Evidence map›Paper›PMID 42124676›Full record

ArticlebioRxiv : the preprint server for biology2026

LEMONmethyl-seq: Targeted long-read DNA methylation profiling reveals dynamics of CRISPR epigenome editing and endogenous DNA methylation patterns.

Anna E Christenson, Nikita S Divekar, Justin P Lubin, Luis G Palma, Peter J Colias, Rithu K Pattali, Da Xu, Akane Hubbard, Katie Lin, Ngan T Phan and 4 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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

14 authors.

Anna E ChristensonDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Nikita S DivekarDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Justin P LubinDepartment of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.
Luis G PalmaDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Peter J ColiasDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Rithu K PattaliDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Da XuDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Akane HubbardDepartment of Radiation Oncology, University of California San Francisco, San Francisco, United States.
Katie LinDepartment of Radiation Oncology, University of California San Francisco, San Francisco, United States.
Ngan T PhanDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Bernardo D MorenoDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Sarah E ChasinsDepartment of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.
S John LiuDepartment of Radiation Oncology, University of California San Francisco, San Francisco, United States.
James K NuñezDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.

Funding

Mechanisms of epigenetic memory in human cellsR35GM155044 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI James Karlo Nunez · 2024 to 2026
$1.2M
NIGMS NIH HHS R35 GM155044
6 · The paper itself

Abstract

backgroundDNA methylation is the most prevalent epigenetic modification in human cells and undergoes dynamic changes during cell differentiation, disease progression, and aging. Here, we introduce Locus-Enriched Mapping Of Nucleotide methylation (LEMONmethyl-seq): an optimized, cost-effective pipeline for single-nucleotide detection of DNA methylation using locus-specific amplification and long-read DNA sequencing.

resultsWe apply LEMONmethyl-seq to profile DNA methylation of endogenous gene promoters across different cell types along with DNA methylation establishment and long-range propagation induced by CRISPR epigenome editing technologies. We profile dynamic changes in DNA methylation patterns on transposable element genomic loci during global epigenetic resetting in stem cells, and we identify site-specific enrichment of non-canonical CpH methylation on genomic sites in stem cells and cultured neurons. Lastly, we apply LEMONmethyl-seq to profile DNA methylation across the

conclusionsTogether, LEMONmethyl-seq serves as a cost-effective, long-read DNA methylation sequencing pipeline that advances methods for detecting DNA methylation patterns and dynamics in mammalian cells. We envision its broad use for studying chromatin pathways, diagnostics, and therapeutic applications.

Indexed as

biomarkerCpH methylationCRISPRDNA methylationepigeneticslong-read sequencing

Identifiers

PMID42124676
PMCPMC13160167

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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.