Abstract
Understanding gene regulation is a key challenge in today's biology. The new technologies of protein-binding microarrays (PBMs) and high-throughput SELEX (HT-SELEX) allow measurement of the binding intensities of one transcription factor (TF) to numerous synthetic double-stranded DNA sequences in a single experiment. Recently, Jolma et al. reported the results of 547 HT-SELEX experiments covering human and mouse TFs. Because 162 of these TFs were also covered by PBM technology, for the first time, a large-scale comparison between implementations of these two in vitro technologies is possible. Here we assessed the similarities and differences between binding models, represented as position weight matrices, inferred from PBM and HT-SELEX, and also measured how well these models predict in vivo binding. Our results show that HT-SELEX- and PBM-derived models agree for most TFs. For some TFs, the HT-SELEX-derived models are longer versions of the PBM-derived models, whereas for other TFs, the HT-SELEX models match the secondary PBM-derived models. Remarkably, PBM-based 8-mer ranking is more accurate than that of HT-SELEX, but models derived from HT-SELEX predict in vivo binding better. In addition, we reveal several biases in HT-SELEX data including nucleotide frequency bias, enrichment of C-rich k-mers and oligos and underrepresentation of palindromes.
Highlights
The questions of how, when and where genes are expressed have been fundamental in the field of cell research in the past decades
We used the SCI09 data set of (16), which includes 115 paired proteinbinding microarrays (PBMs) experiments of 104 mouse transcription factor (TF) [in paired experiments, two array designs are used to study the same TF, and so a model learned on one array can be evaluated on the other, see (15)]
For 128 PBM experiments, an HT-SELEX-derived model was available for the same TF; this set covers 56 different TFs
Summary
The questions of how, when and where genes are expressed have been fundamental in the field of cell research in the past decades. Transcription factors (TFs) are known to be the main regulators of gene transcription and have been a subject for extensive study. These proteins bind to specific short DNA sequence, mainly in the promoter and enhancer regions, and by that impede or encourage transcription. They bind with variable affinity, depending on the sequence and on other factors, and this affinity affects transcription. As opposed to in vivo binding, in vitro binding is purely because of direct TF–DNA interaction (or cooperative binding of specific factors) and allows sampling of the full spectrum of DNA k-mers. A newer technology is high-throughput SELEX (HT-SELEX), which consists of several cycles of incubating the DNA-binding protein with a mixture of DNA sequences, enrichment of the bound DNA sequences, sequencing a sample of them and feeding them to the cycle (6–8)
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