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Identification of E2f1 interactors during early embryonic development in Xenopus tropicalis

ABSTRACT: In this project, we performed E2f1 immunoprecipitation followed by mass spectrometry analysis to identify its interacting partners during early embryonic development in Xenopus tropicalis.

INSTRUMENT(S):

ORGANISM(S): Xenopus Tropicalis

TISSUE(S): Embryo

SUBMITTER: Huanhuan Cui

LAB HEAD: Wei Chen

PROVIDER: PXD051084 | Pride | 2025-12-01

REPOSITORIES: Pride

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			Action	DRS
	E2F1-1.raw	Raw
	E2F1-2.raw	Raw
	checksum.txt	Txt
	ctrl-1.raw	Raw
	ctrl-2.raw	Raw

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Publications

CANTAC-seq analysis reveals E2f1 and Otx1 coordinate zygotic genome activation in Xenopus tropicalis.

Cui Huanhuan H Liang Weizheng W Shi Zhaoying Z Zhang Luming L Li Guipeng G Chen Rui R Tian Chi C Gan Diwen D Shi Xinyao X Sun Zhiyuan Z Zhu Qionghua Q Fang Liang L Huang Hongda H Hu Yuhui Y Chen Yonglong Y Chen Wei W

Nature communications 20251118 1

Zygotic genome activation is tightly associated with the modulation of chromatin accessibility via maternal transcription factors. Understanding how chromatin accessibility is established and identifying key maternal regulators are crucial to comprehending this process. Here, by developing CANTAC-seq, we generate a genome-wide map of accessible chromatin of early Xenopus tropicalis embryos and find that the open chromatin landscape is progressively established at cis-regulatory elements during z ...[more]

PMID: 41253814

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Proteogenomics of Candida tropicalis – an opportunistic pathogen

Project description:Candida tropicalis is an opportunistic pathogen which causes candidiasis in immune-compromised individuals. It is one of the members of the non-albicans group of Candida that are known to be azole resistant and is frequently seen in individuals being treated for cancers, HIV-infection and bone-marrow transplant. Although the genome of C. tropicalis was sequenced in the year 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out in-depth proteomic profiling of C. tropicalis using high-resolution Fourier transform mass spectrometry and mapped ~44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2,740 proteins in the cell lysate of this yeast, we also analysed the proteome of the conditioned media of C. tropicalis culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons and corrected 49 computationally predicted gene models. To our knowledge, this is the first high-throughput proteomic study to refine the genome annotation of C. tropicalis.

2017-05-08 | PXD001071 | Pride

Project description:In quadruplicate for each condition, 10 acbd6 WT, 68 acbd6 crispant and 71 crispant X. tropicalis embryos were incubated with 20 μM YnMyr for 17 h. After labelling, embryos were washed twice with fresh 0.05 x MMR, flash frozen in liquid nitrogen and stored at -80°C until further analysis.

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Deep sequencing of small RNAs in the Xenopus tropicalis gastrula

Project description:Transposable elements comprise a large proportion of animal genomes. Transcripts of transposable elements are a source for the synthesis of endogenous siRNAs and piRNAs. In order to determine if small RNAs mapped to expressed Tc1-like elements are present during early Xenopus tropicalis development, we used Illumina (Solexa) to sequence small RNAs from gastrula-stage embryos. We obtained about 17 million reads that mapped perfectly to the genome. Small RNAs mapped to selected transposable elements were characterized and the expression of selected small RNAs was experimentally verified during development. This is the first deep sequencing experiment for small RNAs in the Xenopus tropicalis gastrula. Analysis of small RNAs expressed in the Xenopus tropicalis gastrula.

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Regulation of filamentation in the human fungal pathogen Candida tropicalis

Project description:The yeast-filament transition is essential for the virulence of a variety of fungi that are pathogenic to humans. N-acetylglucosamine (GlcNAc), a ubiquitous molecule in both the environment and host, is one of the most potent inducers of filamentation in Candida albicans and thermally dimorphic fungi such as Histoplasma capsulatum and Blastomyces dermatitidis. However, GlcNAc suppresses rather than promotes filamentation in Candida tropicalis, a fungal species that is closely related to C. albicans. Furthermore, we discover that glucose induces filamentous growth in C. tropicalis. Mutation and overexpression assays demonstrate that the conserved cAMP signaling pathway plays a central role in the regulation of filamentation in C. tropicalis. Activation of this pathway promotes filamentation in C. tropicalis, while inactivation of this pathway results in a serious growth defect in filamentation. By screening an overexpression library of 154 transcription factors, we have identified approximately 40 regulators of filamentous growth in C. tropicalis. Although most of the regulators (e.g., Tec1, Gat2, Nrg1, Sfl1, Sfl2, and Ash1) demonstrate a conserved role in the regulation of filamentation, similar to their homologs in C. albicans or S. cerevisiae, some of them are specific to C. tropicalis. For example, Czf1 and Efh1 repress filamentation, while Wor1, Zcf3, and Hcm1 promote filamentation in C. tropicalis. Bcr1, Aaf1, and Csr1 play a specific role in the process of GlcNAc-regulated filamentation. Our findings indicate that multiple interconnected signaling pathways are involved in the regulation of filamentation in C. tropicalis. These mechanisms have conserved and divergent features among different Candida species. Total RNA profiles of cells grown in Lee's glucose or Lee's GlcNAc medium.

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Chromatin immunoprecipitation to identify CUG-BP1/EDEN-BP target mRNAs in Xenopus tropicalis eggs

Project description:Identification of RNA bound to the RNA-binding protein CUGBP1/EDENBP in Xenopus tropicalis eggs.

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RNA-seq of a time course of spinal cord regeneration following tail amputation in Xenopus tropicalis tadpoles at stage 50

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Regional expression of X. tropicalis transcription factors in early gastrula embryos

Project description:Purpose: We wished to obtain spatial expression profiles of transcription factor gene expression and expression of other genes. Methods: Embryos were dissected and RNA-seq was performed to determine expression levels of genes. Comparisons between explanted regions permits determination of spatial enrichment of gene expression. mRNA-seq performed on 5 dissected regions of NF stage 10.5 X. tropicalis embryos and stage-matched sibling whole embryos. Experiment performed in duplicate.

2016-08-22 | E-GEOD-81458 | biostudies-arrayexpress

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