Introduction: Decoding Chromatin Regulation in DNA Damage Repair

DNA double-strand breaks (DSBs) are among the most severe forms of DNA damage and must be efficiently repaired to maintain genome stability. Following DNA damage, rapid remodeling of chromatin structure is essential to create an accessible environment for the recruitment of DNA repair factors. Histone post-translational modifications (PTMs), particularly acetylation, are key regulators of chromatin organization and dynamics.

Histone H1 plays an important role in maintaining higher-order chromatin structure by promoting chromatin compaction through its interaction with nucleosomes. However, how PTMs of histone H1 regulate chromatin relaxation and facilitate DNA repair has remained poorly understood.

A study led by Professor Weiguo Zhu and his team at Shenzhen University, published in Nature, titled “Histone H1 deamidation facilitates chromatin relaxation for DNA repair,” has now uncovered a previously unrecognized regulatory mechanism linking histone H1 deamidation to acetylation and chromatin remodeling during DNA damage repair.

Research Discovery: Histone H1 Deamidation Facilitates Chromatin Relaxation

Using a combination of proteomics, PTM profiling, site-specific modification analysis, and antibody-based validation, the researchers identified a critical role for histone H1 deamidation in the DNA damage response.

Following DNA damage, the three major histone H1 isoforms—H1.2, H1.3, and H1.4—showed reduced positive charge, with H1.4 exhibiting the strongest chromatin-condensing activity. Mass spectrometry analysis further revealed that deamidation at Asn76 and Asn77 of H1.4 (H1-N76/N77) was one of the most prominent modification events induced by DNA damage.

Functional experiments demonstrated that this deamidation event is essential for efficient DNA repair. Cells lacking H1.4 displayed impaired DNA repair capacity, whereas expression of the deamidation-mimetic H1.4-2ND mutant restored repair efficiency.

Importantly, the researchers identified CTP synthase 1 (CTPS1) as the enzyme responsible for catalyzing H1 deamidation. Following DNA damage, phosphorylation of CTPS1 at Ser575 promotes its recruitment to DSB sites, where it catalyzes deamidation of H1.4 at N76/N77.

These findings revealed that histone H1 deamidation is not simply a consequence of DNA damage, but instead functions as an active regulatory signal in the DNA damage response.

Core Mechanistic Insight: A Deamidation–Acetylation Cascade Controls Chromatin Accessibility

The study further uncovered a functional connection between H1 deamidation and acetylation.

Using acetylation proteomics together with histone acetylation site-specific antibodies, the researchers found that H1-N76/N77 deamidation is a prerequisite for acetylation at the neighboring H1-K75 site (H1K75ac) following DNA damage.

H1K75 acetylation increased rapidly after DNA damage and closely overlapped with the distribution of H1-N76/N77 deamidation. Further experiments identified p300 as the acetyltransferase responsible for H1K75 acetylation.

Mechanistically, CTPS1-mediated H1 deamidation promotes the interaction between H1.4 and p300, thereby facilitating H1K75 acetylation. This establishes a sequential regulatory cascade:

DNA Damage → CTPS1 Recruitment → H1-N76/N77 Deamidation → p300 Recruitment → H1K75 Acetylation → Chromatin Relaxation → DNA Repair

Functional analyses demonstrated that these modifications contribute directly to chromatin accessibility. Mutations disrupting H1 deamidation or H1K75 acetylation resulted in more compact chromatin, whereas deamidation- or acetylation-mimetic mutants promoted a more relaxed chromatin state.

Together, the findings establish a previously unrecognized deamidation–acetylation cascade that links DNA damage sensing to chromatin remodeling and repair factor recruitment.

PTM BIO Technology Contribution: From Modification Discovery to Site-Specific Validation

The mechanistic insights in this study were supported by an integrated proteomics and PTM analysis workflow, with PTM BIO providing technical support in proteomics, acetylation proteomics, modification site identification, and modification-specific antibody development.

Deep Proteomics Reveals DNA Damage-Responsive Modifications

Mass spectrometry-based proteomic analysis enabled the researchers to systematically investigate protein and PTM changes associated with DNA damage.

The identification of H1.4 N76/N77 deamidation highlighted the power of MS-based proteomics for uncovering modification events that may otherwise remain difficult to detect using conventional approaches.

By combining proteomic discovery with downstream functional experiments, the researchers were able to move from modification profiling to mechanistic investigation of how H1 PTMs influence DNA repair.

Acetylation Proteomics Maps the H1K75ac Regulatory Event

To investigate whether H1 deamidation was linked to other PTMs, the research team employed acetylation proteomics to profile acetylation changes associated with DNA damage.

This analysis helped identify H1K75ac as a critical modification associated with H1 deamidation. Subsequent experiments using histone-specific acetylation antibodies further validated the DNA damage-induced increase of H1K75ac and its dependence on H1-N76/N77 deamidation.

The combination of global modification profiling and targeted validation provided complementary evidence for establishing the sequential relationship between the two PTMs.

Site-Specific Antibody Development Enables Precise Validation

Precise validation of histone modifications is essential for distinguishing specific PTM events from global changes in protein abundance or modification levels.

For this study, PTM BIO provided a site-specific antibody targeting the H1 N76/N77 deamidation state, supporting the validation of this previously characterized modification event.

The integration of mass spectrometry-based site identification, PTM-specific antibody validation, and genetic mutagenesis enabled the researchers to establish a robust connection between individual modification sites and their biological functions.

Scientific Impact: Linking PTM Crosstalk to Cancer Therapy

The discovery extends the current understanding of how histone H1 regulates chromatin dynamics during DNA damage repair.

Rather than acting independently, histone PTMs can function through sequential or interdependent regulatory events. In this study, H1 deamidation and H1K75 acetylation form a coordinated PTM cascade that promotes chromatin relaxation and facilitates DNA repair.

The findings also reveal a potential therapeutic connection. CTPS1-deficient cells showed reduced survival following DNA damage and increased sensitivity to irradiation and VP16 treatment. In vivo, tumors derived from CTPS1-knockout cells exhibited greater growth inhibition following irradiation.

Furthermore, higher CTPS1 expression was associated with increased radioresistance in cancer cell lines and correlated with poorer outcomes in clinical cervical cancer samples.

These findings suggest that CTPS1 may represent a potential target for radiosensitization, providing a new perspective for exploring strategies to improve cancer radiotherapy.

More broadly, the study highlights how integrated proteomics and PTM analysis can uncover functional connections between seemingly distinct modification systems and reveal new layers of regulation in DNA damage responses.

PTM BIO: Empowering PTM Discovery and Mechanistic Research

Understanding the functional roles of protein modifications often requires more than modification profiling alone. Identifying a modification site is only the first step toward establishing its biological significance.

PTM BIO provides integrated research solutions spanning:

Proteomics for comprehensive protein profiling and discovery

Acetylation Proteomics for global characterization of protein acetylation

PTM Site Identification for precise characterization of modification sites

Modification-Specific Antibodies for site-specific experimental validation

Custom Antibody Development for emerging and newly identified PTM sites

Targeted Validation to strengthen mechanistic evidence

By integrating MS-based discovery, modification site identification, antibody-based validation, and bioinformatics analysis, PTM BIO helps researchers build a complete research workflow from:

PTM Discovery → Site Identification → Specific Validation → Mechanistic Investigation

The Nature study by Professor Weiguo Zhu's team demonstrates how this integrated strategy can help uncover previously unknown PTM crosstalk and connect molecular modifications with chromatin remodeling, DNA repair, and therapeutic response.

As a proteomics-driven research partner, PTM BIO is committed to helping scientists decode the complexity of protein modifications and uncover new mechanisms across cancer biology, DNA damage response, epigenetics, and precision medicine.