Genome-Wide Analysis of Soybean JmjC Domain-Containing Proteins Suggests Evolutionary Conservation Following Whole-Genome Duplication.

Yapeng Han,Xiangyong Li,Danxia Ke,Hui Wang,Liangsheng Zhang,Lin Cheng,Lei Wang,Hongyu Yuan,Yanchun Liu

doi:10.3389/fpls.2016.01800

Abstract

Histone modifications, such as methylation and demethylation, play an important role in regulating chromatin structure and gene expression. The JmjC domain-containing proteins, an important family of histone lysine demethylases (KDMs), play a key role in maintaining homeostasis of histone methylation in vivo. In this study, we performed a comprehensive analysis of the jumonji C (JmjC) gene family in the soybean genome and identified 48 JmjC genes (GmJMJs) distributed unevenly across 18 chromosomes. Phylogenetic analysis showed that these JmjC domain-containing genes can be divided into eight groups. GmJMJs within the same phylogenetic group share similar exon/intron organization and domain composition. In addition, 16 duplicated gene pairs were formed by a Glycine-specific whole-genome duplication (WGD) event approximately 13 million years ago (Mya). By investigating the expression profiles of these gene pairs in various tissues, we showed that the expression pattern is conserved in the polyploidy-derived JmjC duplicates, demonstrating that the majority of GmJMJs were preferentially retained after the most recent WGD event and suggesting important roles for demethylase duplications in soybean evolution. These results shed light on the evolutionary history of this family in soybean and provide insights into the JmjCs which will be helpful to reveal their functions in controlling soybean development.

Highlights

Histone methylation and demethylation have important roles in regulating transcription, genome integrity, and epigenetic inheritance (Klose et al, 2006; Klose and Zhang, 2007; Liu et al, 2010)
We identified a total of 48 GmJMJs, which is more than twice the number found in Arabidopsis (21) or rice (20) (Lu et al, 2008)
To better understand the expansion and evolutionary history of GmJMJs, the same methods were used to search for JmjC genes in two other legumes, Medicago and Lotus

Summary

Introduction

Histone methylation and demethylation have important roles in regulating transcription, genome integrity, and epigenetic inheritance (Klose et al, 2006; Klose and Zhang, 2007; Liu et al, 2010). Histone methylation, which is mainly catalyzed by protein families that contain PRMT and SET domains, can have both activating and repressive effects on chromatin function (Ahmad and Cao, 2012; Zhang and Ma, 2012). JmjC Genes from Soybean of the flavin-dependent amine oxidase family (Lee et al, 2005; Metzger et al, 2005; Chen et al, 2011). Genes in the second class of histone demethylases have a JmjC domain with which they catalyze histone lysine demethylation through oxidative reactions dependent on ferrous ion (Fe(II)) and α-ketoglutarate (α-KG) (Elkins et al, 2003; Trewick et al, 2005)

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Discussion

Conclusion