Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes

Mario Pujato, Fabien Kieken, Amanda A. Skiles, Nikos Tapinos, Andras Fiser

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Proper cell functioning depends on the precise spatio-temporal expression of its genetic material. Gene expression is controlled to a great extent by sequence-specific transcription factors (TFs). Our current knowledge on where and how TFs bind and associate to regulate gene expression is incomplete. A structure-based computational algorithm (TF2DNA) is developed to identify binding specificities of TFs. The method constructs homology models of TFs bound to DNA and assesses the relative binding affinity for all possible DNA sequences using a knowledge-based potential, after optimization in amolecularmechanics force field. TF2DNA predictions were benchmarked against experimentally determined binding motifs. Success rates range from 45% to 81% and primarily depend on the sequence identity of aligned target sequences and template structures, TF2DNA was used to predict 1321 motifs for 1825 putative human TF proteins, facilitating the reconstruction of most of the human gene regulatory network. As an illustration, the predicted DNA binding site for the poorly characterized T-cell leukemia homeobox 3 (TLX3) TF was confirmed with gel shift assay experiments. TLX3 motif searches in human promoter regions identified a group of genes enriched in functions relating to hematopoiesis, tissue morphology, endocrine system and connective tissue development and function.

Original languageEnglish (US)
Pages (from-to)13500-13512
Number of pages13
JournalNucleic Acids Research
Volume42
Issue number22
DOIs
StatePublished - Dec 16 2014

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T-Cell Leukemia
Nucleotide Motifs
Homeobox Genes
Transcription Factors
Genes
Transcription Factor 3
Gene Expression
Endocrine System
Gene Regulatory Networks
DNA
Hematopoiesis
Genetic Promoter Regions
Connective Tissue
Gels
Binding Sites
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. / Pujato, Mario; Kieken, Fabien; Skiles, Amanda A.; Tapinos, Nikos; Fiser, Andras.

In: Nucleic Acids Research, Vol. 42, No. 22, 16.12.2014, p. 13500-13512.

Research output: Contribution to journalArticle

Pujato, Mario ; Kieken, Fabien ; Skiles, Amanda A. ; Tapinos, Nikos ; Fiser, Andras. / Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. In: Nucleic Acids Research. 2014 ; Vol. 42, No. 22. pp. 13500-13512.
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