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DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs

ABSTRACT: DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs

PROVIDER: PRJNA649303 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12341124_1.fastq.gz	Fastqsanger.gz
	SRR12341124_2.fastq.gz	Fastqsanger.gz
	SRR12341125_1.fastq.gz	Fastqsanger.gz
	SRR12341125_2.fastq.gz	Fastqsanger.gz
	SRR12341126_1.fastq.gz	Fastqsanger.gz

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DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [PromData]

Project description:DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [PromData]

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DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [GenomeData]

Project description:DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [GenomeData]

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DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [DAP-seq]

Project description:DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [DAP-seq]

| PRJNA649293 | ENA

DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-12-01 | GSE155321 | GEO

DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [GenomeData]

Project description:DNA binding analysis of MYCs using Arabidopsis- and bHLH.specific Protein Binding Microarrays

2020-12-01 | GSE155320 | GEO

DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [PromData]

Project description:DNA binding analysis of MYCs using Arabidopsis- and bHLH.specific Protein Binding Microarrays

2020-12-01 | GSE155318 | GEO

DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [DAP-seq]

Project description:DNA binding analysis of MYCs using Arabidopsis- and bHLH.specific Protein Binding Microarrays

2020-12-01 | GSE155317 | GEO

DNA features beyond the transcription factor binding site specify target recognition by plant MYC2-related bHLH proteins.

Project description:Transcription factors (TFs) regulate gene expression by binding to cis-regulatory sequences in the promoters of target genes. Recent research is helping to decipher in part the cis-regulatory code in eukaryotes, including plants, but it is not yet fully understood how paralogous TFs select their targets. Here we addressed this question by studying several proteins of the basic helix-loop-helix (bHLH) family of plant TFs, all of which recognize the same DNA motif. We focused on the MYC-related group of bHLHs, that redundantly regulate the jasmonate (JA) signaling pathway, and we observed a high correspondence between DNA-binding profiles in vitro and MYC function in vivo. We demonstrated that A/T-rich modules flanking the MYC-binding motif, conserved from bryophytes to higher plants, are essential for TF recognition. We observed particular DNA-shape features associated with A/T modules, indicating that the DNA shape may contribute to MYC DNA binding. We extended this analysis to 20 additional bHLHs and observed correspondence between in vitro binding and protein function, but it could not be attributed to A/T modules as in MYCs. We conclude that different bHLHs may have their own codes for DNA binding and specific selection of targets that, at least in the case of MYCs, depend on the TF-DNA interplay.

| S-EPMC8577090 | biostudies-literature

Candida albicans at Host Barrier Sites: Pattern Recognition Receptors and Beyond.

Project description:Over the last decades, fungal infections have emerged as a growing threat to human health. Although the human body is at potential risk, various body sites host several commensal fungal species, including Candida albicans. In healthy individuals, C. albicans colonizes different mucosal surfaces without causing harm, while under diverse circumstances the fungus can proliferate and cause disease. In this context, the understanding of host?C. albicans interactions in health and during infection may lead to novel therapeutic approaches. Importantly, host cells express pattern recognition receptors (PRRs), which sense conserved fungal structures and orchestrate innate immune responses. Herein, important findings on the topic of the recognition of C. albicans at host barrier sites are discussed. This review briefly summarizes the importance and functions of myeloid PRRs, reviews the fungal recognition and biology of stromal cells, and highlights important C. albicans virulence attributes during site-specific proliferation and invasion.

| S-EPMC6471378 | biostudies-literature

Deconvolving the recognition of DNA shape from sequence

Project description:Binding of transcription factors to DNA is mediated by the recognition of the chemical signatures of the DNA bases and the three-dimensional shape of the DNA molecule. The direct contribution of DNA shape to DNA-binding specificity has been difficult to assess, as DNA shape is a consequence of its sequence. Here, we teased apart these two modes of recognition in the context of Hox-DNA binding. We made a series of mutations in Hox residues that, in a co-crystal structure, only recognize DNA shape, and tested the effect on DNA binding preferences using SELEX-seq. Analysis of shape features of selected sequences revealed that these residues are both necessary and sufficient for selection of sequences with distinct shape features. We used statistical machine learning to show that the accuracy of binding specificity predictions improves by adding shape features to a model that only depends on sequence. We conclude that shape readout is a direct and critical component of binding site selection by Hox proteins. Three rounds of SELEX were performed on a series of Hox mutants as described in Slattery et al, Cell, 2011 (PMID 22153072) and Riley et al, Methods in molecular Biology, 2014 (PMID 25151169). Briefly, His-tagged Scr and Antp mutant proteins were incubated with a randomized 16mer oligonucleotide library, and bound DNA was amplified and sequenced as described (PMID 22153072, PMID 25151169).

2015-01-21 | E-GEOD-65073 | biostudies-arrayexpress

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