA) levels overlap with decreased 24nt sRNA clusters within 100, 50, and 10 kilobases upstream or downstream. These overlaps point to other epialleles, like Pl1-Rh, whose regulatory reprogramming in the absence of RNAP IV persists through meiosis. 10% of these overlapping sRNA clusters correspond to published putative cis-regulatory elements (CREs)7,8,9 while 90% correspond to regions not previously identified as putative CREs. Our findings suggest that Pol IV conditions heritable regulatory patterns of multiple genes and that heritable changes of 24nt sRNAs in the absence of paternal Pol IV may highlight undiscovered regions of regulatory importance.
References:
1. Brink Genetics (1958) | 2. Hollick Nat Rev Gen (2017) | 3. Hollick et al. Genetics (1995) | 4. Hollick et al. Genetics (2005) | 5. Erhard et al. Science (2009) | 6. Erhard et al. Plant Cell (2013) | 7. Oka et al. Genome Biology (2017) | 8. Ricci et al. Nat. Plants (2019) | 9. Lozano et al. G3 (2021)
Keywords: Epigenetic Inheritance, RNA Polymerase IV, small RNAs