Evidence map›Paper›PMID 42642588›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

FENGC: Targeted, Multiplexed, and Integrated Single-Molecule Profiling of Chromatin Accessibility and DNA Methylation.

Mingqi Zhou, Marie-Pierre L Gauthier, Nancy H Nabilsi, Kevin O Murray, Deborah A Morse, Philip A Efron, Alberto Riva, Patrick Concannon, Thomas L Clanton, Jason O Brant and 2 more

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

12 authors.

Mingqi ZhouDepartment of Biochemistry and Molecular Biology, College of Medicine, Genetics Institute, and UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
Marie-Pierre L GauthierDepartment of Biochemistry and Molecular Biology, College of Medicine, and UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
Nancy H NabilsiDepartment of Biochemistry and Molecular Biology, College of Medicine, and UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
Kevin O MurrayDepartment of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA.
Deborah A MorseDepartment of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA.
Philip A EfronDepartment of Surgery, College of Medicine and Sepsis and Critical Illness Research Center, University of Florida, Gainesville, FL, USA.
Alberto RivaBioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA.
Patrick ConcannonGenetics Institute, and Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.
Thomas L ClantonDepartment of Applied Physiology and Kinesiology, College of Health and Human Performance, University of Florida, Gainesville, FL, USA.
Jason O BrantUF Health Cancer Center, and Department of Biostatistics, College of Public Health & Health Professions, University of Florida, Gainesville, FL, USA.
Rhonda BacherGenetics Institute, UF Health Cancer Center, and Department of Biostatistics, College of Public Health & Health Professions, University of Florida, Gainesville, FL, USA.
Michael P KladdeDepartment of Biochemistry and Molecular Biology, College of Medicine, Genetics Institute, UF Health Cancer Center, and Sepsis and Critical Illness Research Center, University of Florida, Gainesville, FL, USA. kladde@ufl.edu.

Funding

Renewal: Dysfunctional Myelopoiesis and Myeloid-Derived Suppressor Cells in Sepsis PathobiologyRM1GM139690 · NIGMS · UNIVERSITY OF FLORIDA · PI Philip A Efron, Michael Paul Kladde · 2021 to 2026
$10.3M
Interplay of Epigenetic Mechanisms in Gene SilencingR01CA155390 · NCI · UNIVERSITY OF FLORIDA · PI KLADDE, MICHAEL PAUL · 2011 to 2015
$1.5M
NCI NIH HHS R01 CA155390NIGMS NIH HHS RM1 GM139690
6 · The paper itself

Abstract

DNA methyltransferase accessibility protocol for individual templates (MAPit) enables localization of DNA-protein interactions by probing the native chromatin architecture in nuclei or permeabilized cells using exogenously applied DNA methyltransferases. By preserving the integrity of DNA in chromatin, MAPit enables simultaneous mapping of nucleosome positioning, transcription factor binding, and endogenous CpG methylation in a single assay-while maintaining linkage between regulatory modules along chromatin fibers. Although MAPit and other sequencing-based approaches can be applied genome-wide, there is a growing demand for orthogonal approaches that validate target discovery and offer deeper molecular resolution at defined loci. Here, we describe a detailed protocol for flap-enabled next-generation capture (FENGC), a cost-effective method for targeted, multiplexed enrichment of DNA sequences for epigenetic and genetic analysis. FENGC precisely excises and enriches tens to hundreds of user-defined targets, generating sequencing-ready libraries with superior on-target rates compared to existing methods, all at a fraction of the cost. When paired with MAPit, the MAPit-FENGC platform enables single-molecule resolution of CpG methylation patterns in the context of chromatin architecture and transcription factor occupancy.

Indexed as

ChromatinDNA MethylationHigh-Throughput Nucleotide SequencingSingle Molecule ImagingAnimalsCpG IslandsDNAHumansSequence Analysis, DNAChromatinDNAChromatin accessibilityDNA methylationEpigeneticsFlap endonucleaseSingle molecule footprintingTargeted sequencing

What OpenQuestion holds

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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.