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Retrograde movements determine effective stem cell numbers in intestinal crypts

ABSTRACT: Retrograde movements determine effective stem cell numbers in intestinal crypts

PROVIDER: PRJNA799997 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17717252_1.fastq.gz	Fastqsanger.gz
	SRR17717252_2.fastq.gz	Fastqsanger.gz
	SRR17717253_1.fastq.gz	Fastqsanger.gz
	SRR17717253_2.fastq.gz	Fastqsanger.gz
	SRR17717254_1.fastq.gz	Fastqsanger.gz

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Retrograde movements determine effective stem cell numbers in intestinal crypts

Project description:Our goal was to compare the transcriptomic profile of lgr5+ high, medium and low cells (corresponding to centre, border and >3 row in crypts) between small and large intestine in mice. We observed differences in the transcriptional profile between centre and border Lgr5+ cells within small and large intestinal crypts and more profound differences between the two intestinal sites.

2022-04-20 | GSE194250 | GEO

Gene expression data from DSS-treated crypts, normal colon crypts and tumor crypts

Project description:Comparative gene expression profiling between DSS-treated crypts and normal colon crypts Comparative gene expression profiling between normal colon crypts and tumor crypts

2017-01-01 | GSE56050 | GEO

The retrograde signals responsible for photoacclimation in the marine diatom Phaeodactylum tricornutum

Project description:Photoacclimation of unicellular algae allows for reversible changes in the number and/or effective absorption cross section of photosynthetic units on time scales of hours to days in response to changes in irradiance. The process involves an enigmatic signaling pathway from the plastid to the nucleus.Our results reveal, for the first time, a fundamental pathway of retrograde signal transduction in a eukaryotic photosynthetic alga.

2019-11-01 | GSE133301 | GEO

Peroxisomal retrograde signaling in C. elegans

Project description:Distinct retrograde signaling pathways have been identified for several cellular organelles. These pathways are important to maintain the function of these organelles in response to organelle-specific stress. Using Caenorhabditis elegans, we show for the first time that such a retrograde signaling also exists for peroxisomes. Analysis of the C. elegans transcriptome revealed that peroxisomal import stress caused by the knock-down of the peroxisomal matrix protein import receptor prx-5/PEX5 induces the compensatory up-regulation of genes involved in defense response and lipid metabolic processes, especially peroxisomal beta oxidation. We, therefore, propose that the peroxisomal retrograde signaling participates in the maintenance of peroxisomal function in response to peroxisomal import stress.

2020-12-19 | GSE156318 | GEO

Peroxisomal retrograde signaling in C. elegans

Project description:Peroxisomal retrograde signaling in C. elegans

| PRJNA657442 | ENA

Sigma2 and Sigma6-mediated plastid retrograde signals control nuclear gene expression in Arabidopsis

Project description:Retrograde signaling from the chloroplast to the nucleus is necessary to regulate the chloroplast proteome during development and fluctuating environmental conditions. Although the specific chloroplast process(es) that must occur and the nature of the signal(s) that exits the chloroplast are not well understood, previous studies using drug inhibitors of chloroplast biogenesis have revealed that normal chloroplast development is required to express Photosynthesis Associated Nuclear Genes (PhANGs). In an attempt to determine which specific steps in chloroplast development are involved in retrograde signaling, we analyzed Arabidopsis mutants defective in the six genes encoding sigma factor (Sig) proteins that are utilized by the plastid-encoded RNA polymerase to transcribe specific sets of plastid genes. Here, we demonstrate that both Sig2 and Sig6 have partially redundant roles in not only plastid transcription, but also tetrapyrrole synthesis and retrograde signaling to control PhANG expression. Normal PhANG expression can be partly restored in the sig2 mutant by increasing heme synthesis. Furthermore, there is a genetic interaction between Sig and GUN (genomes uncoupled) genes to generate chloroplast-retrograde signals. These results demonstrate that defective plastid transcription is the source of at least two retrograde signals to the nucleus; one involving tetrapyrrole synthesis and the other involving the accumulation of an unknown plastid transcript. We also propose that the study of sig mutants (with defects in the expression of specific plastid genes) provides a new genetic system, which avoids the use of harsh inhibitors and their potential side effects, to monitor developmental retrograde signaling and to elucidate its mechanisms.

2012-09-18 | E-MTAB-4338 | biostudies-arrayexpress

Deconvoluting ACS1 retrograde signaling networks that regulate leaf development

Project description:Signals originating within plastids modulate organelle differentiation by transcriptionally regulating nuclear-encoded genes. These retrograde signals are also integral regulators of plant development, including leaf morphology. The clb5 mutant displays severe leaf morphology defects due to Apocarotenoid Signal 1 (ACS1) accumulation in the developmentally arrested plastid. Transcriptomic analysis of clb5 validates ACS1 as a true retrograde signal impacting expression of hundreds of nuclear genes, including suppression of most genes encoding plastid ribosomal proteins.

2021-06-02 | GSE152252 | GEO

Retrograde signalling during caused by heritable mitochondrial dysfunction is partly mediated by ANAC017 and improves plant performance.

Project description:Mitochondria are crucial for plant viability and are able to communicate information on their functional status to the cellular nucleus via retrograde signalling, thereby affecting gene expression. It is currently unclear if retrograde signalling in response to constitutive mitochondrial biogenesis defects is mediated by the same pathways as those triggered during acute mitochondrial dysfunction. Furthermore, it is unknown if retrograde signalling can effectively improve plant performance when mitochondrial function is constitutively impaired. Here we show that retrograde signalling in mutants defective in mitochondrial proteins RNA polymerase rpotmp or prohibitin atphb3 can be suppressed by knocking out the transcription factor ANAC017. Genome-wide RNA-seq expression analysis revealed that ANAC017 is almost solely responsible for the most dramatic transcriptional changes common to rpotmp and atphb3 mutants, regulating both classical marker genes such as alternative oxidase 1a (AOX1a) and also previously-uncharacterised DUF295 genes that appear to be new retrograde markers. In contrast, ANAC017 does not regulate intra-mitochondrial gene expression or transcriptional changes unique to either rpotmp or atphb3 genotype, suggesting the existence of currently unknown signalling cascades. The data show that the role of ANAC017 extends beyond common retrograde transcriptional responses and affects downstream protein abundance and enzyme activity of alternative oxidase, as well as steady state energy metabolism in atphb3 plants. Furthermore, detailed growth analysis revealed that ANAC017-dependent retrograde signalling provides benefits for growth and productivity in plants with mitochondrial defects. In conclusion, ANAC017 plays a key role in both biogenic and operational mitochondrial retrograde signalling, and improves plant performance when mitochondrial function is constitutively impaired.

2016-07-28 | E-MTAB-4655 | biostudies-arrayexpress

Proteomic Analysis of the Peroxisomal Retrograde Signaling in C. elegans

Project description:While retrograde signalling pathways have been identified for several organelles, the existence of such a pathway for peroxisomes remains elusive. We identified a peroxisomal retrograde signalling (PRS) in C. elegans, which is activated in response to peroxisomal import stress. We analyzed the PRS using a proteomic approach.

2021-01-11 | PXD014720 | Pride

RNA Seq In Isolated Crypts from Duodenum, Jejunum, and Ileum

Project description:RNA was extracted from crypts from the three portions of the small intestine

2020-02-26 | GSE131438 | GEO