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CHHM: a Manually Curated Catalogue of Human Histone Modifications Revealing Hotspot Regions and Unique Distribution
Wendong Ma1, Xiaofan Ding1, Jiajia Xu1
1Institute of Translational Medicine, Centre for Precision Medicine Research and Training, MoE Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, 999078, China.
Insights
A new curated catalogue of human histone modifications (CHHM) integrates scattered data, revealing insights into epigenetic control and disease. CHHM provides a user-friendly resource for researchers studying histone modifications and transcriptional regulation.
Area of Science:
- Epigenetics and Molecular Biology
- Genomics and Proteomics
Background:
- Histone modifications are crucial for epigenetic control, regulating biological processes and disease development.
- Existing human histone modification data are fragmented across multiple databases, hindering comprehensive research.
Purpose of the Study:
- To create a unified, curated catalogue of human histone modifications (CHHM).
- To provide a user-friendly resource with evidence confidence levels for researchers.
- To offer new insights into histone modification mechanisms and epigenetic control.
Main Methods:
- Manual retrieval and integration of modification records from 10 knowledgebases/databases and 3 articles.
- Evidence assessment and curation of 6612 nonredundant modification entries.
- Inclusion of 31 modification types, 2 histone-DNA crosslinks, and data across various histone variants (H1, H2A, H2B, H3, H4).
Main Results:
- The CHHM catalogue contains 6612 nonredundant human histone modification entries.
- Acylation modifications represent the most abundant type, highlighting the role of cellular metabolism.
- Uneven distribution across histone families suggests differential susceptibility to modifications, with identified hotspot regions.
Conclusions:
- CHHM serves as a valuable resource for biomedical, clinical, and basic research on histone modifications.
- The catalogue facilitates research on transcriptional regulation and epigenetic mechanisms.
- Findings suggest a significant link between cellular metabolic status and epigenetic control.
Abstract:
Histone modification is one of the key elements in epigenetic control and plays important roles in regulation of biological processes and disease development. Currently, records of human histone modifications with various levels of confidence in evidence are scattered in various knowledgebases and databases. In the present study, a curated catalogue of human histone modifications, CHHM, was obtained by manual retrieval, evidence assessment, and integration of modification records from 10 knowledgebases/databases and 3 complementary articles. CHHM contains 6612 nonredundant modification entries covering 31 types of modifications (including 9 types of emerging modifications) and 2 types of histone-DNA crosslinks, that were identified in 11 H1 variants, 21 H2A variants, 21 H2B variants, 9 H3 variants, and 2 H4 variants. For ease of visualization and accessibility, modification entries are presented with aligned protein sequences in an Excel file. Confidence level in evidence is provided for each entry. Acylation modifications contribute to the highest number of modification entries in CHHM. This supports that cellular metabolic status plays a very important role in epigenetic control. CHHM reveals modification hotspot regions and uneven distribution of the modification entries across the histone families. Such uneven distribution may suggest that a particular histone family is more susceptible to certain types of modifications. CHHM not only serves as an important and user-friendly resource for biomedical and clinical researches involving histone modifications and transcriptional regulation, but also provides new insights for basic researches in the mechanism of human histone modifications and epigenetic control.
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