Evidence map›Paper›PMID 39012589›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities.

Z Begum Yagci, Gautami R Kelkar, Tyler J Johnson, Dilara Sen, Albert J Keung

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Epigenetic editing: from concept to clinic.Nature reviews. Drug discovery · 2026
    Review
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

5 authors.

Z Begum Yagci *Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
Gautami R Kelkar *Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
Tyler J Johnson *Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
Dilara Sen *Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
Albert J KeungDepartment of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA. ajkeung@ncsu.edu.

Funding

The Epigenome in Substance Abuse Disorders: Engineering New Tools to Dissect Function from FormDP1DA044359 · NIDA · NORTH CAROLINA STATE UNIVERSITY RALEIGH · PI KEUNG, ALBERT · 2017 to 2021
$2.7M
Intracellular CRISPR gRNA assembly for massively multiplexed, one pot, (epi)genetic screeningR21CA240162 · NCI · NORTH CAROLINA STATE UNIVERSITY RALEIGH · PI KEUNG, ALBERT · 2019 to 2021
$529k
Engineering locus-specific binders to DNA modificationsR21GM135827 · NIGMS · NORTH CAROLINA STATE UNIVERSITY RALEIGH · PI KEUNG, ALBERT · 2023 to 2024
$418k
NCI NIH HHS R21 CA240162NIDA NIH HHS DP1 DA044359NIGMS NIH HHS R21 GM135827NSF grants EFMA-1830910NSF grants MCB 2144539
6 · The paper itself

Abstract

The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors (EEs) enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus-specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here, we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to: account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus-specificity by considering concentration, affinity, avidity, and sequestration effects.

Indexed as

ChromatinGene EditingAnimalsCRISPR-Cas SystemsEpigenesis, GeneticEpigenomeEpigenomicsGenetic LociHumansChromatinBiochemical specificityChromatin modifiersCRISPRDNA-binding domainEpigenome engineeringLocus specificityTranscription activator-like effectorsZinc finger proteins

Identifiers

PMID39012589

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.