Evidence map›Paper›PMID 38937458›Full record

ArticleNature communications2024

Sequence-specific dynamic DNA bending explains mitochondrial TFAM's dual role in DNA packaging and transcription initiation.

Hyun Huh, Jiayu Shen, Yogeeshwar Ajjugal, Aparna Ramachandran, Smita S Patel, Sang-Hyuk Lee

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Review
  5. TFAM organizes DNA into compact higher order structures.bioRxiv : the preprint server for biology · 2026
    Article
  6. Review
  7. Mechanisms of Protection Against Oxidative Stress During Hibernation.International journal of molecular sciences · 2026
    Review
  8. Article
  9. Review
  10. Review
  11. Article
  12. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Hyun Huh *Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.ORCID 0000-0002-2955-8433
Jiayu Shen *Graduate School of Biomedical Sciences, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA.ORCID 0000-0001-8447-9378
Yogeeshwar AjjugalDepartment of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA.
Aparna RamachandranDepartment of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA.
Smita S PatelDepartment of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854, USA. patelss@rutgers.edu.ORCID 0000-0002-2523-4933
Sang-Hyuk LeeInstitute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA. shlee@physics.rutgers.edu.ORCID 0000-0001-9036-7292

Funding

Mechanistic studies of nucleic acid enzymes involved in DNA replication, transcription, and innate immunity.R35GM118086 · NIGMS · RUTGERS BIOMEDICAL AND HEALTH SCIENCES · PI SMITA S PATEL · 2016 to 2026
$8.9M
NIGMS NIH HHS R35 GM118086U.S. Department of Energy (DOE) DE-SC0019313U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) GM118086
6 · The paper itself

Abstract

Mitochondrial transcription factor A (TFAM) employs DNA bending to package mitochondrial DNA (mtDNA) into nucleoids and recruit mitochondrial RNA polymerase (POLRMT) at specific promoter sites, light strand promoter (LSP) and heavy strand promoter (HSP). Herein, we characterize the conformational dynamics of TFAM on promoter and non-promoter sequences using single-molecule fluorescence resonance energy transfer (smFRET) and single-molecule protein-induced fluorescence enhancement (smPIFE) methods. The DNA-TFAM complexes dynamically transition between partially and fully bent DNA conformational states. The bending/unbending transition rates and bending stability are DNA sequence-dependent-LSP forms the most stable fully bent complex and the non-specific sequence the least, which correlates with the lifetimes and affinities of TFAM with these DNA sequences. By quantifying the dynamic nature of the DNA-TFAM complexes, our study provides insights into how TFAM acts as a multifunctional protein through the DNA bending states to achieve sequence specificity and fidelity in mitochondrial transcription while performing mtDNA packaging.

Indexed as

DNA-Binding ProteinsDNA, MitochondrialDNA PackagingFluorescence Resonance Energy TransferMitochondrial ProteinsNucleic Acid ConformationPromoter Regions, GeneticTranscription FactorsBase SequenceDNA-Directed RNA PolymerasesHumansMitochondriaProtein BindingSingle Molecule ImagingTranscription Initiation, GeneticDNA-Binding ProteinsDNA-Directed RNA PolymerasesDNA, MitochondrialMitochondrial ProteinsTFAM protein, humanTranscription Factors

Identifiers

PMID38937458
PMCPMC11211510

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Registered trials

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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.