Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE133618 | GEO | 2020/02/24
REPOSITORIES: GEO
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Project description:In Arabidopsis thaliana, DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA (sRNA) transcripts. These transcripts are processed by DICER-LIKE3 into 24-nt small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nt epigenetically activated siRNAs (easiRNAs), which likely silence TEs via post-transcriptional mechanisms. Despite this proposed role of Pol IV, its loss of function in Arabidopsis does not cause a discernable pollen defect. Here, we show that the knockout of NRPD1, encoding the largest subunit of Pol IV in the Brassicaceae species Capsella rubella, caused post-meiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were 2 depleted in Capsella nrpd1 microspores. In the wild-type background, the same TEs produced 21/22-nt and 24-nt siRNAs; these processes required Pol IV activity. Arrest of Capsella nrpd1 microspores was accompanied by the deregulation of genes targeted by Pol IV-dependent siRNAs. TEs were much closer to genes in Capsella rubella compared to Arabidopsis thaliana, perhaps explaining the essential role of Pol IV in pollen development in Capsella. Our discovery that Pol IV is functionally required in Capsella microspores emphasizes the relevance of investigating different plant models.
2020-01-23 | GSE136847 | GEO
Project description:Polyploidy, the presence of more than two sets of chromosomes within the nucleus, is a common phenomenon among plants that has shaped genome organization and is thought to be a major driver of speciation. The triploid block acts as a reproductive barrier that prevents successful backcrosses of newly formed polyploids with their progenitors. It is established in the endosperm, an ephemeral tissue that nurtures the developing embryo. Here we show that paternal 21/22 nucleotide epigenetically activated small interfering RNAs (easiRNAs) in Arabidopis thaliana are responsible for the establishment of the triploid block associated seed abortion. This dramatic phenotype is overcome when crosses are performed with a paternal mutant in the plant specific RNA polymerase IV (Pol IV). Loss of Pol IV reduces both easiRNAs and hetsiRNAs in the pollen grain. Seeds derived from crosses between wild type tetraploid fathers and diploid mothers have reduced levels of hetsiRNAs and cytosine methylation at transposable elements (TEs), indicating that they have suffered an excess of epigenetic reprogramming due to an excess of paternally derived easiRNAs. Paternal Pol IV mutants are able to buffer that easiRNA excess and rescue the abortion phenotype by rescuing both the cytosine methylation level at TEs and the 24 nt hetsiRNA accumulation levels. This mechanism highlights the elegant and important TE regulation mechanism controlled by the plant specific Pol IV that takes place pre-fertilization and regulates paternal easiRNAs and maternal hetsiRNAs, and determines the post-fertilization epigenetic stability and seed viability.
2017-12-14 | GSE84122 | GEO
Project description:Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24 nt small RNAs are reduced in TEs and enriched in genes compared to the embryo. We find an inverse relationship between the parent-of-origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs. Disruption of the Pol IV sRNA pathway causes a shift toward maternal allele mRNA expression for many genes. Furthermore, paternal inheritance of an RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. Thus, RNA Pol IV mediates transcriptional balance between maternally and paternally inherited genomes in endosperm.
2017-12-15 | GSE94787 | GEO
Project description:Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24 nt small RNAs are reduced in TEs and enriched in genes compared to the embryo. We find an inverse relationship between the parent-of-origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs. Disruption of the Pol IV sRNA pathway causes a shift toward maternal allele mRNA expression for many genes. Furthermore, paternal inheritance of an RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. Thus, RNA Pol IV mediates transcriptional balance between maternally and paternally inherited genomes in endosperm.
2017-12-15 | GSE94786 | GEO
Project description:To investigate the roles of sRNAs in keeping embryo dormancy or germination in Larix leptolepis, we deciphered the endogenous "sRNAome" in dormant and germinated embryos. High-throughput sequencing of the sRNA libraries showed that dormant embryos exhibited a length bias towards 24-nt, while germinated embryos showed a bias towards a 21-nt and/or 22-nt length. Both of proportions for miRNAs to the non-redundant and redundant sRNAs were higher in germinated embryos than those in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. The proportion of 21-nt and 22-nt sRNAs increased in germinated embryos, which might attribute to the higher expression level of miRNAs. We identified a total of 160 conserved miRNAs from 39 families, 16 novel miRNAs, and 14 plausible miRNA candidates, of which novel and non-conserved known miRNAs might be the main contributors. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during embryo dormancy and germination.
2014-07-19 | GSE49059 | GEO
Project description:Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type (wt) plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV (Pol IV) complex, and is responsible for accumulation of most 24 nucleotide (nt) small interfering RNA (siRNAs). We identified novel MIRNA loci and verified miR399 target conservation in maize. RMR6-dependent 23-24 nt siRNA loci were specifically enriched in the upstream region of the most highly expressed genes. Most genes mis-regulated in rmr6-1 did not show a significant correlation with loss of flanking siRNAs, but we identified one gene supporting existing models of direct gene regulation by TE-derived siRNAs. Long-term drought correlated with changes of miRNA and sRNA accumulation, in particular inducing down-regulation of a set of sRNA loci in the wt leaf.
2016-01-20 | GSE70487 | GEO
Project description:Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type (wt) plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV (Pol IV) complex, and is responsible for accumulation of most 24 nucleotide (nt) small interfering RNA (siRNAs). We identified novel MIRNA loci and verified miR399 target conservation in maize. RMR6-dependent 23-24 nt siRNA loci were specifically enriched in the upstream region of the most highly expressed genes. Most genes mis-regulated in rmr6-1 did not show a significant correlation with loss of flanking siRNAs, but we identified one gene supporting existing models of direct gene regulation by TE-derived siRNAs. Long-term drought correlated with changes of miRNA and sRNA accumulation, in particular inducing down-regulation of a set of sRNA loci in the wt leaf. sRNA profile of maize leaf and shoot apical meristematic area, of wt and rmr6-1 mutant plants grown under 1) control conditions 2) salt stress 3) drought stress 4) salt+drought stress. Each condition was replicated two/three times, after 10 days of treatment and after 7 days of recovery.
2016-01-20 | E-GEOD-70487 | biostudies-arrayexpress
Project description:We report polysomal RNA sequencing data (RNAseq), small RNAseq, and virus-like-particle (VLP) DNA sequencing (DNAseq) and ChIPseq data. Arabidopsis ddm1 mutants produce LTR retrotransposon transcripts that are processed into 21-22 nt easiRNAs by RNA-Dependent RNA polymerase 6 (RDR6). To test if 21-22 nt easiRNAs regulate transcription, translation and reverse transcription of LTR retrotransposons, we compared ddm1 and ddm1rdr6 in polysomal RNAseq, VLP DNAseq and ChIPseq data. We found a handful of ATHILA elements were differentially regulated in ddm1rdr6 for polysomal RNAseq, VLP DNAseq, and ChIPseq datasets. Using short read and long read technologies, we also profiled functional LTR retrotransposons that made full-length DNA by reverse transcription inside VLPs. Small RNAseq data were obtained in pollen and inflorescence tissues in wild-type and ddm1.
2020-03-13 | GSE128932 | GEO
Project description:In Oxytricha, the somatic genome is responsible for vegetative growth, while the germline contributes DNA to the next sexual generation. Somatic nuclear development eliminates all transposons and other so-called "junk DNA", which constitute ~95% of the germline. We demonstrate that Piwi-interacting small RNAs (piRNAs) from the maternal nucleus can specify genomic regions for retention in this process. Oxytricha piRNAs map primarily to the somatic genome, representing the ~5% of the germline that is retained. Furthermore, injection of synthetic piRNAs corresponding to normally-deleted regions leads to their retention in subsequent generations. Our findings highlight small RNAs (sRNAs) as powerful transgenerational carriers of epigenetic information for genome programming. The backcross study here shows that the mating between an IES+ strain with the wild-type stain produces corresponding IES-containing sRNAs at 19 hr, and we provided the mapping to and the sequences of the specific loci of interest in the submission. As a control, wild-type cells do not produce such IES-containing sRNAs, and this analysis can be pulled out from the GSE35018 study since we provided mapping to the whole genome. The purpose of the 20 hr total sRNA sequencing study here is to show that the class of 27 nt sRNA is the major species of total sRNAs in Oxytricha at 20 hr, which we sequenced previously from Otiwi1-associated sRNAs at 12, 19, 23, and 30 hr (GSE35018). In addition, there is a less abundant class of small RNAs of 21-22 nt. These two classes are obvious by simply plotting the length distribution of the sRNA sequences. We sequenced sRNAs from Contig22226.0 IES1+ strain backcrossed to wild-type parental strain at 19hr post-mixing, and found corresponding IES-containing sRNAs. As a control, wild-type cells do not produce such IES-containing sRNAs (see GSE35018). Total RNA from the backcrossing at 19hr were isolated with mirVana small RNA extraction kit (Ambion), and directly used for making Illumina sRNA libraries. Oxytricha total small RNA (sRNA) sequencing at 20 hr post conjugation shows that a class of 27 nt, 5'-U sRNAs dominates the sRNA population at 20 hr, and this class of sRNAs associate with Otiwi1 (see GSE35018 for Otiwi1-interacting sRNAs in Oxytricha). In addition, a much less abundant class of 21-22 nt sRNAs is present according to the length distribution.
2012-09-01 | E-GEOD-40081 | biostudies-arrayexpress
Project description:Small interfering RNAs (siRNAs) are critical for proper development and immunity in eukaryotes1. Plants produce siRNAs with lengths of 21-, 22-, or 24- nucleotides (nt), wherein the 21- and 24-nt siRNAs mediate mRNA cleavage and DNA methylation2,3, respectively. However, the biological functions of 22-nt siRNAs remain elusive. Here we report the identification and characterization of a group of endogenous 22-nt siRNAs generated from the action of DICER-LIKE 2 (DCL2). When cytoplasmic RNA decay and DCL4 are deficient, the massive accumulation of 22-nt siRNAs causes pleiotropic growth disorders, including severe dwarfism, meristem defect, and pigmentation. Notably, two genes that encode nitrate reductases, NIA1 and NIA2, produce nearly half of the total of 22-nt siRNAs. Production of 22-nt siRNA triggers explosive self-amplification that leads to a small RNA storm, and induces dramatic translational repression both gene-specifically and globally. 22-nt siRNAs are also found to preferentially accumulate upon nitrogen deficiency, which acts to restrain plant growth and promote stress responses. Thus, our research uncovers the unique properties of 22-nt siRNAs, a previously unexplored class of plant siRNAs, and highlights the length of small RNA as a major functional determinant.
2020-02-14 | GSE135959 | GEO