Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE155320 | GEO | 2020/12/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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 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

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

| PRJNA649303 | ENA

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]

| PRJNA649298 | ENA

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]

| PRJNA649304 | ENA

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

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

Identification of LIN28-bound mRNAs reveals features of target recognition and regulation

Project description:The conserved human LIN28 RNA-binding proteins function in development, maintenance of pluripotency and oncogenesis. We used PAR-CLIP and a newly developed variant of this method, iDo-PAR-CLIP, to identify LIN28B targets as well as sites bound by the individual RNA binding domains of LIN28B in the human transcriptome at nucleotide resolution. The position of target binding sites reflected the known structural relative orientation of individual LIN28B binding domains, validating iDo-PAR-CLIP. Our data suggest that LIN28B directly interacts with most expressed mRNAs and members of the let-7 microRNA family. The Lin28 binding motif detected in pre-let-7 was enriched in mRNA sequences bound by LIN28B. Upon LIN28B knock down, cell proliferation and the cell cycle were strongly impaired. Quantitative shotgun proteomics of LIN28B depleted cells revealed significant reduction of protein synthesis from its RNA targets that function in translation, mRNA splicing and cell cycle control. Computational analyses provided evidence that the strength of protein synthesis reduction correlated with the location of LIN28B binding sites within target transcripts. We used PAR-CLIP and a newly developed variant of this method, iDo-PAR-CLIP, to identify LIN28B targets as well as sites bound by the individual RNA binding domains of LIN28B in the human transcriptome at nucleotide resolution.

2013-06-25 | E-GEOD-46908 | biostudies-arrayexpress

Identification of LIN28-bound mRNAs reveals features of target recognition and regulation

2013-06-25 | GSE46908 | GEO