Tbx5 paralogues during zebrafish development
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ABSTRACT:
PROVIDER: PRJNA475603 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The goals of this study were to compare the effect on the transcriptome of loss of the Tbx5 paralogues in zebrafish. Methods: Whole embryos were injected with morpholinos targetting either Tbx5a, Tbx5b, or both at the single cell stage. At either 18 or 21 hpf, embryos were pooled and RNA was extracted from the whole embryo. Transcriptomes were generated using Illumina HiSeq 2500. Results: The preliminary experiment produced 632 million reads and a list of 494 differentially expressed genes (detected using Cuffdiff), of which 454 were unique. This final triplicate sequencing gave 309.4 million reads. When using Cuffdiff to produce differential gene expression lists, a list of 162 differentially expressed genes were identified. Conclusions: This study is a detailed analysis of the different transcriptomes of zebrafish deficient in the Tbx5 paralogues and the differential gene expression that occurs as a result of downregulation of the paralogues, both individually and separately.
2018-06-12 | GSE115640 | GEO
Project description:The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ubiquitination of the ribosomal proteins plays a pivotal role in translational control and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To study ribosome ubiquitination during animal development, we generated a zebrafish strain that expresses a FLAG-tagged ribosomal protein Rpl36/eL36 from its endogenous locus. Combining affinity purification of ribosomes from rpl36-FLAG zebrafish embryos with immunoblotting analysis, we analyzed ribosome ubiquitination during zebrafish development. Our data showed that ubiquitination of ribosomal proteins dynamically changed as development proceeded. We further revealed that Znf598, an E3 ubiquitin ligase that triggers RQC, contributed to the ribosome ubiquitination during zebrafish development. LC-MS/MS analysis and immunoblotting analysis identified lysines 139 of ribosomal protein Rps10/eS10 as pivotal ubiquitination sites on the ribosome during development. Finally, we demonstrated that an Rps10 K139/140R mutation reduced overall ribosome ubiquitination pattern. Collectively, these results reveal dynamics and complexity of ribosome ubiquitination in zebrafish development.
2023-10-11 | PXD039560 | JPOST Repository
Project description:T-box transcription factors have been shown to play critical roles in the development and identity of the lungs. Tbx5 has been implicated as an initiator of pulmonary development through direct regulation of signaling molecules of the posterior second heart field (pSHF) and cardiopulmonary progenitors (CPs) (Arora et al. 2012 PLOS Genetics; Steimle et al 2018 PNAS). We hypothesize TBX5 regulates additional targets required for lung development. To this end, we performed ChIP-sequencing to identify localization of TBX5 during fetal lung development.
2021-02-23 | GSE167207 | GEO
Project description:T-box transcription factors play critical roles in the development and identity of the heart. Tbx5 has been implicated as a regulator of the fast-conducting, ventricular conduction system, while Tbx3 has been implicated as a regulator of the slow-conducting node. We hypothesize TBX5 and TBX3 share common binding sites in cardiomyocytes to positively or negatively regulate transcription, respectively, for cardiac cell identity and conduction. To this end, we performed ChIP-sequencing to identify localization of TBX5 during fetal heart development and have compared it with previously published histone (GEO Series: GSE31039; ENCODE Accessions: ENCSR080GQM, ENCSR000CDL, ENCSR000CDM, ENCSR052CDF, ENCSR345RKE, ENCSR007XTC, ENCSR360ANE, ENCSR000CDK, and ENCSR357OED) and TBX3 ChIP-seq (GSM862695).
2020-04-21 | GSE139803 | GEO
Project description:Genome wide localization of RNAs during early zebrafish development
| PRJNA599208 | ENA
Project description:We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA-seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development.
2021-03-30 | GSE143208 | GEO
Project description:We report the m6A methylation maps of zebrafish embryos during early development, and transcriptome-wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A-dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish MZT, highlighting the critical role of the m6A mRNA methylation in animal development.
2017-02-07 | GSE79213 | GEO
Project description:TBX5 is hypomethylated in Rheumatoid Arthritis synovial fibroblasts (RASF). Hypomethylation increased the TBX5 expression in RASF. We performed a microarray expression analysis upon TBX5 overexpression to find TBX5 molecular targets.TBX5 belongs to the T-box transcription factor family all of which possess a T-box DNA binding domain in their sequence. It has been shown to play an important role in tissue development and cancer. We were interested in identifying a possible role of TBX5 overexpression in RA. To that end, OASF were transfected with pcDNA3.1(+)_TBX5 or pcDNA3.1(+) empty vector as a negative control. After 48h, RNA was extracted and cDNA was generated by reverse transcription. The labeled cDNA was hybridized to the Affymetrix microarray.
2014-09-30 | E-GEOD-60162 | biostudies-arrayexpress
Project description:Understanding how the atrial and ventricular chambers of the heart maintain their distinct identity is a prerequisite for treating chamber-specific diseases. Here, we selectively inactivated the transcription factor Tbx5 in the atrial working myocardium of the neonatal mouse heart to show that it is required to maintain atrial identity. Atrial Tbx5 inactivation downregulated highly chamber specific genes such as Myl7 and Nppa, and increased expression of ventricular identity genes including Myl2. Using combined single nucleus transcriptome and open chromatin profiling, we assessed genomic accessibility changes underlying the altered atrial identity expression program, identifying 1846 genomic loci with greater accessibility in control atrial cardiomyocytes compared to KO aCMs. 69% of the control-enriched ATAC regions were bound by TBX5, demonstrating a role for TBX5 in maintaining genomic accessibility. These regions were associated with genes that had higher expression in control aCMs compared to KO aCMs, suggesting they act as TBX5-dependent enhancers. To confirm this hypothesis we analyzed chromatin looping of enhancers marked by H3K27Ac using HiChIP and found 510 chromatin loops that were sensitive to TBX5 dosage. Of the loops enriched in control aCMs, 73.7% contained anchors in control-enriched ATAC regions. Conversely, Tbx5 overexpression in the ventricular myocardium drove atrial gene expression. Together, these data demonstrate a role for TBX5 in maintaining the atrial gene expression program by binding to atrial enhancers to preserve tissue-specific chromatin architecture. We highlight this phenomenon at major atrial identity genes including Nppa, Bmp10 and Myl7. HiChIP for H3K27Ac from atria of TBX5KO and control animals
2023-08-11 | GSE222370 | GEO
Project description:In vertebrates, the heart has two main layers of cardiac muscle, a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5-positive cells and cardiomyoctes with nuclear DsRed (nucDsRed) to distinguish cortical from trabecular myocardium. Then, we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium.
2017-11-08 | GSE87596 | GEO