Identification and characterization of SET domain family genes in bread wheat (Triticum aestivum L.)

Batra, Renu; Gautam, Tinku; Pal, Saikat; Chaturvedi, Deepti; Rakhi,; Jan, Irfat; Balyan, H. S.

doi:10.1038/s41598-020-71526-5

Cited by 20 publications

(14 citation statements)

References 76 publications

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“…Except for the Pre-SET, SET and Post-SET domains, two categories (SUVH and SUVR) of the SUV gene family in Arabidopsis could be obtained by the distribution of two domains, namely SRA and WIYLD [ 3 , 4 , 5 , 13 , 29 ]. So far, most research on the SUV gene family is related to the SET gene family [ 15 , 16 , 17 , 18 , 19 ]. Only the SUV gene family in B. rapa has been reported, but the SUV gene families in B. oleracea and B. napus are still blank.…”

Section: Discussionmentioning

confidence: 99%

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Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Wang

2021

Genes

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SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.

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Section: Discussionmentioning

confidence: 99%

“…At present, the SET gene family has been analyzed in B. rapa [ 15 , 16 ], rice [ 17 ], bread wheat [ 18 ] and apple [ 19 ], etc. With the development of the research on the SET gene family, the role of the Su(var) 3-9 SET gene (SUV gene) family in DNA methylation is gradually revealed.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Wang

2021

Genes

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“…The catalytic activity of the E(z) subunit is conferred by its structurally conserved SET (Su(var)3-9, Enhancer-of-zeste and Trithorax) domain (Dillon et al 2005; Zhang and Ma 2012; Batra et al 2020) of 120-130 amino acids in length, which was first identified in several chromatin-associated proteins (Jones and Gelbart 1993; Tschiersch et al 1994; Jenuwein et al 1998). The SET-domain structure contains β-strands, several α-helices, turns and numerous loops.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

Sharaf

Vijayanathan

Oborník

et al. 2021

Preprint

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Polycomb Repressive Complex 2 (PRC2) is involved in establishing transcriptionally silent chromatin states through its ability to methylate lysine 27 of histone H3 by the catalytic subunit Enhancer of zeste [E(z)]. Polycomb group (PcG) proteins play a crucial role in the maintenance of cell identity and in developmental regulation. Previously, the diversity of PRC2 subunits within some eukaryotic lineages has been reported and its presence in early eukaryotic evolution has been hypothesized. So far however, systematic survey of the presence of PRC2 subunits in species of all eukaryotic lineages is missing. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. In detail, we investigate the SET-domain protein sequences and their evolution across the four domains of life and particularly focus on the structural diversity of the SET-domain subfamily containing E(z), the catalytic subunit of PRC2. We show that PRC2 subunits are already present in early eukaryotic lineages, strengthening the support for PRC2 emergence prior to diversification of eukaryotes. We identify a common presence of E(z) and ESC, suggesting that Su(z)12 may have emerged later and/or may be dispensable from the evolutionarily conserved functional core of PRC2. Furthermore, our results broaden our understanding of the E(z) evolution within the SET-domain protein family, suggesting possibilities of function evolution. Through this, we shed light on a possible emerging point of the PRC2 and the evolution of its function in eukaryotes.

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“…SDG gene family has been identified in many plant species including A. thaliana [11], Brassica rapa [12], Populus trichocarpa [13], Vitis vinifera [14], Zea mays [15], Oryza sativa [16], Solanum lycopersicum [17], Citrus sinensis [18], Litchi chinensis [19], Gossypium raimondii [20], Setaria italic [21], Triticum aestivum [22], and Dendrobium catenatum [23] with 49,67,59,33,43,43,52,47,48,52,53,166, and 44 members, respectively.…”

Section: Introductionmentioning

confidence: 99%

“…The SETD genes cause trimethylation of rubisco and regulate the carbon fixation process during the Calvin cycle [45]. The SDGs are also involved in response to external cues, including both abiotic and biotic stresses [21,22,37,[46][47][48][49]. ATX1 facilitates the H3K4me3 modification and activates the ABA biosynthesis gene named NCED3 to improve Arabidopsis drought tolerance [47].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L.

Sarfraz

Wahid

Xie

et al. 2022

IJMS

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SET domain group encoding proteins function as histone lysine methyltransferases. These proteins are involved in various biological processes, including plant development and adaption to the environment by modifying the chromatin structures. So far, the SET domain genes (SDGs) have not been systematically investigated in Brassica napus (B. napus). In the current study, through genome-wide analysis, a total of 122 SDGs were identified in the B. napus genome. These BnSDGs were subdivided into seven (I–VII) classes based on phylogeny analysis, domain configurations, and motif distribution. Segmental duplication was involved in the evolution of this family, and the duplicated genes were under strong purifying selection. The promoter sequence of BnSDGs consisted of various growth, hormones, and stress-related cis-acting elements along with transcription factor binding sites (TFBSs) for 20 TF families in 59 of the 122 BnSDGs. The gene ontology (GO) analysis revealed that BnSDGs were closely associated with histone and non-histone methylation and metal binding capacity localized mostly in the nucleus. The in silico expression analysis at four developmental stages in leaf, stem root, floral organ, silique, and seed tissues showed a broad range of tissue and stage-specific expression pattern. The expression analysis under four abiotic stresses (dehydration, cold, ABA, and salinity) also provided evidence for the importance of BnSDGs in stress environments. Based on expression analysis, we performed reverse transcription-quantitative PCR for 15 target BnSDGs in eight tissues (young leaf, mature leaf, root, stem, carpel, stamen, sepal, and petals). Our results were in accordance with the in silico expression data, suggesting the importance of these genes in plant development. In conclusion, this study lays a foundation for future functional studies on SDGs in B. napus.

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Identification and characterization of SET domain family genes in bread wheat (Triticum aestivum L.)

Cited by 20 publications

References 76 publications

Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L.

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