START domains generate paralog-specific regulons from a single …

1 day ago · This suggests a model in which HD-ZIPIII TFs use information integrated by their START domain to generate paralog-specific transcriptional outcomes from a shared network …

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Evolution Of Binding Preferences Among Whole-genome …

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Jul 27, 2021 · To provide a genome-scale view, we considered the set of budding yeast TFs classified as whole-genome duplication (WGD)-retained paralogs (~35% of all specific TFs). …

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FAQs about START domains generate paralog-specific regulons from a single … Coupon?

Can gene regulon membership be predicted by DNA sequence-based machine learning?

We developed DNA sequence-based machine learning models for gene regulon membership, resulting in high prediction performance for 40/47 of possible E. coli ICA regulons. Successful models highlight that gene transcriptional regulation can be quantitatively explained by relatively simple promoter sequence features for many regulons. ...

Can paralog upregulation help preserve morphological phenotypes downstream of mutated regulators?

Previous studies have shown that paralog upregulation via transcriptional adaptation can enable the preservation or robustness of molecular and morphological phenotypes downstream of mutated regulators. ...

Are paralogs upregulated in genes with nonsense-induced transcriptional adaptation?

After indel mutations, frameshifts often occur, leading to premature termination codon formation and resultant nonsense-mediated decay. We hypothesized that paralogs may be upregulated in genes with nonsense-induced transcriptional compensation-type transcriptional adaptation. ...

How to extract prognostic associated regulons?

Therefore, we designed a workflow to extract prognostic associated regulons by deconvoluting the patients’ cohorts with matched clinical data and bulk sequencing data. Here, we present and study a computational framework, termed as LPRI, to help prognostic stratification of patients. ...

What if a knockout target shows paralog upregulation?

In this way, caution must be taken in interpreting the phenotypic changes, or lack thereof, if a knockout target shows paralog upregulation. Recent advances in sequencing and genome editing technologies have enabled perturbation and profiling of the molecular makeup of single cells at unprecedented throughput. ...

Do Hox paralogs orchestrate alternative downstream gene regulatory networks?

These findings reveal how Hox paralogs, and perhaps paralogs of other transcription factor families, orchestrate alternative downstream gene regulatory networks with the help of multiple, context-specific cofactors. ...