Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration

ABSTRACT: Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration

PROVIDER: PRJNA1075694 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR27947600.fastq.gz	Fastqsanger.gz
	SRR27947601.fastq.gz	Fastqsanger.gz
	SRR27947590.fastq.gz	Fastqsanger.gz
	SRR27947591.fastq.gz	Fastqsanger.gz
	SRR27947592.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration [Ribo-seq]

Project description:Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration [Ribo-seq]

| PRJNA1083472 | ENA

Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration [RiboMeth-Seq]

Project description:Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration [RiboMeth-Seq]

| PRJNA1075681 | ENA

Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration [Ribo-seq]

Project description:Translational regulation in adult regenerative tissue remains unclear. Planarians, renowned for remarkable cell turnover and tissue regeneration capabilities, are regenerative flatworms that provide an ideal model to address the gap in knowledge between translational control and cell turnover during adult tissue homeostasis and regeneration. Fibrillarin (FBL) is an RNA 2-O’-methyltransferase crucial for rRNA processing, playing a pivotal role in translational regulation. We explored this in planarian Schmidtea mediterranea and identified two FBL homologs: Smed-fbl-1 (fbl-1) and Smed-fbl-2 (fbl-2) are essential for homeostasis and regeneration, but have distinct roles. fbl-1 is enriched in neoblasts and essential for multiple progenitor cell differentiation. Conversely, fbl-2 is expressed in egr5+ epidermal progenitors, crucial for late-stage epidermal lineage specification. Knockdown (KD) of fbl-1 and fbl-2 resulted in different 2-O’-methylation patterns, suggesting their influence on specific mRNA translation during regeneration. Riboseq analysis revealed that fbl-1 KD reduced the translation of genes associated with alternative splicing, cell cycle, and DNA replication, while fbl-2 KD reduced the translation of genes related to protein stability. Interestingly, fbl-2+ cells spatially correlated with wnt-1+ cells, hinting at fbl-2’s role in its localization. Our study indicated that duplicate fbl genes may have a compensatory role in the development of specific cell lineages. This finding underscores the significance of rRNA modification in translation regulation during the maintenance and regeneration of adult tissues.

2024-11-13 | GSE255594 | GEO

Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration [RiboMeth-Seq]

2024-11-13 | GSE255590 | GEO

Fibrillarin homologs regulate translation in divergent cell lineages during planarian homeostasis and regeneration

Project description:Abstract: Tissue homeostasis and regeneration involve complex cellular changes. The role of rRNA modification-dependent translational regulation in these processes remains largely unknown. Planarians, renowned for their ability to undergo remarkable tissue regeneration, provide an ideal model for the analysis of differential rRNA regulation in diverse cell types during tissue homeostasis and regeneration. We investigated the role of RNA 2'-O-methyltransferase, Fibrillarin (FBL), in the planarian Schmidtea mediterranea and identified two FBL homologs: Smed-fbl-1 (fbl-1) and Smed-fbl-2 (fbl-2). Both are essential for planarian regeneration, but play distinct roles: fbl-1 is crucial for progenitor cell differentiation, while fbl-2 is important for late-stage epidermal lineage specification. Different 2'-O-methylation patterns were observed upon fbl-1 and fbl-2 knockdown, suggesting their roles in translation of specific mRNA pools during regeneration. Ribo-seq analysis further revealed differing impacts of fbl-1 and fbl-2 knockdown on gene translation. These findings indicate divergent roles of the duplicate fbl genes in specific cell lineage development in planarians and suggest a role of rRNA modifications in translational regulation during tissue maintenance and regeneration.

| S-SCDT-10_1038-S44318-024-00315-X | biostudies-other

Fibrillarin homologs are required for divergent cell lineage development by translational regulation in planarian homeostasis and regeneration

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

2024-11-13 | GSE255595 | GEO

Fibrillarin RIP-seq in PA1 cells

Project description:We have used fibrillarin RIP-seq to explore snoRNA related transcripts in PA1 cells.

2016-10-13 | GSE85852 | GEO

HOX gene complement and expression in the planarian Schmidtea mediterranea

Project description:Background: Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi. Results: Because the planarian Schmidtea mediterranea (S. med) is unsegmented, appendage-less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement. Here we argue against this hypothesis and show that S. med has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly-sensitive method. In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially-restricted expression. Finally, we confirm HOX gene axial expression by RNA-deep-sequencing 6 anterior-to-posterior “zones” of the animal, which we provide as a dataset to the community to discover other axially-restricted transcripts. Conclusions: Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented. However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates. Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior-posterior axis of adult planarians.

2016-03-08 | GSE78937 | GEO

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

Project description:The head-regeneration transcriptome of the planarian Schmidtea mediterranea

2011-07-15 | E-MTAB-607 | biostudies-arrayexpress

454 Life Sciences/Roche and Illumina sequencing of small RNAs from planarian samples

Project description:Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration and tissue homeostasis have been shown to depend on PIWI, a molecule required for piRNA expression in planarians. Nevertheless, the full complement of piRNAs, and microRNAs (miRNAs) in this organism has yet to be defined. Here, we report on the large scale cloning and sequencing of small RNAs from the planarian Schmidtea mediterranea, yielding altogether millions of sequenced unique small RNAs. We show that piRNAs are in part organized in genomic clusters and that they share characteristic features with mammalian and fly piRNAs. We further identify 61 novel miRNA genes and thus double the number of known planarian miRNAs. Sequencing, as well as quantitative PCR of small RNAs uncovered ten miRNAs enriched in planarian stem cells. These miRNAs are down-regulated in animals in which stem cells have been abrogated by irradiation, and thus constitute miRNAs likely associated with specific stem cell functions. Altogether, we present the first comprehensive small RNA analysis in animals belonging to the third animal superphylum, the Lophotrochozoa, and single out a number of miRNAs that may function in regeneration. Several of these miRNAs are deeply conserved in animals. Small RNAs were sequenced from FACS-sorted neoblast stem cells, untreated planarians and irradiated planarians, depleted of neoblasts

2009-06-30 | E-GEOD-16159 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data