MainA 2018 survey of putative human TFs concluded that over one-quarter of the estimated 1,600 TFs lacked established binding motifs1. This proportion represents a striking deficit given that most of the conserved DNA in the human genome is noncoding3 and that a primary hypothesis for the function of noncoding DNA is gene regulation4. Moreover, most of the uncharacterized and putative TFs are not close paralogues of any established TF. Thus, despite possessing either literature evidence of DNA binding or protein domains that would typically bind DNA (DNA-binding domains (DBDs)), their binding motifs cannot be readily inferred. However, it cannot be excluded that these putative TFs lack DNA sequence specificity entirely.TF DNA-binding motifs are commonly modelled as position weight matrices (PWMs), which describe the relative preference of a TF for each nucleotide base pair in the binding site5,6. Different methods for measuring TF binding, and for deriving PWMs from the resultant data, have different inherent limitations and biases5. There is also long-standing controversy regarding the contribution of the inherent sequence specificity of a TF to its cellular binding relative to the influence of chromatin and cofactors2. These uncertainties represent fundamental hurdles for the analysis of gene regulation and for a myriad of related tasks in genome analyses, including the interpretation of conserved genomic elements and sequence variants.To address these issues, we analyse a large majority of the poorly characterized human TFs1 (defined here as having no confidently known binding motif) and several dozen previously studied control TFs7,8 using a panel of assays that provide different perspectives on DNA sequence specificity. We refer to this international collaborative project as the ‘Codebook–GRECO-BIT Collaboration’. The reagent set and laboratory experiments were initiated as the ‘Codebook project’, which alludes to the fact that TFs decode individual ‘words’ in the genome. Meanwhile, the Benchmarking Initiative by the Gene Regulation Consortium, GRECO-BIT rooted in GRECO9, was engaged for much of the data analyses.In this paper, we present an overview of the Codebook data, major outcomes of the study and examples of prevalent phenomena and applications. We discuss the following findings:
An expanded codebook of human transcription factor DNA-binding specificity - Nature
Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.
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