Skip to content
DraconiticResearch
Search Sources API
194,161 studies31 sourcesUpdated 59 min ago
PreprintCC BYbioRxiv

methylTFR: Computational quantification of transcription factor activity from DNA methylation

  • I. B. Gunduz
  • R. Nitsch
  • S. K. Murugan
  • F. Mueller1
  1. 1Saarland University
Read full textPDFDOICite

Abstract

DNA methylation modulates transcription factor (TF) binding, and plays an important role in regulating gene expression. We developed methylTFR, an R package for quantifying TF activity from DNA methylation across TF-binding sites, providing a low-dimensional and interpretable activity profile. Across 147 human immune cell methylomes, methylTFR identified cell-type-specific regulators, including CEBP and ETS family activity in myeloid cells. In CD4+ T cells, TF activity scores resolved the naive-to-memory trajectory and highlighted AP-1 factors as important memory regulators. We applied methylTFR to sparse single-cell methylome data, and we integrated derived activity scores with gene expression and accessibility into joint factor models yielding multimodal views of lineage regulators.

Related

  1. Transcription-driven establishment of DNA methylation at the PWS/AS imprinted region
    J. Haake, A. Lederhof, C. Pommerenke +1
    bioRxivPreprintAll rights reservedFull textGenetics & genomicsbioRxiv
  2. Nascent transcription profiling identifies H3K36 methylation as a custodian of the somatic transcriptome
    H. Sultana, V. Vandadi, H. R. Salzler +7
    bioRxivPreprintCC BY-NCFull textGenetics & genomicsbioRxiv
  3. Transcription factor CCTF1 plays an important role in regulating proteasome activity during archaeal cell division
    Yunfeng Yang, Zixin Geng, Shikuan Liang +5
    Nucleic Acids ResearchPeer-reviewedCC BY-NC 4.0Full textMicrobiologyHAL
  4. VIGAT: VLM-guided gene activity quantification from single-cell ATAC-seq
    B. Ji, Z. Ji
    bioRxivPreprintCC BYFull textBioinformatics & computational biologybioRxiv
  5. Acute Octodrine (DMHA) Exposure Disrupts Cardiac Function, Locomotor Activity, and Neuronal Activity-Responsive Transcription in Zebrafish Larvae.
    Eduardo Kennedy Carrão-Dantas, Ouwais Aljabasini, Eva Prats +3
    International journal of molecular sciencesPeer-reviewedCC BYFull textCell biologyEurope PMC

Cite

BibTeXRIS
BibTeX
@misc{gunduz2026methyltfr,
  title = {{methylTFR: Computational quantification of transcription factor activity from DNA methylation}},
  author = {I. B. Gunduz and R. Nitsch and S. K. Murugan and F. Mueller},
  howpublished = {bioRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.29.755279},
  url = {https://www.biorxiv.org/content/10.64898/2026.09.29.755279v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - methylTFR: Computational quantification of transcription factor activity from DNA methylation
AU  - I. B. Gunduz
AU  - R. Nitsch
AU  - S. K. Murugan
AU  - F. Mueller
PY  - 2026
DA  - 2026/09/29
PB  - bioRxiv
DO  - 10.64898/2026.09.29.755279
UR  - https://www.biorxiv.org/content/10.64898/2026.09.29.755279v1
AB  - DNA methylation modulates transcription factor (TF) binding, and plays an important role in regulating gene expression. We developed methylTFR, an R package for quantifying TF activity from DNA methylation across TF-binding sites, providing a low-dimensional and interpretable activity profile. Across 147 human immune cell methylomes, methylTFR identified cell-type-specific regulators, including CEBP and ETS family activity in myeloid cells. In CD4+ T cells, TF activity scores resolved the naive-to-memory trajectory and highlighted AP-1 factors as important memory regulators. We applied methylTFR to sparse single-cell methylome data, and we integrated derived activity scores with gene expression and accessibility into joint factor models yielding multimodal views of lineage regulators.
ER  -