Constrained Open Chromatin Regions Reveal Functional Elements Shaping Human Traits Article Swipe
Kohei Tomizuka
,
Masaru Koido
,
Akari Suzuki
,
Soichiro Yoshino
,
Nao Tanaka
,
Yuki Ishikawa
,
Xiaoxi Liu
,
Satoshi Koyama
,
Kazuyoshi Ishigaki
,
Yasuhiro Murakawa
,
Kazuhiko Yamamoto
,
Chikashi Terao
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.10.31.621195
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.10.31.621195
Open chromatin regions (OCRs) define cell-type-specific regulatory elements across the genome, yet their functional significance varies, making it challenging to pinpoint biologically essential regions. Here, we introduce CAMBUS (Chromatin Accessibility Mutation Burden Score), a machine-learning framework that identifies active and evolutionarily constrained OCRs by leveraging surrounding DNA sequences. Applying CAMBUS to 29 immune cell types, we identified 66,043 constrained OCRs, which were substantially enriched in the known constraint genome (odds ratio=11.45 (95% confidence interval 9.33-14.05), P=4.7 x 10-68), while 90% of these OCRs were not prioritized by existing constraint metrics. These OCRs were highly enriched for known enhancers and super-enhancers, independent of known epigenetic markers and annotated regions, and overlapped with regulatory elements implicated in immune-mediated diseases and experimentally validated functional variants, including rare variants, particularly in leukocyte-related traits. Furthermore, CAMBUS revealed cell-type-specific transcriptional regulatory landscapes, linking genetic constraint with gene regulation in immune cells and identifying plausible connections between 1,533 causal variants and 70 complex traits. By defining biologically constrained regulatory elements at high resolution, CAMBUS provides a framework for understanding the selective pressures shaping the non-coding genome and its role in human health and disease.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.10.31.621195
- https://www.biorxiv.org/content/biorxiv/early/2024/11/01/2024.10.31.621195.full.pdf
- OA Status
- green
- References
- 74
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4403964620Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2024.10.31.621195Digital Object Identifier
- Title
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Constrained Open Chromatin Regions Reveal Functional Elements Shaping Human TraitsWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2024Year of publication
- Publication date
-
2024-11-01Full publication date if available
- Authors
-
Kohei Tomizuka, Masaru Koido, Akari Suzuki, Soichiro Yoshino, Nao Tanaka, Yuki Ishikawa, Xiaoxi Liu, Satoshi Koyama, Kazuyoshi Ishigaki, Yasuhiro Murakawa, Kazuhiko Yamamoto, Chikashi TeraoList of authors in order
- Landing page
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https://doi.org/10.1101/2024.10.31.621195Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2024/11/01/2024.10.31.621195.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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-
greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2024/11/01/2024.10.31.621195.full.pdfDirect OA link when available
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| publication_year | 2024 |
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