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The application of a reverse transcriptase inhibitor suppresses LTR retrotransposon mobilization in plants [ALE-seq]

ABSTRACT: Recently developed methods applied to plant material, for example tissue culture during plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. Here we tested the use of Reverse Transcriptase inhibitors to avoid LTR-TE mobilization in plants. We demonstrated that the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. We propose the use of Tenofovir as a new tool to both study LTR-TE transposition and to regenerate more genetically stable plant lines from tissue culture.

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE196868 | GEO | 2023/01/06

REPOSITORIES: GEO

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The application of a reverse transcriptase inhibitor suppresses LTR retrotransposon mobilization in plants [RNA-seq]

Project description:Recently developed methods applied to plant material, for example tissue culture during plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. Here we tested the use of Reverse Transcriptase inhibitors to avoid LTR-TE mobilization in plants. We demonstrated that the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. We propose the use of Tenofovir as a new tool to both study LTR-TE transposition and to regenerate more genetically stable plant lines from tissue culture.

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Project description:Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals—tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs—both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, underscoring the need for cautious interpretation of the connection between TEs and genomic imprinting.

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Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm (WGBS aerial)

Project description:Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals—tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs—both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, underscoring the need for cautious interpretation of the connection between TEs and genomic imprinting.

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Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis

Project description:Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently e v olv ed in the en- dosperm of flo w ering plants and the placenta of mammals—tissues crucial f or nurturing embry os. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct in v estigations of the impact of de no v o TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana . Through the combination of chemical TE mobilization and doubled haploid induction, we gener- ated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs—both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdo wn of MEG imprinting. T his study pro vides insights into the consequences of chemically induced TE remobilization in the endosperm, re v ealing that chemically-induced epigenome changes can ha v e long-term consequences on imprinted gene expression.

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Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

Project description:Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome. Examination of small RNA populations in the sugarcane leaves that show matches against sugarcane LTR-RTs.

2012-04-16 | E-GEOD-35143 | biostudies-arrayexpress

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