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Genome-Wide Assessment of the Binding Effects of Artificial Transcriptional Activators by Utilizing the Power of High-Throughput Sequencing

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Advancing Development of Synthetic Gene Regulators

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Abstract

One of the major goals in DNA-based personalized medicine is the development of sequence-specific small molecules to target the genome by means of synthetic biology; SAHA-PIPs belong to such class of small molecules. In a complex eukaryotic genome, the differential biological effects of SAHA-PIPs remain unclear. These questions can be addressed by directly identifying the binding regions of small molecules across the genome; however, it is a challenge to enrich specifically the small-molecule-bound DNA without chemical cross-linking. Here, we developed a method using high-throughput sequencing to map the binding area of non-cross-linked small molecules throughout the chromatinized human genome. Analysis of the sequenced data confirmed the presence of specific binding sites for SAHA-PIPs among the enriched sequence reads. Mapping the binding sites and enriched regions on the human genome clarifies the origin of the distinctive biological effects of SAHA-PIP. This approach will be useful for identifying the functionality of other small molecules on a large scale.

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Authors and Affiliations

  1. Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan

    Anandhakumar Chandran

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  1. Anandhakumar Chandran
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Correspondence to Anandhakumar Chandran .

Appendix

Appendix

Extended Fig. 3.1.

Extended Fig. 3.1
figure 5figure 5

Identified genomic regions of PIP conjugates 3 and 4 binding and enrichment in a DPPA4 b EPCAM c PIWIL2 d TDRD9 e GAPDH

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Extended Fig. 3.2.

Extended Fig. 3.2
figure 6

Comparison of genomic binding and enriched region with binding rule based binding site. a For compound 3. b For compound 4

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Chandran, A. (2018). Genome-Wide Assessment of the Binding Effects of Artificial Transcriptional Activators by Utilizing the Power of High-Throughput Sequencing. In: Advancing Development of Synthetic Gene Regulators. Springer Theses. Springer, Singapore. https://doi.org/10.1007/978-981-10-6547-7_3

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