Smed-myb-1 specifies early temporal identity during planarian epidermal differentiation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA486438 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7704560.fastq.gz | Fastqsanger.gz | |||
| SRR7704561.fastq.gz | Fastqsanger.gz | |||
| SRR7704562.fastq.gz | Fastqsanger.gz | |||
| SRR7704563.fastq.gz | Fastqsanger.gz | |||
| SRR7704554.fastq.gz | Fastqsanger.gz |
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Project description:The planarian epidermis provides an excellent model to explore adult stem cell (ASC) lineage development due to well-characterized and distinct spatiotemporal phases during lineage progression. Using flow cytometry-isolated cells enriched in epidermal progenitors, we performed transcriptional profiling and RNAi screening to uncover regulators of epidermal differentiation. We identified a MYB-type transcription factor (Smed-myb-1) required for specification of the first temporal phase of post-mitotic maturation. Knockdown of myb-1 abolished the early progenitor phase of differentiation without ceasing production of subsequent epidermal progenitors or homeostatic turnover and regeneration of the epidermis. Further examination revealed accelerated maturation of ASC descendants, with premature entry into subsequent progeny phases and ultimately the epidermis. These results demonstrate that a spatiotemporal shift in lineage progression occurs in the absence of the early progenitor state after myb-1 RNAi, and identify myb-1 as a critical regulator of the early temporal window in the step-wise specification during planarian epidermal differentiation.
2018-08-18 | GSE118674 | GEO
Project description:Epidermis is essential for animal survival, providing both a protective barrier and cellular sensor to the external environment. Interestingly, the epidermes of different species show broad morphological and functional diversity yet it is unclear whether this diversity came from modification of an existing gene regulatory network or de novo innovation of new genes. Here we identify the transcriptional regulators underlying the differentiation program of planarian epidermal lineage. We classify Smed-p53 as the most upstream molecule in this transcriptional cascade, suggesting a potentially conserved role for this gene in epidermal differentiation similar to TP63 in vertebrates. Moreover, we find that homologs of Sox and Pax family transcription factors, Smed-soxP-3 and Smed-pax-5, act cooperatively to activate the expression of epidermal markers. Together, these data show that planarian epidermal differentiation is regulated by a combination of conserved elements (p53/p63), recruitment of a non-conventional transcription module (soxP-3/pax-5), and novel genes (prog); they also suggest that specialized adpatations, such as epidermal mucus-secretion, arise from complex changes to gene networks.
2016-09-01 | GSE80543 | GEO
Project description:Epidermis is essential for animal survival, providing both a protective barrier and cellular sensor to the external environment. Interestingly, the epidermes of different species show broad morphological and functional diversity yet it is unclear whether this diversity came from modification of an existing gene regulatory network or de novo innovation of new genes. Here we identify the transcriptional regulators underlying the differentiation program of planarian epidermal lineage. We classify Smed-p53 as the most upstream molecule in this transcriptional cascade, suggesting a potentially conserved role for this gene in epidermal differentiation similar to TP63 in vertebrates. Moreover, we find that homologs of Sox and Pax family transcription factors, Smed-soxP-3 and Smed-pax-5, act cooperatively to activate the expression of epidermal markers. Together, these data show that planarian epidermal differentiation is regulated by a combination of conserved elements (p53/p63), recruitment of a non-conventional transcription module (soxP-3/pax-5), and novel genes (prog); they also suggest that specialized adpatations, such as epidermal mucus-secretion, arise from complex changes to gene networks. This experiment aims to identify regulators involved in epidermal differentiation at the neoblast stage by using RNA Seq to examine transcriptional changes in neoblasts (X1 population) isolated from animals treated with zfp-1 or p53 dsRNA.
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Project description:Here, we analyze the RNA-binding preferences of the planarian smed-mbnl-like-2, smed-mbnl-1 (isoform X1), smed-bruli, smed-mbnl-1 (isoform Xins), and smed-mbnl-like-1 protein using RNAcompete.
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Project description:The adult brain of the planarian Schmidtea mediterranea (a freshwater flatworm) is a dynamic structure with constant cell turnover as well as the ability to completely regenerate de novo. Despite this, function and pattern is achieved in a reproducible manner from individual to individual in terms of the correct spatial and temporal production of specific neuronal subtypes. Although several signalling molecules have been found to be key to scaling and cell turnover, the mechanisms by which specific neural subtypes are specified remain largely unknown. Here we performed a 6 day RNAseq time course on planarians that were regenerating either 0, 1, or 2 heads in order to identify novel regulators of brain regeneration. Focusing on transcription factors, we identified a TCF/LEF factor, Smed-tcf1, which was required to correctly pattern the dorsal-lateral cell types of the regenerating brain. The most severely affected neurons in Smed-tcf1(RNAi) animals were the dorsal GABAergic neurons, which failed to regenerate, leading to an inability of the animals to phototax away from light. Together, Smed-tcf1 is a critical regulator, required to pattern the dorsal-lateral region of the regenerating planarian brain.
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Project description:Here, we analyze the RNA-binding preferences of the planarian smed-mbnl-like-2, smed-mbnl-1 (isoform X1), smed-bruli, smed-mbnl-1 (isoform Xins), and smed-mbnl-like-1 protein using RNAcompete. In the RNAcompete assay, a purified GST-tagged protein is incubated with an excess of RNA pool and bound RNA from individual pulldown experiments are directly labeled and hybridized to a custom Agilent 244K microarray.
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Project description:Epidermis is essential for animal survival, providing both a protective barrier and cellular sensor to the external environment. Interestingly, the epidermes of different species show broad morphological and functional diversity yet it is unclear whether this diversity came from modification of an existing gene regulatory network or de novo innovation of new genes. Here we identify the transcriptional regulators underlying the differentiation program of planarian epidermal lineage. We classify Smed-p53 as the most upstream molecule in this transcriptional cascade, suggesting a potentially conserved role for this gene in epidermal differentiation similar to TP63 in vertebrates. Moreover, we find that homologs of Sox and Pax family transcription factors, Smed-soxP-3 and Smed-pax-5, act cooperatively to activate the expression of epidermal markers. Together, these data show that planarian epidermal differentiation is regulated by a combination of conserved elements (p53/p63), recruitment of a non-conventional transcription module (soxP-3/pax-5), and novel genes (prog); they also suggest that specialized adpatations, such as epidermal mucus-secretion, arise from complex changes to gene networks. The purpose of this experiment is to identify genes associated with neoblasts (stem cells). Worms are exposed to 6k rad of gamma radiation, allowed to recover for 24, 48, 72, or 96 hours, and compared to the pre-cursor un-exposed population by RNA Seq to identify genes with decreased expression following radiation exposure.
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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.
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