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Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (ChIP-seq data set)

ABSTRACT: Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (ChIP-seq data set)

PROVIDER: PRJNA418944 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6303490.fastq.gz	Fastqsanger.gz
	SRR6303510.fastq.gz	Fastqsanger.gz
	SRR6303520.fastq.gz	Fastqsanger.gz
	SRR6303530.fastq.gz	Fastqsanger.gz
	SRR6303491.fastq.gz	Fastqsanger.gz

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Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors

Project description:Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors

| PRJNA434197 | ENA

Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (ChIP-seq data set)

Project description:A key model for understanding how large transcription complexes are targeted is the Drosophila dosage compensation system in which the Male-Specific Lethal (MSL) transcription complex specifically identifies and regulates the male X-chromosome. MSL complex is targeted to GA-containing sequences, but the most well-studied GA-binding transcription factor, GAGA Associated Factor (GAF), does not physically associate with MSL complex. Instead the Chromatin Linked Adapter for MSL Proteins (CLAMP) zinc-finger protein specifically targets MSL complex to GA-rich sequences on the X-chromosome. Here, we compare the binding relationships of CLAMP, GAF, and the MSL3 dosage compensation complex protein using ChIP-seq.

2018-02-01 | GSE107059 | GEO

Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (protein binding microarray data set)

Project description:Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (protein binding microarray data set)

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Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors (protein binding microarray data set)

Project description:To more specifically define the sequence content that favors direct binding of GAF, a genomic-context protein binding microarray (gcPBM) was used to detect GST-tagged GAF binding to double stranded DNA probes using a fluorescently conjugated anti-GST secondary antibody

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Sequence variation within similar cis-elements promotes context-specific functions of two Drosophila GA-binding transcription factors

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

2018-02-15 | GSE110654 | GEO

Sequence reliance of a Drosophila context-dependent transcription factor

Project description:Despite binding similarciselements in multiple locations, transcription factors often perform context-dependent functions at different loci. How factors integratecissequence and genomic context is still poorly understood and has implications for off-target effects in genetic engineering. TheDrosophilacontext-dependent transcription factor CLAMP targets similar GA-richciselements on the X-chromosome and at the histone gene locus but recruits very different, loci-specific factors. We discover that CLAMP leverages information from bothciselement and local sequence to perform context-specific functions. Our observations imply the importance of other cues, including protein-protein interactions and the presence of additional cofactors.

2023-12-15 | GSE249797 | GEO

Transcriptome analysis on OVA-GA(10) immunized GA-CFP mice

Project description:The goal of the study is to perform unbiased transcriptome analysis on spinal cord samples of immunized GA-CFP mice to configure the effect of OVA-GA(10) vaccination in a C9orf72 mouse model.

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Early GA response genes in Arabidopsis thaliana

Project description:The phytohormone GA controls multiple important developmental processes in plants such as germination, elongation growth and flowering time. In this experiment, we look for early GA response genes in 7 day-old light-grown Arabidopsis seedlings. To this end we compare four data sets: (1) a GA biosynthesis mutant ga-1 (SALK_109115) mock treated for 1 hr; (2) a GA biosynthesis mutant ga-1 (SALK_109115) treated for 1 hr with 100 µM GA3; (3) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant mock treated for 1 hr; (4) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant treated for 1 hr with 100 µM GA3. In a comparison of the two ga-1 samples, GA regulated genes can be identified, and the assumption is that bona fide GA regulated genes are not responding in the gid1a-1 gid1b-1 gid1c-2 GA receptor mutant. Keywords: phytohormone response

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Gibberellin (GA) Treatment of Arabidopsis Root Tips

Project description:The plant hormone gibberellin (GA) represents an important regulator of growth and development. Early transcriptional events controlled by GA are not well characterised. Previous microarray studies have identified genes responsive to GA treatment in the whole seedling. The whole seedling represents many tissues where subtle effects of GA treatment in specific tissues may be masked. When treated with GA, an effect on the growth rate of roots was observed. More specifically, the shorter root of a GA-deficient plant can be rescued to wild-type length by the application of GA. This experiment was designed to identify GA-regulated genes in the root tips of Arabidopsis. The use of a GA-deficient mutant provides a greater potential to identify genes responding to GA treatment. Root tips are ideally suited for the quick uptake of the hormone treatment. There will be two biological replicates which will each consist of a control treatment at 0 minutes and 2 hours, as well as the experimental GA-treated 2 hour time point. This system provides an opportunity to compare gene expression between treated and non-treated root tips and allow the identification of early GA-responsive genes.

2010-04-20 | GSE20223 | GEO

Expression data from leaves of GA-deficient and GA-insensitive transgenic poplar

Project description:We used whole-genome microarrays to identify differentially expressed genes in leaves of GA-deficient (35S::PcGA2ox) and/or GA-insensitive (35S::rgl1) transgenics as compared to WT poplar (717-1B4 genotype). Our work suggests that the molecular machinery that reduces gibberellins (GAs) concentration and signaling is a major route for restraining growth under both immediate and imminent adverse conditions. We show that inhibition of growth as a result of water deprivation and short days (SDs) coincides with up-regulation of several DELLA and GA2ox encoding genes in poplar. Likewise, GA-deficient and GA-insensitive transgenics, with up-regulated GA2ox and DELLA domain proteins, elicited a hypersensitive growth inhibition in response to both drought and SDs. Because the GA-modified transgenic showed accelerated response to drought and SD, we hypothesized that the mechanisms associated with these responses are constitutively elevated even under control conditions (well-watered, long day photoperiod). Therefore, we used whole-genome poplar microarray to study transcriptome level changes in the leaves of transgenic compared to WT plants grown under control environment.

2014-01-01 | GSE38390 | GEO

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