Arabidopsis thaliana
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PROVIDER: PRJNA117275 | ENA |
REPOSITORIES: ENA
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Project description:Hight throughput techniques have revealed huge complexity in antisense RNAs in many organisms. We have explored the complexity of this class of transcripts and functional links to Polycomb silencing thought analysis of non-coding RNAs of Arabidopsis FLC. FLC is repressed and epigenetically silenced by prolonged cold, enabling plants to undergo the floral transition. Single nucleotide resolution tiling array revealed long non-coding transcripts covering the entire FLC locus. The most abundant of these are capped and polyadenylated, initiate over a 100 nucleotide window just downstream of the sense polyA site, are differentially spliced and terminate either within the sense gene or its promoter. Their levels correlate with FLC sense transcripts in all mutants and conditions tested except cold treatment. The antisense transcripts were strongly but transiently cold-induced, much earlier than other vernalization markers, and this coincided with reduction in sense FLC transcription but not sense FLC mRNA levels. Addition of the FLC antisense 5'/sense 3' region to a GFP transgene was sufficient to confer cold-induced silencing of thet fusion; however this silencing was not epigenetically manteined. These processes were all independent of the function of the Polycomb proteins required for maintenance of FLC silencing. Our data suggest that FLC antisense transcripts induce transient FLC transcriptional silencing, possibly through promoter interference, with the epigenetic silencing requiring subsequent recruitment of Polycomb machinery. Total seedling RNA from different genotypes and different conditions: WT, FRIGIDA, 35s::FCA (giving overexpression of FCA), FRIGIDA + 2 weeks cold, FRIGIDA + 2 weeks cold + 7 days warm.
2009-12-31 | E-GEOD-16977 | biostudies-arrayexpress
Project description:Hight throughput techniques have revealed huge complexity in antisense RNAs in many organisms. We have explored the complexity of this class of transcripts and functional links to Polycomb silencing thought analysis of non-coding RNAs of Arabidopsis FLC. FLC is repressed and epigenetically silenced by prolonged cold, enabling plants to undergo the floral transition. Single nucleotide resolution tiling array revealed long non-coding transcripts covering the entire FLC locus. The most abundant of these are capped and polyadenylated, initiate over a 100 nucleotide window just downstream of the sense polyA site, are differentially spliced and terminate either within the sense gene or its promoter. Their levels correlate with FLC sense transcripts in all mutants and conditions tested except cold treatment. The antisense transcripts were strongly but transiently cold-induced, much earlier than other vernalization markers, and this coincided with reduction in sense FLC transcription but not sense FLC mRNA levels. Addition of the FLC antisense 5'/sense 3' region to a GFP transgene was sufficient to confer cold-induced silencing of thet fusion; however this silencing was not epigenetically manteined. These processes were all independent of the function of the Polycomb proteins required for maintenance of FLC silencing. Our data suggest that FLC antisense transcripts induce transient FLC transcriptional silencing, possibly through promoter interference, with the epigenetic silencing requiring subsequent recruitment of Polycomb machinery.
2009-12-31 | GSE16977 | GEO
Project description:• Polycomb (PcG) regulation is crucial for development across eukaryotes, but how PcG targets are specified is still incompletely understood. The slow timescale of cold-induced Polycomb Repressive Complex 2 silencing during vernalization at Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate the sequence of events. Association of the DNA binding protein VAL1 to an FLC intronic RY motif within the PcG nucleation region is an important step. VAL1 is associated in vivo with APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and Polycomb Repressive Complex 1 (PRC1). Here, we show that ASAP and PRC1 functions are necessary for co-transcriptional repression and chromatin regulation during FLC silencing. ASAP mutants affect FLC transcription in warm conditions, but the rate of FLC silencing in the cold is unaffected. PRC1-mediated H2Aub accumulation increases at the nucleation region upon exposure to cold, but unlike the PRC2-delivered H3K27me3 does not spread across the locus. H2Aub is thus involved in the transition to epigenetic silencing at FLC facilitating H3K27me3 accumulation, which in turn is necessary for long-term epigenetic memory. Overall, our work highlights the importance of the DNA sequence-specific binding protein VAL1 as an assembly platform coordinating the co-transcriptional repression and chromatin regulation necessary for the epigenetic silencing of FLC.
2022-10-13 | PXD036548 | Pride
Project description:Polycomb (PcG) silencing is crucial for development, but how targets are specified remains incompletely understood. The cold-induced Polycomb Repressive Complex 2 (PRC2) silencing of Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate PcG regulation. Association of the DNA binding protein VAL1 to the PcG nucleationregion at FLC is an important step. VAL1 interacts with APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and PRC1. Here, we show that ASAP and PRC1 are necessary for co-transcriptional repression and chromatin regulation during FLC silencing. ASAP mutants affect FLC transcription in warm conditions, but the rate of FLC silencing in the cold is unaffected. PRC1-mediated H2Aub accumulates at FLC nucleation region during cold, but unlike the PRC2-delivered H3K27me3 does not spread across the locus. H2Aub thus marks the transition to epigenetic silencing, while H3K27me3 is necessary for long-term epigenetic memory. Overall, our work highlights the importance of VAL1 as an assembly platform co-ordinating the co-transcriptional repression and chromatin regulation necessary for the epigenetic silencing of FLC.
2022-08-15 | PXD036057 |
Project description:Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the Poly(A) signal (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing (RNA-seq) during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady state RNA techniques to identify biologically relevant players in stress responses.
2024-06-04 | GSE252832 | GEO
Project description:In this work, we present the first comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process in Arabidopsis thaliana. Six major clusters of genes exhibiting distinctive features were identified. Temporary changes in histone H3K4me3 levels were observed that likely coordinate photosynthesis and prevent oxidative damage during cold. In addition, vernalization induced a stable accumulation of H3K27me3 over genes encoding many development-related transcription factors, resulting in either inhibition of transcription or a bivalent status of the genes. Lastly, FLC-like and VIN3-like genes were identified that appear to be novel components of the vernalization pathway.
2020-08-01 | GSE130291 | GEO
Project description:Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1) and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states.
2020-05-30 | GSE151449 | GEO
Project description:We were interested in identifying targets of novel putative miRNAs we identified from small RNA sequencing libraries of Arabidopsis shoots. The small RNA (smRNA) sequencing libraries were made to identify changes in abundance of specific smRNAs in response to developmental transitions in Arabidopsis thaliana shoots, with special focus on vegetative phase change. We specifically wanted to separate the temporal changes in gene expression that result from vegetative phase change and those from flowering. Because of the close timing between the juvenile-to-adult and adult-to-reproductive developmental transitions in Arabidopsis grown under long day conditions, we used the late-flowering genotype FRI;FLC developed by the lab of Richard Amasino by introgressing the FRI allele from Sf-2 into the Col-0 genetic background, which is fri;FLC. For the early flowering genotype, we used FRI;flc-3, also developed by the Amasino lab by EMS-mutagenizing FRI;FLC, identifying early flowering mutants, and backcrossing multiple times to eliminate other EMS-induced mutations. The onset of vegetative phase change in FRI;FLC and FRI;flc-3 under our growth conditions was identical, but the progression was slower in FRI;FLC. By sequencing small RNAs from shoot apices at different time points and fully-expanded leaves at different positions on the shoot and comparing the results between the two genotypes, we were able to obtain a clear picture of changes in small RNA abundance in response to vegetative phase change and flowering in Arabidopsis. We then used the remaining RNA to make genome-wide mapping of uncapped and cleaved transcripts (GMUCT) 2.0 libraries of a subset of our samples. GMUCT 2.0 allows you to identify RNAs that are 1) uncapped and in the process of 5’->3’ exonuclease degradation and 2) miRNA and siRNA-mediated cleavage products. We wanted to use these GMUCT 2.0 libraries to identify targets of novel putative miRNAs discovered by our smRNA sequencing, thereby supporting the idea that these novel putative miRNAs are in fact functional.
2016-02-01 | GSE72505 | GEO