Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana.

Yichao Li,Allan M. Showalter,Frank Drews,Lonnie R. Welch,Maxwell Mullin,Yingnan Zhang

doi:10.3390/plants9121751

Yichao Li, Allan M. Showalter + Show 4 more

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https://doi.org/10.3390/plants9121751

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Journal: Plants (Basel, Switzerland)	Publication Date: Dec 10, 2020
Citations: 3	License type: CC BY 4.0

Affiliation: Ohio University

Abstract

Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall structural proteins that function in various aspects of plant growth and development, including pollen tube growth. We have previously characterized protein sequence signatures for three family members in the HRGP superfamily: the hyperglycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). However, the mechanism of pollen-specific HRGP gene expression remains unexplored. To this end, we developed an integrative analysis pipeline combining RNA-seq gene expression and promoter sequences to identify cis-regulatory motifs responsible for pollen-specific expression of HRGP genes in Arabidopsis thaliana. Specifically, we mined the public RNA-seq datasets and identified 13 pollen-specific HRGP genes. Ensemble motif discovery identified 15 conserved promoter elements between A. thaliana and A. lyrata. Motif scanning revealed two pollen related transcription factors: GATA12 and brassinosteroid (BR) signaling pathway regulator BZR1. Finally, we performed a regression analysis and demonstrated that the 15 motifs provided a good model of HRGP gene expression in pollen (R = 0.61). In conclusion, we performed the first integrative analysis of cis-regulatory motifs in pollen-specific HRGP genes, revealing important insights into transcriptional regulation in pollen tissue.

Highlights

Tissue-specific gene expression patterns are maintained by the combinatorial binding of transcription factors (TFs) to DNA motifs in a cooperative and competitive manner
Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall proteins involved in various aspects of plant growth and development [4]
To answer the question of what cis-regulatory motifs control pollen-specific HRGP gene expression, we developed a systematic bioinformatic pipeline for interactive analysis of pollen-specific HRGP genes and de novo promoter motifs (Figure 1) based on several published databases and tools, including the gene expression database Araport11 [5]; the known transcription factor binding sites (TFBSs) database plantTFDB [8]; and the motif discovery tool Emotif-Alpha [7], which is an ensemble motif discovery pipeline that integrates 11 motif discovery tools, such as GimmeMotifs [10], DECOD [11], and DME [12]

Summary

Introduction

Tissue-specific gene expression patterns are maintained by the combinatorial binding of transcription factors (TFs) to DNA motifs in a cooperative and competitive manner. Extensive studies have been done to characterize regulatory factors and sequences responsible for tissue-specific gene expression in human and in mouse [2,3]. To our knowledge, there is no such study that elucidates transcriptional regulatory motifs responsible for pollen-specific gene expression, for hydroxyproline-rich glycoproteins (HRGPs) in Arabidopsis thaliana. Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall proteins involved in various aspects of plant growth and development [4].

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