A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization

• Published in: Genome research Vol. 28; no. 8; pp. 1158 - 1168
• Main Authors: Blumberg, Amit, Danko, Charles G, Kundaje, Anshul, Mishmar, Dan
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.08.2018
• Subjects: Animals; CD34 antigen; Cell Line; Chromatin; Chromatin - genetics; Deoxyribonuclease; Deoxyribonucleases - genetics; Deoxyribonucleic acid; DNA; DNA Footprinting - methods; DNA, Mitochondrial - genetics; DNA-Binding Proteins - genetics; Fetuses; Footprinting; G-Quadruplexes; Gene Expression Regulation; Genome, Human; HeLa Cells; Histones; Humans; Interleukin 3; Mice; Mitochondria - genetics; Mitochondrial DNA; Mitochondrial Proteins - genetics; Regulatory sequences; Synteny; Transcription Factors - genetics
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.230409.117

Human mitochondrial DNA (mtDNA) is believed to lack chromatin and histones. Instead, it is coated solely by the transcription factor TFAM. We asked whether mtDNA packaging is more regulated than once thought. To address this, we analyzed DNase-seq experiments in 324 human cell types and found, for the first time, a pattern of 29 mtDNA Genomic footprinting (mt-DGF) sites shared by ∼90% of the samples. Their syntenic conservation in mouse DNase-seq experiments reflect selective constraints. Colocalization with known mtDNA regulatory elements, with G-quadruplex structures, in TFAM-poor sites (in HeLa cells) and with transcription pausing sites, suggest a functional regulatory role for such mt-DGFs. Altered mt-DGF pattern in interleukin 3-treated CD34 cells, certain tissue differences, and significant prevalence change in fetal versus nonfetal samples, offer first clues to their physiological importance. Taken together, human mtDNA has a conserved protein-DNA organization, which is likely involved in mtDNA regulation.