High-throughput characterization of the role of non-B DNA motifs on promoter function
Ilias Georgakopoulos-Soares,
Jesus Victorino,
Guillermo E. Parada,
Vikram Agarwal,
Jingjing Zhao,
Hei Yuen Wong,
Mubarak Ishaq Umar,
Orry Elor,
Allan Muhwezi,
Joon-Yong An,
Stephan J. Sanders,
Chun Kit Kwok,
Fumitaka Inoue,
Martin Hemberg,
Nadav Ahituv
Affiliations
Ilias Georgakopoulos-Soares
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
Jesus Victorino
Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain; Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
Guillermo E. Parada
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
Vikram Agarwal
Calico Life Sciences LLC, South San Francisco, CA, USA
Jingjing Zhao
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
Hei Yuen Wong
Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
Mubarak Ishaq Umar
Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
Orry Elor
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
Allan Muhwezi
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
Joon-Yong An
Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
Stephan J. Sanders
Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA; Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
Chun Kit Kwok
Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
Fumitaka Inoue
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
Martin Hemberg
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Corresponding author
Nadav Ahituv
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA; Corresponding author
Summary: Alternative DNA conformations, termed non-B DNA structures, can affect transcription, but the underlying mechanisms and their functional impact have not been systematically characterized. Here, we used computational genomic analyses coupled with massively parallel reporter assays (MPRAs) to show that certain non-B DNA structures have a substantial effect on gene expression. Genomic analyses found that non-B DNA structures at promoters harbor an excess of germline variants. Analysis of multiple MPRAs, including a promoter library specifically designed to perturb non-B DNA structures, functionally validated that Z-DNA can significantly affect promoter activity. We also observed that biophysical properties of non-B DNA motifs, such as the length of Z-DNA motifs and the orientation of G-quadruplex structures relative to transcriptional direction, have a significant effect on promoter activity. Combined, their higher mutation rate and functional effect on transcription implicate a subset of non-B DNA motifs as major drivers of human gene-expression-associated phenotypes.
