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Transcriptomic effects of the expression in Arabidopsis of a TCP15-EAR fusion controlled by its own promoter (two-color experiment)

ABSTRACT: TCP proteins are transcription factors that participate in plant development (Martin-Trillo ad Cubas, 2010; Uberti-Manassero et al., 2013). Previous studies demonstrated that the Arabidopsis thaliana TCP protein TCP15 affects the development of leaves, stems and flowers (Kieffer et al., 2011; Uberti-Manassero et al., 2013). To obtain further insight into the molecular mechanisms involved in TCP15 action, we performed a transcriptional profiling of plants that express a repressor form of TCP15 under the control of the TCP15 promoter (P15::TCP15-EAR), previously described in Uberti-Manassero et al. (2012). For this purpose, gene expression was quantified in RNA extracted from complete rosettes of 25-day-old P15::TCP15-EAR plants and compared with that in RNA extracted from wild-type (Col-0) plants of the same age. Two genotype experiment: wild type vs. P15::TCP15-EAR plants. Biological replicates: 2 wild type replicates, 2 P15::TCP15-EAR replicates.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Agustin Arce

PROVIDER: E-GEOD-57743 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptomic effects of the expression in Arabidopsis of a TCP15-EAR fusion controlled by its own promoter (one-color experiment)

Project description:TCP proteins are transcription factors that participate in plant development (Martin-Trillo ad Cubas, 2010; Uberti-Manassero et al., 2013). Previous studies demonstrated that the Arabidopsis thaliana TCP protein TCP15 affects the development of leaves, stems and flowers (Kieffer et al., 2011; Uberti-Manassero et al., 2013). To obtain further insight into the molecular mechanisms involved in TCP15 action, we performed a transcriptional profiling of plants that express a repressor form of TCP15 under the control of the TCP15 promoter (P15::TCP15-EAR), previously described in Uberti-Manassero et al. (2012). For this purpose, gene expression was quantified in RNA extracted from complete rosettes of 25-day-old P15::TCP15-EAR plants and compared with that in RNA extracted from wild-type (Col-0) plants of the same age. Two genotype experiment: wild type vs. P15::TCP15-EAR plants. Biological replicates: 1 wild type replicate, 1 P15::TCP15-EAR replicate.

2015-05-16 | E-GEOD-57742 | biostudies-arrayexpress

Transcriptomic effects of the expression in Arabidopsis of a TCP15-EAR fusion controlled by its own promoter (two-color experiment)

2015-05-16 | GSE57743 | GEO

Transcriptomic effects of the expression in Arabidopsis of a TCP15-EAR fusion controlled by its own promoter (one-color experiment)

2015-05-16 | GSE57742 | GEO

Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1)-target genes in Arabidopsis

Project description:NAC transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) functions as a master regulator in DNA damage response of Arabidopsis. However, the signaling pathway controlled by SOG1 remains elusive. To identify target genes of SOG1, we used wild-type plants harboring the transgene ProSOG1:SOG1-Myc, which expresses the SOG1-Myc fusion gene under the 2-kb SOG1 promoter. It was previously demonstrated that SOG1-Myc can complement the sog1-1 mutation (Yoshiyama et al., 2013). After treatment of plants with 15 µM zeocin for 2 hours, chromatin fragments bound to SOG1-Myc were immunoprecipitated with the anti-Myc antibody, and were subjected to next generation sequencing. We identified 778 SOG1-binding peak summits, which displayed peak values 16-fold higher than those in wild-type plants without the transgene. The genomic regions between 5-kb upstream and downstream of each peak summit included 1514 genes among which we found SMR5, SMR7 and CYCB1;1 that were previously identified as SOG1 target genes (Yi et al., 2014; Weimer et al., 2016). Among 1514 genes identified by ChIP-sequencing, 146 genes were overlapped with the SOG1-regulated genes extracted from the microarray data (GSE106154); therefore, we concluded that the 146 genes are SOG1 ditrect target genes.

2017-11-02 | GSE106415 | GEO

DNMT1 mutant ants develop normally, but have disrupted oogenesis and decreased survival

Project description:While DNA methylation is an important gene regulatory mechanism in mammals (Razin and Riggs 1980; Moore, Le, and Fan 2013), its function in arthropods remains poorly understood. Studies in eusocial insects have argued for its role in caste development by regulating gene expression and splicing (Elango et al. 2009; Lyko et al. 2010; Bonasio et al. 2012; Flores et al. 2012; Foret et al. 2012; Li-Byarlay et al. 2013; Marshall, Lonsdale, and Mallon 2019; Shi et al. 2013)(Alvarado et al. 2015; Kucharski et al. 2008). However, such findings are not always consistent across studies, and have therefore remained controversial (Arsenault, Hunt, and Rehan 2018; Cardoso-Junior et al. 2021; Harris et al. 2019; Herb et al. 2012; Libbrecht et al. 2016; Oldroyd and Yagound 2021b; Patalano et al. 2015). Here we use CRISPR/Cas9 to mutate the maintenance DNA methyltransferase DNMT1 in the clonal raider ant, Ooceraea biroi. Mutants have greatly reduced DNA methylation but no obvious developmental phenotypes, demonstrating that, unlike mammals (Brown and Robertson 2007; En Li, Bestor, and Jaenisch 1992; Jackson-Grusby et al. 2001; Panning and Jaenisch 1996), ants can undergo normal development without DNMT1 or DNA methylation. Additionally, we find no evidence of DNA methylation regulating caste development. However, mutants are sterile, while in wildtypes, DNMT1 is localized to the ovaries and maternally provisioned into nascent oocytes. This supports the idea that DNMT1 plays a crucial but unknown role in the insect germline (Amukamara et al. 2020; Arsala et al. 2021; Bewick et al. 2019; Schulz et al. 2018; Ventós-Alfonso et al. 2020; Washington et al. 2020).

2023-03-23 | GSE182212 | GEO

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Project description:Hmx1 is a transcription factor expressed in the developing eye and ear and in some other parts of the nervous system. Dumbo mice are carrying the Hmx1 p.Q64X loss-of-function mutation (Munroe et al., 2009. BMC Developmental Biology). Transcriptomic analyses of this mouse model allows to decipher biological pathways under the control of Hmx1. In our study, we used it to better understand the role of Hmx1 in the retina and to identify several of its target genes. Wild-type and dumbo mice were maintained in a 12-hours light/12-hours dark cycle with free access to food and water. Animals were sacrified at P15 for retina isolation and RNA extraction.

2013-07-24 | E-GEOD-47002 | biostudies-arrayexpress

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2024-05-16 | GSE230836 | GEO

Auxin-triggered changes in the Arabidopsis root tip (phospho)proteome reveal novel root growth regulators

Project description:Canonical auxin signalling starts with auxin binding to the receptor complex, followed by modulation of gene transcription and protein abundance (Tan et al., 2007; Chapman and Estelle, 2009; Slade et al., 2017). However, recent studies also showed an alternative mechanism in roots involving intra-cellular auxin perception, but not transcriptional reprogramming (Fendrych et al., 2018). Despite knowledge on effects of auxin on Arabidopsis root growth at the protein and phosphorylation level is increasing (Zhang et al., 2013; Mattei et al., 2013; Slade et al., 2017), it still remains incomplete. To address this gap in our knowledge, we explored the impact of auxin on the root tip proteome and phosphoproteome.

2021-09-09 | PXD021267 | Pride

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ATAC-seq on HSV-1 infected primary human fibroblasts (time course)

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2018-03-08 | GSE100611 | GEO

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