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

ABSTRACT: 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. In addition, we show that GLYCINE-RICH PROTEIN 8 promotes hair cell fate while alleviating phosphate starvation stress. In total, this global analysis reveals post-transcriptional regulators of plant root epidermal cell fate.

SUBMITTER: Foley SW

PROVIDER: S-EPMC5605909 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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

Foley Shawn W SW Gosai Sager J SJ Wang Dongxue D Selamoglu Nur N Sollitti Amelia C AC Köster Tino T Steffen Alexander A Lyons Eric E Daldal Fevzi F Garcia Benjamin A BA Staiger Dorothee D Deal Roger B RB Gregory Brian D BD

Developmental cell 20170401 2

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 ...[more]

PMID: 28441533

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Project description:Abscission, organ separation, is a developmental process that is modulated by endogenous and environmental factors. To better understand the molecular events underlying the progression of abscission in soybean, an agriculturally important legume, we performed RNA sequencing (RNA-seq) of RNA isolated from the leaf abscission zones (LAZ) and petioles (Non-AZ, NAZ) after treating stem/petiole explants with ethylene for 0, 12, 24, 48, and 72 h. As expected, expression of several families of cell wall modifying enzymes and many pathogenesis-related (PR) genes specifically increased in the LAZ as abscission progressed. Here, we focus on the 5,206 soybean genes we identified as encoding transcription factors (TFs). Of the 5,206 TFs, 1,088 were differentially up- or down-regulated more than eight-fold in the LAZ over time, and, within this group, 188 of the TFs were differentially regulated more than eight-fold in the LAZ relative to the NAZ. These 188 abscission-specific TFs include several TFs containing domains for homeobox, MYB, Zinc finger, bHLH, AP2, NAC, WRKY, YABBY, and auxin-related motifs. To discover the connectivity among the TFs and highlight developmental processes that support organ separation, the 188 abscission-specific TFs were then clustered based on a >four-fold up- or down-regulation in two consecutive time points (i.e., 0 and 12 h, 12 and 24 h, 24 and 48 h, or 48 and 72 h). By requiring a sustained change in expression over two consecutive time intervals and not just one or several time intervals, we could better tie changes in TFs to a particular process or phase of abscission. The greatest number of TFs clustered into the 0 and 12 h group. Transcriptional network analysis for these abscission-specific TFs indicated that most of these TFs are known as key determinants in the maintenance of organ polarity, lateral organ growth, and cell fate. The abscission-specific expression of these TFs prior to the onset of abscission and their functional properties as defined by studies in Arabidopsis indicate that these TFs are involved in defining the separation cells and initiation of separation within the AZ by balancing organ polarity, roles of plant hormones, and cell differentiation.

Dataset Information

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

Publications

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

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