The bone marrow (BM) is a crucial tissue involved in hematopoiesis and immune cell development. The construction of a comprehensive bone marrow atlas is essential to understand the regulatory mechanisms and functional characteristics of different cell types. My thesis is a contribution to a larger effort aimed at the generation of a Bone Marrow Atlas, with a special interest in non-hematopoietic cells. My contribution fo-cuses in the chromatin accessibility part based on Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data, therefore offering valuable insights into chromatin accessibility and gene regulation by transcription factors (TFs).
The work developed in the thesis can be divided in three parts: (i) identification of da-tasets of interest (data collection); (ii) processing the data: implementation of ATAC-seq pipeline, and (iii) a proof-of-concept on how to make sure of this data collection in research: a Shiny application and a use case.
The data collection included in the atlas have both in-house and publicly available ATAC-seq human paired data encompassing various cell types. ATAC-seq pipeline was imple-mented to process and analyze bone marrow samples, facilitating the identification of cell type-specific accessible chromatin regions. This analysis is composed by several es-sential steps to extract valuable information about chromatin accessibility and regulato-ry elements. These steps involve the preprocessing of raw sequencing data, alignment to a reference genome (hg38), peak calling to detect open chromatin regions (OCRs), and downstream analysis to associate TFs with the identified peaks.
The BM atlas incorporates the ATAC-seq data generated through this pipeline along with gene expression profiles produced from RNA-seq another project as part of the BM atlas. The combination of these techniques offers a comprehensive understanding of the bone marrow's molecular landscape and uncover the interplay between chromatin accessibility and gene expression.
To facilitate a user-friendly exploration of the BM atlas, we have developed an interac-tive R Shiny app. This app empowers researchers to navigate the atlas, visualize gene expression patterns, and investigate regulatory networks associated with bone marrow cell types. It serves as a powerful tool to unravel the intricate interplay between chro-matin accessibility, gene regulation, and TFs within the bone marrow context. Addition-ally, we created a user case study focusing on H1 linker histones, demonstrating their impact on chromatin accessibility, gene expression, and cell fate decisions across di-verse bone marrow cell types. This case study highlights the utility of the BM atlas in uncovering the role of specific epigenetic regulators in this tissue.
|Date of Award||Jun 2023|
|Original language||English (US)|
- Biological, Environmental Sciences and Engineering