The roles of T and Tbx6 during gastrulation and determination of left/right asymmetry

Concepcion, Daniel

doi:10.7916/d8s75fpt

Cited by 1 publication

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“…Consistent with expectations, many of the TFs whose motifs are enriched (Fig. 5B) are known to be important in lineage specification and pattern formation, such as Pou3f1 [11], Sox2 and Sox3 [57][58][59] in ectoderm; Sox17, Foxa1 [60,61], Gata3 [62], Gata1 [63], Gata6 [64], Eomes [65], Fox-factors [60,[66][67][68] in endoderm, Msgn1 [69], Twist2 [70], Lef1 [71], and Tbx1 [72], Tcf12 [73,74] in mesoderm. Interestingly, within enriched TF binding sequence motifs (Fig.…”

Section: Inferring Lineage-specific Driver Tfs From Motifs In Putativ...supporting

confidence: 86%

Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation

Abnizova,

Stapel,

Boekhorst

et al. 2024

BMC Biol

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Background Regulation of transcription is central to the emergence of new cell types during development, and it often involves activation of genes via proximal and distal regulatory regions. The activity of regulatory elements is determined by transcription factors (TFs) and epigenetic marks, but despite extensive mapping of such patterns, the extraction of regulatory principles remains challenging. Results Here we study differentially and similarly expressed genes along with their associated epigenomic profiles, chromatin accessibility and DNA methylation, during lineage specification at gastrulation in mice. Comparison of the three lineages allows us to identify genomic and epigenomic features that distinguish the two classes of genes. We show that differentially expressed genes are primarily regulated by distal elements, while similarly expressed genes are controlled by proximal housekeeping regulatory programs. Differentially expressed genes are relatively isolated within topologically associated domains, while similarly expressed genes tend to be located in gene clusters. Transcription of differentially expressed genes is associated with differentially open chromatin at distal elements including enhancers, while that of similarly expressed genes is associated with ubiquitously accessible chromatin at promoters. Conclusion Based on these associations of (linearly) distal genes’ transcription start sites (TSSs) and putative enhancers for developmental genes, our findings allow us to link putative enhancers to their target promoters and to infer lineage-specific repertoires of putative driver transcription factors, within which we define subgroups of pioneers and co-operators.

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Section: Inferring Lineage-specific Driver Tfs From Motifs In Putativ...supporting

confidence: 86%

Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation

Abnizova,

Stapel,

Boekhorst

et al. 2024

BMC Biol

View full text Add to dashboard Cite

show abstract

The roles of T and Tbx6 during gastrulation and determination of left/right asymmetry

Cited by 1 publication

References 0 publications

Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation

Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation

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