التفاصيل البيبلوغرافية
| العنوان: |
An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome. |
| المؤلفون: |
Marinov GK; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Ramalingam V; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Greenleaf WJ; Department of Genetics, Stanford University, Stanford, CA 94305, USA.; Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA.; Department of Applied Physics, Stanford University, Stanford, California 94305, USA.; Chan Zuckerberg Biohub, San Francisco, California, USA., Kundaje A; Department of Genetics, Stanford University, Stanford, CA 94305, USA.; Department of Computer Science, Stanford University, Stanford, CA 94305, USA. |
| المصدر: |
BioRxiv : the preprint server for biology [bioRxiv] 2024 Jun 06. Date of Electronic Publication: 2024 Jun 06. |
| نوع المنشور: |
Journal Article; Preprint |
| اللغة: |
English |
| بيانات الدورية: |
Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| مستخلص: |
In most eukaryotes, mitochondrial organelles contain their own genome, usually circular, which is the remnant of the genome of the ancestral bacterial endosymbiont that gave rise to modern mitochondria. Mitochondrial genomes are dramatically reduced in their gene content due to the process of endosymbiotic gene transfer to the nucleus; as a result most mitochondrial proteins are encoded in the nucleus and imported into mitochondria. This includes the components of the dedicated mitochondrial transcription and replication systems and regulatory factors, which are entirely distinct from the information processing systems in the nucleus. However, since the 1990s several nuclear transcription factors have been reported to act in mitochondria, and previously we identified 8 human and 3 mouse transcription factors (TFs) with strong localized enrichment over the mitochondrial genome using ChIP-seq (Chromatin Immunoprecipitation) datasets from the second phase of the ENCODE (Encyclopedia of DNA Elements) Project Consortium. Here, we analyze the greatly expanded in the intervening decade ENCODE compendium of TF ChIP-seq datasets (a total of 6,153 ChIP experiments for 942 proteins, of which 763 are sequence-specific TFs) combined with interpretative deep learning models of TF occupancy to create a comprehensive compendium of nuclear TFs that show evidence of association with the mitochondrial genome. We find some evidence for chrM occupancy for 50 nuclear TFs and two other proteins, with bZIP TFs emerging as most likely to be playing a role in mitochondria. However, we also observe that in cases where the same TF has been assayed with multiple antibodies and ChIP protocols, evidence for its chrM occupancy is not always reproducible. In the light of these findings, we discuss the evidential criteria for establishing chrM occupancy and reevaluate the overall compendium of putative mitochondrial-acting nuclear TFs. |
| معلومات مُعتمدة: |
U01 HG009431 United States HG NHGRI NIH HHS; R01 HG008140 United States HG NHGRI NIH HHS; U19 AI057266 United States AI NIAID NIH HHS; P50 HG007735 United States HG NHGRI NIH HHS; UM1 HG009436 United States HG NHGRI NIH HHS; UM1 HG009442 United States HG NHGRI NIH HHS |
| تواريخ الأحداث: |
Date Created: 20240619 Latest Revision: 20240624 |
| رمز التحديث: |
20240624 |
| مُعرف محوري في PubMed: |
PMC11185660 |
| DOI: |
10.1101/2024.06.04.597442 |
| PMID: |
38895386 |
| قاعدة البيانات: |
MEDLINE |
