Ilias Georgakopoulos-Soares, Jesus Victorino, Guillermo E Parada, Vikram Agarwal, Jingjing Zhao et al.
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.
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. High-throughput characterization of the role of non-B DNA motifs on promoter function. 2022-04-13. https://doi.org/10.1016/j.xgen.2022.100111
Three isogenic HepG2 replicates tested a library of 200-bp genomic elements in an integrated lentiMPRA reporter. RNA/DNA activity measurements are joined to the original ENCODE reference sequences and annotated for non-B DNA motif features.
Three isogenic K562 replicates tested a library of 200-bp genomic elements in an integrated lentiMPRA reporter. RNA/DNA activity measurements are joined to the original ENCODE reference sequences and annotated for non-B DNA motif features.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 16 files (ZIP)ENCODE_ENCFF285OWV_metadata.jsonENCODE_ENCFF788GLA_metadata.jsonENCODE_ENCSR460LZI_activity_GRCh38.bed.gzENCODE_ENCSR460LZI_K562_element_quantifications.tsvENCODE_ENCSR460LZI_metadata.jsonENCODE_ENCSR460LZI_reference_original.fasta.gzENCODE_ENCSR463IRX_activity_GRCh38.bed.gzENCODE_ENCSR463IRX_HepG2_element_quantifications.tsvENCODE_ENCSR463IRX_metadata.jsonENCODE_ENCSR463IRX_reference_original.fasta.gzgithub_MPRA_scripts_functions.pygithub_MPRA_scripts_README.txtHEK293T_K562_NonB_Library.fastaNPC_Autism_Library.fastaPRJNA763774_ENA_run_manifest.tsvsupplementary_mmc1_tables_s1_s2.pdf