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Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

Amit Blumberg, Edward J. Rice, Anshul Kundaje, Charles G. Danko, Dan Mishmar
doi: https://doi.org/10.1101/054031
Amit Blumberg
1.Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105 Israel.
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Edward J. Rice
2.Baker Institute for Animal Health, Cornell University, Ithaca, New York, 14853, USA.
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Anshul Kundaje
3.Department of Genetics, Stanford University, Stanford, California, 94305-5120, USA.
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Charles G. Danko
2.Baker Institute for Animal Health, Cornell University, Ithaca, New York, 14853, USA.
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Dan Mishmar
1.Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105 Israel.
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  • For correspondence: dmishmar@bgu.ac.il
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Abstract

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 18, 2016.
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Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution
Amit Blumberg, Edward J. Rice, Anshul Kundaje, Charles G. Danko, Dan Mishmar
bioRxiv 054031; doi: https://doi.org/10.1101/054031
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Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution
Amit Blumberg, Edward J. Rice, Anshul Kundaje, Charles G. Danko, Dan Mishmar
bioRxiv 054031; doi: https://doi.org/10.1101/054031

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