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DNA Methylation Across Primary Motor Cortex at Single-cell Resolution

Shi, Dengxiaoyu (2022) DNA Methylation Across Primary Motor Cortex at Single-cell Resolution. Master's Thesis, University of Pittsburgh. (Unpublished)

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As an essential epigenetic modification, DNA methylation is involved in many disease progressions that are not yet well understood. Recently developed single-nucleus methyl-3C sequencing (snm3C-seq) enables us to profile DNA methylation and 3D genome structures simultaneously from single cells. With this technology, we can picture gene regulation, which provides insights to possible causes and potential treatment targets for human diseases.

In this paper, we analyzed the snm3C-seq data from two tissue samples of the human primary motor cortex (M1) using the Allcools package. We identified 29 cell types in M1 based on 100kb-bin level CG and non-CG (CH) DNA methylation. We also identified and compared the top 2 and top 10 differentially methylated genes for each cluster compared to the rest clusters. Comparing the methylation patterns of AD-related genes between these clusters, we observed that the CG methylation of APOE is significantly low in Astrocytes, and CG methylation of PSEN1 is significantly different between most neurons and non-neurons. Our findings could provide a new path for further studies of the cell type-specific or region-specific methylation signatures in brain diseases.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Shi, Dengxiaoyudes220@pitt.edudes2200000-0001-6373-7198
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairCarlson, Jenna C.jnc35@pitt.edujnc35
Committee MemberPark, Hyun Junghyp15@pitt.eduhyp15
Committee MemberYouk, Ada O.ayouk@pitt.eduayouk
Committee MemberBuchanich, Jeanine M.jeanine@pitt.edujeanine
Date: 16 May 2022
Date Type: Publication
Defense Date: 25 April 2022
Approval Date: 16 May 2022
Submission Date: 29 April 2022
Access Restriction: 2 year -- Restrict access to University of Pittsburgh for a period of 2 years.
Number of Pages: 78
Institution: University of Pittsburgh
Schools and Programs: School of Public Health > Biostatistics
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: Methylation, Single cell, Alzheimer's
Related URLs:
Date Deposited: 16 May 2022 13:55
Last Modified: 16 May 2024 05:15


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