ArticlePloS one2014
Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 45 citations in OpenAlex.
- Article
- KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome.Genome research · 2025Article
- An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome.PloS one · 2025Article
- Multi-faceted regulation of CREB family transcription factors.Frontiers in molecular neuroscience · 2024Review
- The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebrates.BMC genomics · 2023Article
- Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells.Nucleic acids research · 2023Article
- Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models.Cancer research · 2023Article
- Mitochondrial Kinases and the Role of Mitochondrial Protein Phosphorylation in Health and Disease.Life (Basel, Switzerland) · 2021Review
- Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Structure, mechanism, and regulation of mitochondrial DNA transcription initiation.The Journal of biological chemistry · 2020Review
- Transposable elements, circular RNAs and mitochondrial transcription in age-related genomic regulation.Development (Cambridge, England) · 2020Review
- Mitochondrial DNA Mutation Analysis in Breast Cancer: Shifting From Germline Heteroplasmy Toward Homoplasmy in Tumors.Frontiers in oncology · 2020Article
- Hypoxia induces rapid, STAT3 and ROS dependent, mitochondrial translocation of RelA(p65) and IκBα.Bioscience reports · 2019Article
- MOTS-c: A Mitochondrial-Encoded Regulator of the Nucleus.BioEssays : news and reviews in molecular, cellular and developmental biology · 2019Review
- Transcription, Processing, and Decay of Mitochondrial RNA in Health and Disease.International journal of molecular sciences · 2019Review
- Review
- A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization.Genome research · 2018Article
- ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation.Briefings in functional genomics · 2018Review
- Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data.Genome biology · 2016Article
- Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Mitochondria contain their own circular genome, with mitochondria-specific transcription and replication systems and corresponding regulatory proteins. All of these proteins are encoded in the nuclear genome and are post-translationally imported into mitochondria. In addition, several nuclear transcription factors have been reported to act in mitochondria, but there has been no comprehensive mapping of their occupancy patterns and it is not clear how many other factors may also be found in mitochondria. Here we address these questions by using ChIP-seq data from the ENCODE, mouseENCODE and modENCODE consortia for 151 human, 31 mouse and 35 C. elegans factors. We identified 8 human and 3 mouse transcription factors with strong localized enrichment over the mitochondrial genome that was usually associated with the corresponding recognition sequence motif. Notably, these sites of occupancy are often the sites with highest ChIP-seq signal intensity within both the nuclear and mitochondrial genomes and are thus best explained as true binding events to mitochondrial DNA, which exist in high copy number in each cell. We corroborated these findings by immunocytochemical staining evidence for mitochondrial localization. However, we were unable to find clear evidence for mitochondrial binding in ENCODE and other publicly available ChIP-seq data for most factors previously reported to localize there. As the first global analysis of nuclear transcription factors binding in mitochondria, this work opens the door to future studies that probe the functional significance of the phenomenon.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.