Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing

Xudong Liu; Ying Ni; Dandan Wang; Silin Ye; Mengsu Yang; Xuan Sun; Anskar Yu Hung Leung; Runsheng Li

doi:10.1038/s41597-023-02431-5

Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing

Xudong Liu (Co-first Author)
, Ying Ni (Co-first Author)
, Dandan Wang
, Silin Ye
, Mengsu Yang
, Xuan Sun
, Anskar Yu Hung Leung^*
, Runsheng Li^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

5 Citations (Scopus)

76 Downloads (CityUHK Scholars)

Abstract

Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%-80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders.

© The Author(s) 2023

Original language	English
Pages (from-to)	532
Journal	Scientific Data
Volume	10
Online published	10 Aug 2023
DOIs	https://doi.org/10.1038/s41597-023-02431-5
Publication status	Published - 2023

Bibliographical note

Funding

This work was supported by the Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (SMSEGL20SC02), Early career scheme (project number 9048204) from the Hong Kong Research Grant Council, Hong Kong Health and Medical Research Fund (project number 9211280) and new Research Initiatives support from City University of Hong Kong (project number 9610497) to R.L, and was supported by Hetao Shenzhen-Hong Kong Science and Technology Innovation Cooperation Zone Shenzhen Park Project (HZQB-KCZYZ-2021017) and City University of Hong Kong (project number 9680217 and number 9678223) to M.Y; and was supported by Theme-based Research Scheme (T12-702/20-N), Technology Start-up Support Scheme for Universities (TSSSU/HKU/22/12/1), Incu-Bio Programme, HKSTP, and NSFC/RGC Joint Research Scheme (N_HKU745/21) to A.Y.H.L.

Research Keywords

Animals
CpG Islands
DNA Methylation
Epigenesis, Genetic
High-Throughput Nucleotide Sequencing/methods
Nanopore Sequencing
Sequence Analysis, DNA/methods
Zebrafish/genetics
Hematopoiesis/genetics

Publisher's Copyright Statement

This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

RGC Funding Information

RGC-funded

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10.1038/s41597-023-02431-5

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1 Finished
1 Active

HMRF: Subtyping CN-AML with Modification Biomarkers Using Nanopore Sequencing
LI, R. (Principal Investigator / Project Coordinator) & Leung, A. Y. H. (Co-Investigator)
1/11/21 → …
Project: Research
ECS: Towards A Better Understanding of rDNA in Caenorhabditis Species Using Long-Read Sequencing
LI, R. (Principal Investigator / Project Coordinator)
1/01/22 → 22/12/25
Project: Research

Cite this

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title = "Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing",

abstract = "Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4\% vs 70\%-80\%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders. {\textcopyright} The Author(s) 2023",

keywords = "Animals, CpG Islands, DNA Methylation, Epigenesis, Genetic, High-Throughput Nucleotide Sequencing/methods, Nanopore Sequencing, Sequence Analysis, DNA/methods, Zebrafish/genetics, Hematopoiesis/genetics",

author = "Xudong Liu and Ying Ni and Dandan Wang and Silin Ye and Mengsu Yang and Xuan Sun and Leung, \{Anskar Yu Hung\} and Runsheng Li",

note = "{\textcopyright} 2023. Springer Nature Limited.",

year = "2023",

doi = "10.1038/s41597-023-02431-5",

language = "English",

volume = "10",

pages = "532",

journal = "Scientific Data",

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TY - JOUR

T1 - Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing

AU - Liu, Xudong

AU - Ni, Ying

AU - Wang, Dandan

AU - Ye, Silin

AU - Yang, Mengsu

AU - Sun, Xuan

AU - Leung, Anskar Yu Hung

AU - Li, Runsheng

PY - 2023

Y1 - 2023

N2 - Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%-80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders. © The Author(s) 2023

AB - Zebrafish is a widely used model organism for investigating human diseases, including hematopoietic disorders. However, a comprehensive methylation baseline for zebrafish primary hematopoietic organ, the kidney marrow (KM), is still lacking. We employed Oxford Nanopore Technologies (ONT) sequencing to profile DNA methylation in zebrafish KM by generating four KM datasets, with two groups based on the presence or absence of red blood cells. Our findings revealed that blood contamination in the KM samples reduced read quality and altered methylation patterns. Compared with whole-genome bisulfite sequencing (WGBS), the ONT-based methylation profiling can cover more CpG sites (92.4% vs 70%-80%), and exhibit less GC bias with more even genomic coverage. And the ONT methylation calling results showed a high correlation with WGBS results when using shared sites. This study establishes a comprehensive methylation profile for zebrafish KM, paving the way for further investigations into epigenetic regulation and the development of targeted therapies for hematopoietic disorders. © The Author(s) 2023

KW - Animals

KW - CpG Islands

KW - DNA Methylation

KW - Epigenesis, Genetic

KW - High-Throughput Nucleotide Sequencing/methods

KW - Nanopore Sequencing

KW - Sequence Analysis, DNA/methods

KW - Zebrafish/genetics

KW - Hematopoiesis/genetics

U2 - 10.1038/s41597-023-02431-5

DO - 10.1038/s41597-023-02431-5

M3 - RGC 21 - Publication in refereed journal

C2 - 37563176

SN - 2052-4463

VL - 10

SP - 532

JO - Scientific Data

JF - Scientific Data

ER -

Unraveling the whole genome DNA methylation profile of zebrafish kidney marrow by Oxford Nanopore sequencing

Abstract

Bibliographical note

Funding

Research Keywords

Publisher's Copyright Statement

RGC Funding Information

Access Output

Other Access Options

Permanent Link

Fingerprint

Projects

HMRF: Subtyping CN-AML with Modification Biomarkers Using Nanopore Sequencing

ECS: Towards A Better Understanding of rDNA in Caenorhabditis Species Using Long-Read Sequencing

Cite this