Histone crotonylation in neurobiology: to be or not to be?

Have you ever wondered how a single stem cell in an embryo becomes the billions of specialized neurons in your brain? The answer lies in epigenetics—the chemical changes that control which genes are turned on or off without altering DNA itself. While histone acetylation and methylation are well-known epigenetic players, a lesser-known modification called histone crotonylation is emerging as a key regulator of brain development and function. But what exactly does crotonylation do in the nervous system, and why does it matter for our health?

What is histone crotonylation?

Histones are proteins that package DNA into a compact structure called chromatin. Crotonylation is a chemical modification that attaches a crotonyl group (a short-chain fatty acid) to specific lysine (K) amino acids on histones. Think of it as a “loosening” signal: when crotonylation occurs, it opens up chromatin, making DNA more accessible to the molecular machinery that reads genes (a process called transcription).

Scientists categorize the molecules that control crotonylation into three groups:

Writers: Enzymes like P300 and GCN5 that add crotonyl groups to histones.
Erasers: Enzymes like class I histone deacetylases (HDACs) and Sirtuins 1–3 that remove crotonyl groups.
Regulators: Proteins like ECHS1 (short-chain enoyl-CoA hydratase) and CDYL (chromodomain-Y-like) that control the availability of crotonyl-CoA—the molecule needed for crotonylation.

Key crotonylation sites on histones include H3K18cr, H2BK12cr, H3K9cr, and H3K27cr—specific spots that act like molecular switches for gene activity. What makes crotonylation unique? Even though it shares tools with acetylation (another histone modification), it acts differently: crotonylation and acetylation occur at different times and places in chromatin, meaning they control distinct sets of genes.

Crotonylation’s role in neurobiology: The case of neural stem cells

Neural stem cells (NSCs) are the “building blocks” of the brain—they can either stay in a “stem” state (able to divide) or differentiate into neurons, astrocytes, or oligodendrocytes. Recent research from Liu’s lab at the Institute of Zoology (Chinese Academy of Sciences) has shed light on how crotonylation guides this decision.

Using multi-omics techniques—including RNA sequencing (to map gene activity), ChIP-seq (to track histone modifications), and ATAC-seq (to measure chromatin accessibility)—the team analyzed embryonic forebrain tissue. They found that H3K9cr (crotonylation at lysine 9 of histone H3) enriches in the promoter regions (gene “start sites”) of genes linked to NSC maintenance and differentiation.

Here’s the breakthrough: NSCs rely on bivalent promoters—regions of DNA that are “poised” to turn genes on or off. Crotonylation activates these promoters by:

Loosening chromatin (making DNA accessible),
Recruiting RNA polymerase II (the enzyme that reads DNA into RNA),
Reprogramming the “transcriptome” (all active genes) to push NSCs toward neuronal differentiation.

A follow-up study from the same group mapped how crotonylation and another modification, lactylation (H3K18la), change dynamically during neural development. Together, these studies create an epigenetic blueprint for how NSCs make fate decisions—expanding our understanding of brain development at the molecular level.

Open questions: What we still don’t know

For all the progress, crotonylation’s role in neurobiology is far from fully understood. Key unanswered questions include:

Which sites matter most? While “pan-crotonylation” (crotonylation across all histone sites) is linked to NSC stemness, we don’t know which specific sites (e.g., H3K9cr vs. H3K18cr) are critical for guiding NSC fate in living organisms (in vivo).
How does crotonylation interact with other epigenetics? NSCs are regulated by multiple modifications—acetylation (H3K9ac), methylation (H3K4me3), lactylation (H3K18la), and DNA methylation. Integrating these data with single-cell RNA sequencing could reveal how they work together, but it’s a complex puzzle.
What’s the mechanism? While a “histone Kcr-miR-203-Bmi1” axis has been suggested, we don’t know exactly how crotonylation controls specific genes (via promoters, enhancers, or other elements) to reshape the transcriptome.

Clinical implications: Crotonylation and neurological disease

The real promise of crotonylation lies in its potential to explain—and treat—neurological disorders. Here’s what we know so far:

1. Developmental brain disorders

Mice with BTBR T+Itpr3tf/J, a model for conditions like autism, have elevated crotonylation in their brains. This suggests dysregulation could contribute to abnormal neuroanatomy and function.

2. Neurodegeneration

Mutations in ECHS1 (a crotonylation regulator) cause Leigh syndrome, a devastating childhood neurodegenerative disease. ECHS1 knockout mice die in embryos, likely due to defects in neuronal development—linking crotonylation to survival.

3. Epilepsy

CDYL, another crotonylation regulator, suppresses epilepsy in mice by reducing axonal sodium channel (Nav1.6) activity. A genome-wide study linked CDYL to responsiveness to ketogenic diets in drug-resistant epilepsy—hinting that crotonylation could be a target for improving treatment.

4. Depression

CDYL-mediated crotonylation also regulates stress-induced depressive behaviors in mice. While how this translates to humans is unclear, it opens a new avenue for studying mood disorders.

5. Gut-brain axis

Crotonate, the molecule needed for crotonylation, is produced by gut bacteria. This suggests that gut health could influence brain development and function via crotonylation—a rapidly growing area of research with implications for conditions like anxiety and Alzheimer’s.

Conclusion: Crotonylation is here to stay

Histone crotonylation is no longer a niche topic—it’s a central player in neurobiology. Studies from Liu’s lab and others have shown it controls NSC fate by activating key genes, but we’re just beginning to unravel its full potential.

The next steps are clear: identify which crotonylation sites are most critical for NSC behavior in vivo, map how crotonylation interacts with other epigenetic marks, and translate these findings into treatments for neurological diseases. For example, targeting crotonylation regulators like ECHS1 or CDYL could help restore normal gene activity in conditions like Leigh syndrome or epilepsy.

One thing is certain: crotonylation is “to be”—a vital area of research that could transform our understanding of the brain and offer new hope for patients with neurological disorders.

Cechuan Deng1,2, Jia-Hua Qu3, InKyeom Kim4,5,6, Xiaoqiang Tang1
1Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China;
2Department of Medical Genetics, Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China;
3Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA;
4Department of Pharmacology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea;
5Cardiovascular Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea;
6Department of Biomedical Science, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.

Original study published in: Chinese Medical Journal 2022;135(9):1036–1038.
doi.org/10.1097/CM9.0000000000001945

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