Transcription factors bind negatively selected sites within human mtDNA genes

Amit Blumberg, Badi Sri Sailaja, Anshul Kundaje, Liron Levin, Sara Dadon, Shimrit Shmorak, Eitan Shaulian, Eran Meshorer, Dan Mishmar*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

39 Scopus citations


Transcription of mitochondrial DNA (mtDNA)-encoded genes is thought to be regulated by a handful of dedicated transcription factors (TFs), suggesting that mtDNA genes are separately regulated from the nucleus. However, several TFs, with known nuclear activities, were found to bind mtDNA and regulate mitochondrial transcription. Additionally, mtDNA transcriptional regulatory elements, which were proved important in vitro, were harbored by a deletion that normally segregated among healthy individuals. Hence, mtDNA transcriptional regulation is more complex than once thought. Here, by analyzing ENCODE chromatin immunoprecipitation sequencing (ChIP-seq) data, we identified strong binding sites of three bona fide nuclear TFs (c-Jun, Jun-D, and CEBPb) within human mtDNAprotein-coding genes.Wevalidated the binding of two TFs byChIP-quantitative polymerase chain reaction (c- Jun and Jun-D) and showed their mitochondrial localization by electron microscopy and subcellular fractionation. As a step toward investigating the functionality of these TF-binding sites (TFBS),weassessed signaturesof selection. By analyzing 9,868humanmtDNA sequences encompassing allmajor globalpopulations,we recordedgenetic variants in tipsandnodesofmtDNAphylogeny within the TFBS.We next calculated the effects of variants on binding motif prediction scores. Finally, the mtDNA variation pattern in predicted TFBS,occurring withinChIP-seqnegative-binding sites,was comparedwithChIP-seqpositive-TFBS(CPR). Motifs withinCPRsof c-Jun, Jun-D, and CEBPb harbored either only tip variants or their nodal variants retained high motif prediction scores. This reflects negative selection within mtDNA CPRs, thus supporting their functionality. Hence, human mtDNA-coding sequences may have dual roles, namely coding for genes yet possibly also possessing regulatory potential.

Original languageAmerican English
Pages (from-to)2634-2646
Number of pages13
JournalGenome Biology and Evolution
Issue number10
StatePublished - Oct 2014

Bibliographical note

Publisher Copyright:
© The Author(s) 2014.


  • CEBPb
  • ChIP-seq
  • Jun-D
  • c-Jun
  • mitochondrial DNA
  • negative selection
  • transcription.


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