RT Journal Article
SR Electronic
T1 Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 054031
DO 10.1101/054031
A1 Amit Blumberg
A1 Edward J. Rice
A1 Anshul Kundaje
A1 Charles G. Danko
A1 Dan Mishmar
YR 2016
UL http://biorxiv.org/content/early/2016/05/18/054031.abstract
AB Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. Surprisingly, accurate detection of human mtDNA transcription initiation sites (TIS) in the heavy and light strands revealed a novel conserved transcription pausing site near the light strand TIS, upstream to the transcription-replication transition region. This pausing site correlated with the presence of a bacterial pausing sequence motif, yet the transcription pausing index varied quantitatively among the cell lines. Analysis of non-human organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. Whereas mammals (chimpanzee, rhesus macaque, rat, and mouse) showed a human-like mtDNA transcription pattern, the invertebrate pattern (Drosophila and C. elegans) profoundly diverged. Our approach paves the path towards in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes.