Distribution of reads over the human mitochondrial genome for factors previously reported to bind to mitochondria in ENCODE ChIP-seq data.

<p>Reads mapping to the forward strand are represented in black, reads mapping to the reverse strand are represented in yellow. The unique mappability track for the mitochondrial genome is shown in red in the outside track (see Methods for details). Protein-coding, rRNA and tRNA genes are shown as colored bars. The innermost circle shows the motif occurrences in the mitochondrial genome for each factor as black vertical bars. (A) CREB; (B) STAT3; (C) GR in A549 cells treated with different concentrations of dexamethasone (Dex) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Reddy1" target="_blank">[60]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Reddy2" target="_blank">[61]</a>; (D) ER<i>α</i> in untreated (DMSO) ECC1 cells and ECC1 cells treated with bisphenol A (BPA), genistein (Gen) or 17<i>β</i>-estradiol (E2) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Gertz1" target="_blank">[31]</a>; (E) IRF3; (F) NF<i>κ</i>B in GM12878 cells treated with TNF<i>α </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Kasowski1" target="_blank">[37]</a>. The reads per million (RPM) tracks are shown, scaled to the maximum signal level (for both strands) for each dataset. Plots were generated using Circos version 0.60 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Krzywinski1" target="_blank">[41]</a>.</p

Signal distribution over the mitochondrial genome in human FAIRE-seq, DNAse-seq and MNAse-seq datasets.

<p>Shown is the maximum z-score for each individual replicate for each cell line (left) and the z-score profile along the mitochondrial chromosome for the replicate with the highest z-score (right). (A) FAIRE data; (B) DNAse data; (C) MNAse data. “UNC”, “UW” and “SYDH” refer to the ENCODE production groups which generated the data. Z-scores larger than 100 are shown as 100. No read enrichment over the D-loop is observed, suggesting that the D-loop signal found in TF ChIP-seq datasets is not due to sequencing biases but is a result of the immunoprecipitation process.</p

Unique mappability of the mitochondrial genome (chrM) in ENCODE and modENCODE species.

<p>(A) human; (B) mouse; (C) <i>C. elegans</i>; (D) <i>D. melanogaster</i>. The 36 bp mappability track (see Methods for details) is shown. The annotated protein coding and rRNA and tRNA genes are shown in the inner circles as follows: forward-strand genes are shown as green lines, while reverse-strand genes are shown as red lines, with the exception of mouse and human rRNA and tRNAs (blue). The D-loop region in human is shown in black. Gene annotations were obtained from ENSEMBL (version 66). Plots were generated using Circos version 0.60 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Krzywinski1" target="_blank">[41]</a>.</p

Signal distribution over the mitochondrial genome in human ChIP-seq datasets.

<p>The maximum z-score for each individual TF ChIP-seq replicate in each cell line is shown on the left (factors are sorted by average z-score, with control datasets always shown on the bottom in red, below the red horizontal line). The z-score profile along the mitochondrial chromosome for the replicate with the highest z-score is shown on the right. “SYDH” and “HA” refer to the ENCODE production groups which generated the data. Z-scores ≥100 are shown as equal to 100. (A) GM12878 cells; (B) K562 cells.</p

Distribution of reads over the mouse mitochondrial genome for MEF2D isoforms MEF2Da1 and MEF2Da2 in C2C12 myoblasts.

<p>Reads mapping to the forward strand are represented in black, reads mapping to the reverse strand are represented in yellow. The unique mappability track for the mitochondrial genome is shown in red in the outside track (see Methods for details). Protein-coding, rRNA and tRNA genes are shown as colored bars. The innermost circle shows the MEF2D motif occurrences in the mitochondrial genome as black vertical bars. Data was obtained from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Sebastian1" target="_blank">[65]</a>, GSE43223. Plots were generated using Circos version 0.60 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Krzywinski1" target="_blank">[41]</a>.</p

Signal distribution over the mitochondrial genome in mouse ChIP-seq datasets.

<p>Shown is the maximum z-score for each individual replicate for each cell line (left) and the z-score profile along the mitochondrial chromosome for the replicate with the highest z-score (right). Control datasets are shown in red on the bottom, below the red horizontal line. (A) CH12 cells; (B) MEL cells.</p

Representative USCS Genome Browser snapshots of nuclear transcription factor ChIP-seq datasets exhibiting strong enrichment in the mitochondrial genome.

<p>(A) GM12878 GCN5 shows high signal intensity in the D-loop (the region between coordinates 16030 and 580, i.e. the non-coding regions on the left and right ends of the snapshot) representative of the D-loop enrichment observed for a large number of transcription factors (B) In contrast, a large MafK peak is observed in a coding region outside of the D-loop in HepG2 cells. Upper track (black) shows reads aligning to the forward strand, lower track (gray) shows read aligning to the reverse strand.</p

Distribution of reads over the human and mouse mitochondrial genome for p53 in publicly available ChIP-seq datasets.

<p>Reads mapping to the forward strand are represented in black, reads mapping to the reverse strand are represented in yellow. The unique mappability track for the mitochondrial genome is shown in red in the outside track (see Methods for details). Protein-coding, rRNA and tRNA genes are shown as colored bars. The innermost circle shows the motif occurrences in the mitochondrial genome for each factor as black vertical bars. (A) p53 in mouse embryionic fibroblasts (MEFs), data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-KenzelmannBroz1" target="_blank">[38]</a>, GSE46240. (B) p53 in mouse embryonic stem cells (mESC), data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Li1" target="_blank">[45]</a>, GSE26361; (C) p53 in human IMR90 cells, data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Aksoy1" target="_blank">[2]</a>, GSE42728. The reads per million (RPM) tracks are shown, scaled to the maximum signal level (for both strands) for each dataset. Plots were generated using Circos version 0.60 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Krzywinski1" target="_blank">[41]</a>.</p

Signal distribution over the mitochondrial genome in <i>C.elegans</i> ChIP-seq datasets.

<p>(A) Shown is the maximum z-score for each individual replicate for each cell line (left) and the z-score profile along the mitochondrial chromosome for the replicate with the highest z-score (right). Control datasets are shown in red on the bottom, below the red horizontal line; (B) Forward and reverse strand read distribution over the <i>C.elegans</i> mitochondrial genome for W03F9.2 (“Young Adult” stage). Reads mapping to the forward strand are represented in black, reads mapping to the reverse strand are represented in yellow. The unique mappability track for the mitochondrial genome is shown in red in the outside track (see Methods for details). Plots generated using Circos version 0.60 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084713#pone.0084713-Krzywinski1" target="_blank">[41]</a>.</p

Signal distribution over the mitochondrial genome in human ChIP-seq datasets.

<p>The maximum z-score for each individual TF ChIP-seq replicate in each cell line is shown on the left (factors are sorted by average z-score, with control datasets always shown on the bottom in red, below the red horizontal line). The z-score profile along the mitochondrial chromosome for the replicate with the highest z-score is shown on the right. “SYDH” and “HA” refer to the ENCODE production groups which generated the data. Z-scores ≥100 are shown as equal to 100. (A) H1-hESC cells; (B) IMR90.</p