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RNA Seq analysis following RNAi perturbation of Hox genes in flatworm

ABSTRACT: RNA Seq analysis following RNAi perturbation of Hox genes in flatworm

PROVIDER: PRJNA670704 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12879714.fastq.gz	Fastqsanger.gz
	SRR12879715.fastq.gz	Fastqsanger.gz
	SRR12879716.fastq.gz	Fastqsanger.gz
	SRR12879717.fastq.gz	Fastqsanger.gz
	SRR12879718.fastq.gz	Fastqsanger.gz

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RNA Seq analysis following RNAi perturbation of Hox genes in flatworm

Project description:Hox genes are highly conserved transcription factors renowned for their roles in the segmental patterning of the embryonic anterior-posterior (A/P) axis1. Emerging evidence for Hox gene expression and function in postnatally derived structures has fueled interest in their additional roles beyond embryogenesis2,3. We report novel functions for Hox genes in A/P directed adult tissue segmentation and transverse fission behavior underlying asexual reproduction in the planaria, Schmidtea mediterranea. Silencing of each of the 13 planarian Hox family members revealed 5 Hox genes required for asexual reproduction. Amongst these, silencing of hox3 genes resulted in supernumerary segments, while silencing of post2b eliminated segmentation altogether. The opposing roles of hox3 and post2b in segmentation are paralleled in the regulation of fission behavior. Silencing of hox3 increases the frequency of fission behavior initiation, while silencing of post2b eliminates fission behavior entirely. Furthermore, we identified a network of downstream effector genes mediating Hox gene regulation of asexual reproduction, thereby providing insight into their respective mechanisms of action. In summation, our study identifies roles for planarian Hox genes as mediators of adult tissue segmentation and behavior, as well as providing the first lines of evidence that Hox genes function post-embryonically to regulate asexual reproduction.

2021-08-13 | GSE159876 | GEO

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Project description:stk25 and tao genes came out of an RNAi screen in the parasitic flatworm Schistosoma mansoni, and these genes shared a similar knockdown phenotype. To test for a functional relationship, we compared transcriptomes of early knockdown worms for each gene, compared to mock controls.

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Project description:This study aimed to ascertain the effect of CTCF RNAi on gene expression, chromatin conformation and the chromatin environment in prostate cancer cell line, LNCaP This study aimed to confirm loss of CTCF sites following CTCF RNAi in IMR90 cells

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Temporary bioadhesion in the proseriate flatworm Minona ileanae

Project description:Flatworms can very rapidly attach to and detach from many substrates. In the presented work, we analyzed the adhesive system of the marine proseriate flatworm Minona ileanae. We used light-, scanning-, and transmission electron microscopy to analyze the morphology of the adhesive organs, which are located at the ventral side of the tail plate. We performed transcriptome sequencing and differential RNA-seq for the identification of tail-specific transcripts. Using in situ hybridization expression screening, we identified nine transcripts that were expressed in the cells of the adhesive organs. Knock-down of five of these transcripts by RNA interference led to a reduction of the animal's attachment capacity. Adhesive proteins in footprints were confirmed using mass spectrometry and antibody staining. Additionally, lectin labelling of footprints revealed the presence of several sugar moieties. Furthermore, we determined a genome size of about 560 megabases for M. ileanae. We demonstrated the potential of Oxford Nanopore sequencing of genomic DNA as a cost-effective tool to identify the number of repeats within an adhesive protein and to combine transcripts that were fragments of larger genes. A better understanding of the molecules involved in flatworm bioadhesion paves the way towards developing innovative glues with reversible adhesive properties.

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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.

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