Evidence map›Paper›PMID 38965385›Full record

ArticleNature chemical biology2025

Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1.

Kwangwoon Lee, Marco Barone, Amanda L Waterbury, Hanjie Jiang, Eunju Nam, Sarah E DuBois-Coyne, Samuel D Whedon, Zhipeng A Wang, Jonatan Caroli, Katherine Neal and 7 more

Abstract read
In one paragraph

Article in Nature chemical biology, 2025. 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. Review
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. Review
  9. Article
  10. Circular Engineered Sortase for Interrogating Histone H3 in Chromatin.Journal of the American Chemical Society · 2024
    Article
  11. A circular engineered sortase for interrogating histone H3 in chromatin.bioRxiv : the preprint server for biology · 2024
    Article
  12. 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

17 authors.

Kwangwoon Lee *Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.ORCID 0000-0002-2021-5186
Marco Barone *Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy.ORCID 0000-0001-7184-2940
Amanda L WaterburyDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.ORCID 0000-0002-4473-2866
Hanjie JiangDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.ORCID 0000-0001-6090-4552
Eunju NamDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.ORCID 0000-0003-0801-9331
Sarah E DuBois-CoyneDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
Samuel D WhedonDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.ORCID 0000-0002-3745-5645
Zhipeng A WangDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.ORCID 0000-0002-5693-7359
Jonatan CaroliDepartment of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy.
Katherine NealDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.ORCID 0000-0003-4171-1944
Brian IbeabuchiDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
Zuzer DhoondiaDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.ORCID 0000-0002-0390-8140
Mitzi I KurodaDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.ORCID 0000-0003-0840-3608
Brian B LiauDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.ORCID 0000-0002-2985-462X
Samuel BeckDepartment of Dermatology, Boston University School of Medicine & Boston Medical Center, Boston, MA, USA. sambeck@bu.edu.ORCID 0000-0002-0184-8367
Andrea MatteviDepartment of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy. andrea.mattevi@unipv.it.ORCID 0000-0002-9523-7128
Philip A ColeDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA. pacole@bwh.harvard.edu.ORCID 0000-0001-6873-7824

Funding

Protein Acylation and Methylation Mechanisms_Administrative SupplementR37GM062437 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI COLE, PHILIP A · 2013 to 2022
$4.1M
Mechanisms &Inhibition of Histone AcetyltransferasesR01GM062437 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI COLE, PHILIP A · 2001 to 2012
$3.8M
Epigenetic regulation of transcriptional programmingR35GM126944 · NIGMS · BRIGHAM AND WOMEN'S HOSPITAL · PI KURODA, MITZI I · 2018 to 2022
$3.3M
Mapping Structure-Activity Relationships of Chemical Inhibitors via Genome-EditingDP2GM137494 · NIGMS · HARVARD UNIVERSITY · PI LIAU, BRIAN · 2019 to 2019
$2.5M
Loss of transcriptional homeostasis of genes lacking CpG islands during agingR01AG068179 · NIA · MOUNT DESERT ISLAND BIOLOGICAL LAB · PI BECK, SAMUEL · 2021 to 2025
$2.3M
Chemical Genetic Approaches to Study Chromatin ComplexesR01CA274437 · NCI · HARVARD UNIVERSITY · PI Brian Liau · 2023 to 2026
$2.2M
Chemical Approaches to Understanding Reversible Lysine ModificationsR35GM149229 · NIGMS · BRIGHAM AND WOMEN'S HOSPITAL · PI PHILIP A COLE · 2023 to 2026
$1.9M
Chromatin architecture disruption and the vicious cycle of aging.R56AG082796 · NIA · BOSTON UNIVERSITY MEDICAL CAMPUS · PI BECK, SAMUEL · 2023 to 2023
$413k
American Cancer Society (American Cancer Society, Inc.) PF20-105-01-DMCAmerican Heart Association (American Heart Association, Inc.) 826614Charles A. King Trust N/ALeukemia and Lymphoma Society (Leukemia & Lymphoma Society) SCORNIA NIH HHS R01 AG068179NIA NIH HHS R56 AG082796NIGMS NIH HHS DP2 GM137494NIGMS NIH HHS R01 GM062437NIGMS NIH HHS R35 GM126944NIGMS NIH HHS R35 GM149229NIGMS NIH HHS R37 GM062437U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) DP2GM137494U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) GM126944U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) GM149229U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging) AG068179
6 · The paper itself

Abstract

Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.

Indexed as

Histone CodeHistone DemethylasesHistonesProtein EngineeringAcetylationEpigenesis, GeneticHumansK562 CellsLysineHistone DemethylasesHistonesKDM1A protein, humanLysine

Identifiers

PMID38965385
PMCPMC11699879

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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.