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ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis [Methyl-seq]

ABSTRACT: We examed the methylation level of SUCSUL, SUCSUL amp1lamp1 and Col in Arabidopsis to study the role of AMP1 in siRNA-mediated gene regulation

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE233872 | GEO | 2025/01/02

REPOSITORIES: GEO

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ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis [small RNA-seq]

Project description:We profiled the small RNA of SUCSUL, SUCSUL amp1lamp1 and Col in Arabidopsis to study the role of AMP1 in siRNA-mediated gene regulation

2025-01-02 | GSE233873 | GEO

ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-01-02 | GSE233874 | GEO

ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis [Methyl-seq]

Project description:ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis [Methyl-seq]

| PRJNA978428 | ENA

ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis

Project description:ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis

| PRJNA978425 | ENA

ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis [small RNA-seq]

Project description:ALTERED MERISTEM PROGRAM1 impairs RNA silencing through repressing the biogenesis of inverted repeats-derived siRNAs in Arabidopsis [small RNA-seq]

| PRJNA978430 | ENA

Transcriptom analyses of Arabidopsis altered meritem program1-32 (amp1-32) mutant as well as wild-type Columbia-0 plants via next-generation sequencing (NGS).

Project description:Purpose:The goals of this study are to compare transcriptome of amp1-32 mutant with that of wild-type Columbia-0 plant and to identify genes whose expression are tightly regualted by AMP1 in Arabidopsis. Methods: mRNA profiles of 3-week-old wild-type Col-0 and amp1-32 mutant plants were generated by deep sequencing, in duplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method : TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30~53 million sequence reads per sample to the Arabidopsis genome (TAIR10). From the 2 biological replicates, we detected 135 up-regulated genes, and 36 down-regulated genes, in the amp1-32 mutant plant. Conclusions: Our study represents the first detailed analysis of transcriptome of amp1 mutant plants, with biologic replicates. Our results show that AMP1 protein had weak, but significant, effects on transcription of genes important for plant development and responses to stresses.

2017-05-30 | GSE81618 | GEO

Recombination-restarted replication makes inverted chromosome fusions at inverted repeats.

Project description:Impediments to DNA replication are known to induce gross chromosomal rearrangements (GCRs) and copy-number variations (CNVs). GCRs and CNVs underlie human genomic disorders and are a feature of cancer. During cancer development, environmental factors and oncogene-driven proliferation promote replication stress. Resulting GCRs and CNVs are proposed to contribute to cancer development and therapy resistance. When stress arrests replication, the replisome remains associated with the fork DNA (stalled fork) and is protected by the inter-S-phase checkpoint. Stalled forks efficiently resume when the stress is relieved. However, if the polymerases dissociate from the fork (fork collapse) or the fork structure breaks (broken fork), replication restart can proceed either by homologous recombination or microhomology-primed re-initiation. Here we ascertain the consequences of replication with a fork restarted by homologous recombination in fission yeast. We identify a new mechanism of chromosomal rearrangement through the observation that recombination-restarted forks have a considerably high propensity to execute a U-turn at small inverted repeats (up to 1 in 40 replication events). We propose that the error-prone nature of restarted forks contributes to the generation of GCRs and gene amplification in cancer, and to non-recurrent CNVs in genomic disorders.

| S-EPMC3605775 | biostudies-literature

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs.

Project description:Small RNAs regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). Although miniature inverted-repeat transposable elements (MITEs) are closely associated with euchromatic genes, the broader functional impact of these short TE insertions in genes is largely unknown. We identified 22 families of MITEs in the Solanaceae (MiS1-MiS22) and found abundant MiS insertions in Solanaceae genomic DNA and expressed sequence tags (EST). Several Solanaceae MITEs generate genome changes that potentially affect gene function and regulation, most notably, a MiS insertion that provides a functionally indispensable alternative exon in the tobacco mosaic virus N resistance gene. We show that MITEs generate small RNAs that are primarily 24 nt in length, as detected by Northern blot hybridization and by sequencing small RNAs of Solanum demissum, Nicotiana glutinosa, and Nicotiana benthamiana. Additionally, we show that stable RNAi lines silencing DICER-LIKE3 (DCL3) in tobacco and RNA-dependent RNA polymerase 2 (RDR2) in potato cause a reduction in 24-nt MITE siRNAs, suggesting that, as in Arabidopsis, TE-derived siRNA biogenesis is DCL3 and RDR2 dependent. We provide evidence that DICER-LIKE4 (DCL4) may also play a role in MITE siRNA generation in the Solanaceae.

| S-EPMC2612961 | biostudies-literature

Fast cloning inverted repeats for RNA interference.

Project description:Double-stranded RNA (dsRNA) can induce post-transcriptional gene silencing in a wide variety of organisms. Commonly, inverted repeats are used to produce dsRNA to silence genes of interest. However, cloning inverted repeats still remains a rate-limiting step for widely applying this technique. Here we describe a pGEM-T-based vector, pGEM-WIZ, designed to produce inverted repeats for any Drosophila gene. pGEM-WIZ has a high efficiency in assembling inverted repeats and the repeats in this vector are stable in regular Escherichia coli strains. Furthermore, we have developed a method for rapid selection of clones with an inverted repeat based on size and relative copy number of the vector with or without an insert. This method further eases the cloning process. The inverted repeat cassette assembled in pGEM-WIZ can be easily transferred to commonly available expression vectors suitable for stably expressing inverted repeats in vitro and in vivo.

| S-EPMC1624905 | biostudies-literature

Concentration of inverted repeats along human DNA.

Project description:This work aims to describe the observed enrichment of inverted repeats in the human genome; and to identify and describe, with detailed length profiles, the regions with significant and relevant enriched occurrence of inverted repeats. The enrichment is assessed and tested with a recently proposed measure (z-scores based measure). We simulate a genome using an order 7 Markov model trained with the data from the real genome. The simulated genome is used to establish the critical values which are used as decision thresholds to identify the regions with significant enriched concentrations. Several human genome regions are highly enriched in the occurrence of inverted repeats. This is observed in all the human chromosomes. The distribution of inverted repeat lengths varies along the genome. The majority of the regions with severely exaggerated enrichment contain mainly short length inverted repeats. There are also regions with regular peaks along the inverted repeats lengths distribution (periodic regularities) and other regions with exaggerated enrichment for long lengths (less frequent). However, adjacent regions tend to have similar distributions.

| S-EPMC10561070 | biostudies-literature

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