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

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

PROVIDER: PRJNA649293 | 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

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

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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 binding analysis of MYCs using Arabidopsis- and bHLH.specific Protein Binding Microarrays

2020-12-01 | GSE155317 | GEO

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 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.

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Peptidoglycan metabolite photoaffinity reporters reveal direct binding to intracellular pattern recognition receptors and Arf GTPases

Project description:Extensive structure-activity studies of iE-DAP and MDP have demonstrated their selective activation of NOD1- and NOD2-expressing cells, respectively. Nonetheless, the direct binding of iE-DAP and MDP to NOD1 and NOD2, respectively, as well as other proteins in mammalian cells has not been systematically investigated. To address the direct interaction of iE-DAP and MDP with NOD1 and NOD2 in living cells, we synthesized a series of peptidoglycan metabolite photoaffinity chemical reporters containing a diazirine for photocrosslinking in cells and an alkyne tag for bioorthogonal detection of covalently-labeled proteins. The analysis of these peptidoglycan metabolite photoaffinity reporters demonstrate that iE-DAP and MDP can directly bind to NOD1 and NOD2 in mammalian cells. The crosslinking of these peptidoglycan metabolite photoaffinity reporters only occur with active variants of NOD1 and NOD2. Beyond direct binding to NOD2, the active MDP photoaffinity reporter selectively crosslinked Arf GTPases in NOD2-expressing cells and did so most prominently with GTP-bound Arf6, revealing the Arf proteins as novel direct pattern recognition receptors. Additional labeling and co-precipitation experiments suggest that MDP induces a complex between NOD2 and GTP-Arf6. This study highlights the utility of peptidoglycan metabolite photoaffinity reporters for characterizing their direct binding to intracellular pattern recognition receptors and identifying unpredicted cellular cofactors. The applications of these microbial-specific metabolite reporters should enable the discovery of other receptors, transporters and regulatory enzymes in host cells and microbes.

2020-05-26 | PXD012350 | Pride

SWIZ DAP-Seq

Project description:SWIZ DAP-Seq

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