Other

Dataset Information

0

Deconvolving the recognition of DNA shape from sequence


ABSTRACT: 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.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE65073 | GEO | 2015/01/21

SECONDARY ACCESSION(S): PRJNA272858

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
Other
Items per page:
1 - 1 of 1

Similar Datasets

2015-01-21 | E-GEOD-65073 | biostudies-arrayexpress
2018-01-16 | GSE93662 | GEO
2014-11-04 | E-GEOD-59845 | biostudies-arrayexpress
2023-12-31 | GSE227873 | GEO
2016-12-31 | GSE85757 | GEO
2016-12-31 | GSE86088 | GEO
2014-10-01 | GSE61920 | GEO
2021-06-10 | GSE169222 | GEO
2018-08-23 | GSE102981 | GEO
2012-12-06 | E-GEOD-42709 | biostudies-arrayexpress