Fig 1.
Global assessment of the evidence for association of human nuclear TFs with the mitochondrial genome. (A) Summary of the known human TFs and available ENCODE TF ChIP datasets. The TF classification of human TFs of Lambert et al. 2018 [1] was followed. (B) Hierarchical clustering of ChIP-seq profiles over the mitochondrial genome for 6,513 TF ChIP-seq datasets. Datasets that show evidence for non-artefactual association with mitochondrial DNA are highlighted at the bottom.
Fig 2.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) ATF2 (bZIP); (B) ATF3 (bZIP); (C) ATF4 (bZIP); (D) ATF7 (bZIP).
Fig 3.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) CREB1 (bZIP); (B) FOS (bZIP); (C) FOSL1 (bZIP); (D) FOSL2 (bZIP).
Fig 4.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) CEBPB (bZIP); (B) CEBPG (bZIP); (C) JUN (bZIP); (D) JUND (bZIP).
Fig 5.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) MAFF (bZIP); (B) MAFG (bZIP); (C) MAFK (bZIP); (D) NFE2 (bZIP).
Fig 6.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) NFE2L1 (bZIP); (B) NFE2L2 (bZIP); (C) NRL (bZIP); (D) BHLHE40 (bHLH).
Fig 7.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) MAX (bHLH); (B) MITF (bHLH); (C) SREBF1 (bHLH); (D) RFX1 (RFX).
Fig 8.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) RFX5 (RFX); (B) FOXA1 (Forkhead); (C) FOXA2 (Forkhead); (D) ZNF316 (C2H2 ZNF).
Fig 9.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) DZIP1 (C2H2 ZNF); (B) HIVEP1 (C2H2 ZNF); (C) ZNF225 (C2H2 ZNF); (D) ZNF263 (C2H2 ZNF).
Fig 10.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) ZNF274 (C2H2 ZNF); (B) ZNF280B (C2H2 ZNF); (C) ZNF350 (C2H2 ZNF); (D) ZNF598 (C2H2 ZNF).
Fig 11.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) ZNF768 (C2H2 ZNF); (B) ZNF839 (C2H2 ZNF); (C) ZNF891 (C2H2 ZNF); (D) THAP9 (THAP finger).
Fig 12.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) NFKB2 (Rel); (B) RXRA (nuclear receptor); (C) RUNX3 (Runt); (D) HSF1 (HSF).
Fig 13.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) MEIS2 (Homeodomain); (B) PKNOX1 (Homeodomain); (C) CUX1 (Homeodomain); (D) E2F1 (E2F).
Fig 14.
Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) ARID1B (ARID/BRIGHT) (B) TFAP2C (AP-2); (C) C11orf30; (D) ATM.
Fig 15.
Summary of the available evidence for the physical association of nuclear TFs with the mitochondrial genome. All TFs with ChIP-seq evidence for chrM occupancy are listed in the “any” column. “BPNet confirmed” indicates that the observed ChIP-Seq pattern is corroborated in its key aspects by BPNet models. The “discordant” TFs are those for which not all available ChIP-seq experiments show chrM peaks.