A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate

Abstract

SUMMARY The Arabidopsis thaliana root epidermis is comprised of two cell types, hair and nonhair cells, which differentiate from the same precursor. Although the transcriptional programs regulating these events are well studied, post-transcriptional factors functioning in this cell fate decision are mostly unknown. Here, we globally identify RNA-protein interactions and RNA secondary structure in hair and nonhair cell nuclei. This analysis reveals distinct structural and protein binding patterns across both transcriptomes, allowing identification of differential RNA binding protein (RBP) recognition sites. Using these sequences, we identify two RBPs that regulate hair cell development. Specifically, we find that SERRATE functions in a microRNA-dependent manner to inhibit hair cell fate, while also terminating growth of root hairs mostly independent of microRNA biogenesis. Additionally, we show that GLYCINE-RICH PROTEIN 8 promotes hair cell fate while alleviating phosphate starvation stress. In total, this global analysis reveals novel post-transcriptional regulators of plant root epidermal cell fate.

Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C4 grass

“…These results indicate strong conservation of components of GI protein‐interaction partners across different plant species. We also identified additional interesting candidates, such as an essential light signal receptor PHYTOCHROME C ( PHYC ; Woods, Ream, Minevich, Hobert, & Amasino, ), an RNA‐directed DNA methylation pathway gene ARGONAUTE 4 ( AGO4 ; Lahmy et al, ), a cold response and root hair regulator GLYCINE RICH PROTEIN 8 ( GRP8 ; Carpenter, Kreps, & Simon, ; Foley et al, ), and a cell wall modification gene EXPANSIN 13 ( EXP13 ; Lee, Choi, & Kende, ), with strong coexpression patterns with PhGI under SD, LD, or both conditions (Table S11). The functional diversity of these coexpressed genes might help to understand the pleiotropic roles of GI in the external coincidence model.…”

“…Arabidopsis , showed coexpression patterns with PhGI coexpression genes. The full lines represent five co-expression genes that identified as GI interaction partners in previous reports hair regulator GLYCINE RICH PROTEIN 8 (GRP8;Carpenter, Kreps, & Simon, 1994;Foley et al, 2017), and a cell wall modification gene EXPANSIN 13 (EXP13; Lee, Choi, & Kende, 2001), with strong coexpression patterns with PhGI under SD, LD, or both conditions (Table S11). The functional diversity of these coexpressed genes might help to understand the pleiotropic roles of GI in the external coincidence model.…”

Nuclear Transcriptomes at High Resolution Using Retooled INTACT

“…INTACT can enable profiling all of these levels of regulation from the same preparation of nuclei, as shown for mouse neuronal cells (Mo et al, 2015). Access to nuclei can also improve chromatin immunopurification and chromosome conformation studies (Rodriguez-Granados et al, 2016), enable RNAprotein interaction analyses (Foley et al, 2017), as well as refine proteomic analyses by allowing access to nuclei of discrete cell-or tissue-types (Amin et al, 2014). INTACT and other methods for isolation of nuclei vary in their advantages and disadvantages.…”

“…Others have compared nuclear poly(A) + (Zhang et al, 2008) and total nuclear RNA (Deal and Henikoff, 2010) to total poly(A) + mRNA of Arabidopsis (Arabidopsis thaliana) using microarrays. More recently, two studies have used nuclear RNAs to evaluate their structure and RNA-protein interactions (Gosai et al, 2015;Foley et al, 2017). To date, there has been no comparison of nuclear RNA with total cellular poly(A) + RNA using high-throughput RNA-seq for any plant.…”

Nuclear transcriptomes at high resolution using retooled INTACT

“…More recently, two studies have used nuclear RNAs to evaluate their structure and RNAprotein interactions (Gosai et al, 2015;Foley et al, 2017). To date, there has been no comparison of nuclear RNA with total cellular poly(A) + RNA using high-throughput RNA-seq for any plant.…”