Temporal Changes in Transcripts of MITE Transposable Elements during Rice Endosperm Development

The repression of transcription from transposable elements (TEs) by DNA methylation is necessary to maintain genome integrity and prevent harmful mutations. However, under certain circumstances, TEs are thought to escape from the host defense system and reactivate their transcription. In Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), DNA demethylases target the sequences derived from TEs in the central cell, the progenitor cell for the endosperm in the female gametophyte. This genome-wide DNA demethylation is also observed in the endosperm after fertilization. In this study, we used a custom microarray to survey the transcripts generated from TEs during the rice endosperm development and at selected timepoints in the embryo as a control. The expression patterns of TE transcripts are dynamically up- and downregulated during endosperm development, especially for miniature inverted-repeat transposable elements (MITEs). Surprisingly, some TE transcripts were directionally controlled, while the other DNA transposons and retrotransposons were not. We also discovered the NF-Y binding motif, CCAAT, in the region near the 5′ terminal inverted repeat of Youren, one of the transcribed MITEs in the endosperm. Our results uncover dynamic changes in TE activity during endosperm development in rice.

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Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

BMC Plant Biology ◽

10.1186/s12870-021-03194-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lianyu Lin ◽

Anupma Sharma ◽

Qingyi Yu

Keyword(s):

Transposable Elements ◽

Inverted Repeat ◽

Sequence Similarity ◽

Genome Structure ◽

Terminal Inverted Repeat ◽

Essential Information ◽

Dna Transposon ◽

Genome Wide ◽

Identification And Characterization

Abstract Background Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. Results We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. Conclusions Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.

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Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions

Scientific Reports ◽

10.1038/s41598-017-02855-1 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 6

Author(s):

Cheng Guo ◽

Matthew Spinelli ◽

Congting Ye ◽

Qingshun Q. Li ◽

Chun Liang

Keyword(s):

Arabidopsis Thaliana ◽

Comparative Analysis ◽

Transposable Elements ◽

Inverted Repeat ◽

Genome Wide

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Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla)

Planta ◽

10.1007/s00425-016-2544-0 ◽

2016 ◽

Vol 244 (4) ◽

pp. 775-787 ◽

Cited By ~ 5

Author(s):

Mingbing Zhou ◽

Guiyun Tao ◽

Peiyao Pi ◽

Yihang Zhu ◽

Youhuang Bai ◽

...

Keyword(s):

Transposable Elements ◽

Inverted Repeat ◽

Moso Bamboo ◽

Evolution Analysis ◽

Genome Wide ◽

Phyllostachys Heterocycla

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Genome-Wide Identification and Analysis on YUCCA Gene Family in Isatis indigotica Fort. and IiYUCCA6-1 Functional Exploration

International Journal of Molecular Sciences ◽

10.3390/ijms21062188 ◽

2020 ◽

Vol 21 (6) ◽

pp. 2188

Author(s):

Miaomiao Qin ◽

Jing Wang ◽

Tianyi Zhang ◽

Xiangyang Hu ◽

Rui Liu ◽

...

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Control Group ◽

Binding Motif ◽

Isatis Indigotica ◽

Rate Limiting Step ◽

Genome Wide ◽

Transgenic Lines ◽

Gene Structures ◽

High Auxin

Auxin is one of the most critical hormones in plants. YUCCA (Tryptophan aminotransferase of Arabidopsis (TAA)/YUCCA) enzymes catalyze the key rate-limiting step of the tryptophan-dependent auxin biosynthesis pathway, from IPA (Indole-3-pyruvateacid) to IAA (Indole-3-acetic acid). Here, 13 YUCCA family genes were identified from Isatis indigotica, which were divided into four categories, distributing randomly on chromosomes (2n = 14). The typical and conservative motifs, including the flavin adenine dinucleotide (FAD)-binding motif and flavin-containing monooxygenases (FMO)-identifying sequence, existed in the gene structures. IiYUCCA genes were expressed differently in different organs (roots, stems, leaves, buds, flowers, and siliques) and developmental periods (7, 21, 60, and 150 days after germination). Taking IiYUCCA6-1 as an example, the YUCCA genes functions were discussed. The results showed that IiYUCCA6-1 was sensitive to PEG (polyethylene glycol), cold, wounding, and NaCl treatments. The over-expressed tobacco plants exhibited high auxin performances, and some early auxin response genes (NbIAA8, NbIAA16, NbGH3.1, and NbGH3.6) were upregulated with increased IAA content. In the dark, the contents of total chlorophyll and hydrogen peroxide in the transgenic lines were significantly lower than in the control group, with NbSAG12 downregulated and some delayed leaf senescence characteristics, which delayed the senescence process to a certain extent. The findings provide comprehensive insight into the phylogenetic relationships, chromosomal distributions, and expression patterns and functions of the YUCCA gene family in I. indigotica.

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Genome-wide distribution and potential regulatory functions of AtATE, a novel family of miniature inverted-repeat transposable elements in Arabidopsis thaliana

Molecular Genetics and Genomics ◽

10.1007/s00438-002-0675-4 ◽

2002 ◽

Vol 267 (4) ◽

pp. 459-471 ◽

Cited By ~ 25

Author(s):

A. El Amrani ◽

L. Marie ◽

A. Aïnouche ◽

J. Nicolas ◽

I. Couée

Keyword(s):

Arabidopsis Thaliana ◽

Transposable Elements ◽

Inverted Repeat ◽

Wide Distribution ◽

Genome Wide ◽

Regulatory Functions

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A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome

Genes ◽

10.3390/genes12060859 ◽

2021 ◽

Vol 12 (6) ◽

pp. 859

Author(s):

Alicja Macko-Podgórni ◽

Gabriela Machaj ◽

Dariusz Grzebelus

Keyword(s):

Transposable Elements ◽

Inverted Repeat ◽

Splice Variants ◽

Untranslated Regions ◽

Plant Genomes ◽

Bioinformatic Tools ◽

Genome Wide ◽

Gene Structure And Expression ◽

Coding Capacity ◽

Reference Genomes

Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack of coding capacity, the identification of MITEs has been demanding. However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes. We mined MITEs in the carrot reference genome DH1 using MITE-hunter and developed a curated carrot MITE repository comprising 428 families. Of the 31,025 MITE copies spanning 10.34 Mbp of the carrot genome, 54% were positioned in genic regions. Stowaways and Tourists were frequently present in the vicinity of genes, while Mutator-like MITEs were relatively more enriched in introns. hAT-like MITEs were relatively more frequently associated with transcribed regions, including untranslated regions (UTRs). Some carrot MITE families were shared with other Apiaceae species. We showed that hAT-like MITEs were involved in the formation of new splice variants of insertion-harboring genes. Thus, carrot MITEs contributed to the accretion of new diversity by altering transcripts and possibly affecting the regulation of many genes.

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