Survey of transposable elements from rice genomic sequences

Transposable elements are powerful mutagens. Along with genomic sequences, knock-out phenotypes and expression patterns are important information to elucidate the function of genes. In this review, I propose a strategy to develop tranposant lines on a large scale by combining genetic cross and tissue culture of Ac and Ds lines. Based on the facts that Ds tends to be inactive in F2 or later generation and Ds becomes reactivated via tissue culture, a large scale of transposants can be produced by tissue culture of seeds carrying Ac and inactive Ds. In this review, I describe limitations and considerations in operating transposon tagging systems in rice. Also, I discuss the efficiency of our gene trap system and technical procedures to clone Ds flanking DNA.

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Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

10.1101/2021.07.31.454434 ◽

2021 ◽

Author(s):

Jaemyung Choi ◽

David Bruce Lyons ◽

Daniel Zilberman

Keyword(s):

Dna Methylation ◽

Transposable Elements ◽

Small Rna ◽

Histone H3 ◽

Histone H1 ◽

Dna Methyltransferases ◽

Flowering Plants ◽

Genomic Sequences ◽

Rna Molecules ◽

Rna Biogenesis

Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically required for small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.

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Software Evaluation for de novo Detection of Transposons

10.1101/2021.02.08.430290 ◽

2021 ◽

Author(s):

Matias Rodriguez ◽

Wojciech Makałowski

Keyword(s):

Transposable Elements ◽

Genome Evolution ◽

De Novo ◽

Simulated Data ◽

Genomic Sequences ◽

Software Evaluation ◽

Easy Task ◽

Eukaryotic Genomes

AbstractTransposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.

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MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

Nucleic Acids Research ◽

10.1093/nar/gkq862 ◽

2010 ◽

Vol 38 (22) ◽

pp. e199-e199 ◽

Cited By ~ 210

Author(s):

Y. Han ◽

S. R. Wessler

Keyword(s):

Transposable Elements ◽

Inverted Repeat ◽

Genomic Sequences

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Evolution and diversity of transposable elements in fish genomes

Scientific Reports ◽

10.1038/s41598-019-51888-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 6

Author(s):

Feng Shao ◽

Minjin Han ◽

Zuogang Peng

Keyword(s):

Species Diversity ◽

Transposable Elements ◽

Long Terminal Repeat ◽

Genome Size ◽

Fish Species ◽

Significant Variation ◽

Genomic Sequences ◽

Fish Genome ◽

Long Interspersed Nuclear Elements ◽

Fish Species Diversity

Abstract Transposable elements (TEs) are genomic sequences that can move, multiply, and often form sizable fractions of vertebrate genomes. Fish belong to a unique group of vertebrates, since their karyotypes and genome sizes are more diverse and complex, with probably higher diversity and evolution specificity of TE. To investigate the characteristics of fish TEs, we compared the mobilomes of 39 species, and observed significant variation of TE content in fish (from 5% in pufferfish to 56% in zebrafish), along with a positive correlation between fish genome size and TE content. In different classification hierarchies, retrotransposons (class), long terminal repeat (order), as well as Helitron, Maverick, Kolobok, CMC, DIRS, P, I, L1, L2, and 5S (superfamily) were all positively correlated with fish genome size. Consistent with previous studies, our data suggested fish genomes to not always be dominated by DNA transposons; long interspersed nuclear elements are also prominent in many species. This study suggests CR1 distribution in fish genomes to be obviously regular, and provides new clues concerning important events in vertebrate evolution. Altogether, our results highlight the importance of TEs in the structure and evolution of fish genomes and suggest fish species diversity to parallel transposon content diversification.

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Software Evaluation for De Novo Detection of Transposons

10.21203/rs.3.rs-179452/v1 ◽

2021 ◽

Author(s):

Matias Rodríguez ◽

Wojciech Makalowski

Keyword(s):

Transposable Elements ◽

Genome Evolution ◽

De Novo ◽

Simulated Data ◽

Genomic Sequences ◽

Software Evaluation ◽

Easy Task ◽

Eukaryotic Genomes

Abstract Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo!TE detection and compared their performance on both simulated data and well curated genomic sequences. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.

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Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

eLife ◽

10.7554/elife.72676 ◽

2021 ◽

Vol 10 ◽

Author(s):

Jaemyung Choi ◽

David B Lyons ◽

Daniel Zilberman

Keyword(s):

Dna Methylation ◽

Transposable Elements ◽

Small Rna ◽

Histone H3 ◽

Histone H1 ◽

Dna Methyltransferases ◽

Flowering Plants ◽

Genomic Sequences ◽

Rna Molecules ◽

Rna Biogenesis

Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.

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SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction

Frontiers in Genetics ◽

10.3389/fgene.2020.594318 ◽

2021 ◽

Vol 11 ◽

Author(s):

Jerzy K. Kulski ◽

Shingo Suzuki ◽

Takashi Shiina

Keyword(s):

Transposable Elements ◽

Mhc Class I ◽

Human Leukocyte ◽

Genomic Region ◽

Class I ◽

Genomic Sequences ◽

Prime Model ◽

Sequence Alignments ◽

Human Major Histocompatibility Complex ◽

Haplotype Blocks

The genomic region (~4 Mb) of the human major histocompatibility complex (MHC) on chromosome 6p21 is a prime model for the study and understanding of conserved polymorphic sequences (CPSs) and structural diversity of ancestral haplotypes (AHs)/conserved extended haplotypes (CEHs). The aim of this study was to use a set of 95 MHC genomic sequences downloaded from a publicly available BioProject database at NCBI to identify and characterise polymorphic human leukocyte antigen (HLA) class I genes and pseudogenes, MICA and MICB, and retroelement indels as haplotypic lineage markers, and single-nucleotide polymorphism (SNP) crossover loci in DNA sequence alignments of different haplotypes across the Olfactory Receptor (OR) gene region (~1.2 Mb) and the MHC class I region (~1.8 Mb) from the GPX5 to the MICB gene. Our comparative sequence analyses confirmed the identity of 12 haplotypic retroelement markers and revealed that they partitioned the HLA-A/B/C haplotypes into distinct evolutionary lineages. Crossovers between SNP-poor and SNP-rich regions defined the sequence range of haplotype blocks, and many of these crossover junctions occurred within particular transposable elements, lncRNA, OR12D2, MUC21, MUC22, PSORS1A3, HLA-C, HLA-B, and MICA. In a comparison of more than 250 paired sequence alignments, at least 38 SNP-density crossover sites were mapped across various regions from GPX5 to MICB. In a homology comparison of 16 different haplotypes, seven CEH/AH (7.1, 8.1, 18.2, 51.x, 57.1, 62.x, and 62.1) had no detectable SNP-density crossover junctions and were SNP poor across the entire ~2.8 Mb of sequence alignments. Of the analyses between different recombinant haplotypes, more than half of them had SNP crossovers within 10 kb of LTR16B/ERV3-16A3_I, MLT1, Charlie, and/or THE1 sequences and were in close vicinity to structurally polymorphic Alu and SVA insertion sites. These studies demonstrate that (1) SNP-density crossovers are associated with putative ancestral recombination sites that are widely spread across the MHC class I genomic region from at least the telomeric OR12D2 gene to the centromeric MICB gene and (2) the genomic sequences of MHC homozygous cell lines are useful for analysing haplotype blocks, ancestral haplotypic landscapes and markers, CPSs, and SNP-density crossover junctions.

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