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Volume 9
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10.3390/plants9121751
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Article

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

by
Yichao Li
1,*,
Maxwell Mullin
1,
Yingnan Zhang
1,
Frank Drews
1,
Lonnie R. Welch
1,* and
Allan M. Showalter
2,*
1
School of Electrical Engineering and Computer Science, Russ College of Engineering, Ohio University, Athens, OH 45701, USA
2
Department of Environmental and Plant Biology, Molecular and Cellular Biology Program, College of Arts and Sciences, Ohio University, Athens, OH 45701, USA
*
Authors to whom correspondence should be addressed.
Plants 2020, 9(12), 1751; https://doi.org/10.3390/plants9121751
Submission received: 31 October 2020 / Revised: 26 November 2020 / Accepted: 7 December 2020 / Published: 10 December 2020
(This article belongs to the Special Issue Advances in Functional Genomics of Plant Cell Wall Metabolism)
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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.
Keywords: hydroxyproline-rich glycoproteins; cis-regulatory motifs; pollen-specific; machine learning; tissue-specific expression hydroxyproline-rich glycoproteins; cis-regulatory motifs; pollen-specific; machine learning; tissue-specific expression

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MDPI and ACS Style

Li, Y.; Mullin, M.; Zhang, Y.; Drews, F.; Welch, L.R.; Showalter, A.M. Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana. Plants 2020, 9, 1751. https://doi.org/10.3390/plants9121751

AMA Style

Li Y, Mullin M, Zhang Y, Drews F, Welch LR, Showalter AM. Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana. Plants. 2020; 9(12):1751. https://doi.org/10.3390/plants9121751

Chicago/Turabian Style

Li, Yichao, Maxwell Mullin, Yingnan Zhang, Frank Drews, Lonnie R. Welch, and Allan M. Showalter. 2020. "Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana" Plants 9, no. 12: 1751. https://doi.org/10.3390/plants9121751

APA Style

Li, Y., Mullin, M., Zhang, Y., Drews, F., Welch, L. R., & Showalter, A. M. (2020). Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana. Plants, 9(12), 1751. https://doi.org/10.3390/plants9121751

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