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Dissertation/Thesis Abstract

The Formation and Function of Lineage Specific Nuclear Topologies during Cellular Differentiation
by Neems, Daniel, Ph.D., Northwestern University, 2016, 145; 10044036
Abstract (Summary)

DNA is the physical medium for information storage inside of cells. Sub-regions of the DNA composed of linear stretches of nucleic acid sequences (DNA sequences), known as genes are the basic unit of storage in the human genome. Genes contain a myriad different types of information, of which a major class is protein coding genes. As the name suggests these genes hold the information required to make proteins, which then go on to perform cellular function and consequently dictate cellular activity and identity. Genes themselves are further grouped through the physical lineage of being contained on the same macromolecule known as chromosomes. The entire complement of chromosomes makes up the genome of the organism. In the case of humans, which are diploid, the genome is made up of 22 sets of autosomes and one set of sex chromosomes, a total of 46 discrete chromosomes. During interphase of the cell cycle all 46 of these chromosomes are found inside the nucleus in partially condensed, largely discrete regions known as chromosome territories.

The positioning of chromosome territories and the genes within them is non-random and has previously been demonstrated to be a function of gene expression. In order for a gene to be expressed, its sequence must be accessible to the RNA polymerases (RNAPs) that transcribe it, not tightly compacted around histones in an inaccessible form known as heterochromatin. As different types of cells need different types of proteins to function, and thus different genes to be expressed, the regions of the genome that are found in heterochromatin are cell type specific. The location of gene locus inside the nucleus relative to other sub-nuclear features such as RNAPII foci, known as transcription factories, also dictate expression. This relationship results in the interphase genome forming a cell type specific topology which is the result of the expressed genes. In spite of the persistent observation of cell type specific nuclear topologies, the factors that guide the formation and the function of observed topologies remains unclear.

Here, we test the relationship between linear and three-dimensional (3D) organization of gene regulation during myogenesis. Our analysis indicates that a subset of human chromosomes is significantly enriched for topologically associated domains (TADs) that contain muscle-specific genes. These lineage-enriched TADs demonstrate an expression dependent pattern of nuclear organization that also affects the positioning of non-enriched TADs. Therefore, lineage-enriched TADs affect cell-specific genome organization during myogenesis. The allelic spatial proximity of one of these domains, which encodes myogenin, reduces transcriptional variability. Moreover, this cell-specific nuclear topology is dependent on cell division. We propose that the linear and spatial organization of gene locus is functionally inter-dependent and that mitosis is critical in establishing this behavior during cellular differentiation.

We then extend this analysis into murine lymphocyte development. Specifically, we look at naturally occurring suppressive T-regulatory cells (Tregs ) that dampen the strength/severity of the immune response and have been demonstrated to be clinically relevant in the emergence and pathogenesis of auto-immune disorders. T-regulatory cells are an interesting model for studying lineage specific nuclear topologies because during an active immune response they are a mixed population of natural Tregs and induced Tregs that phenocopy each other but have different developmental histories. There is also clinical interest in finding a reliable means to make a distinction between these two cell types for the potential treatment of auto-immune disease. By studying features of nuclear organization for two candidate genes, FoxP3 and Helios, and the chromosomes they reside on, X and one respectively, we were able to distinguish these two populations of cells on the basis of nuclear topologies. We propose this distinction is the result of differing nuclear topologies in the progenitor population in conjunction with only a sub-set of regions, such as LE-TADs, showing lineage specific localizations. This would lead to remnants of progenitor topologies in terminal lineages. We also make the interesting observation of unexpectedly high rates of coalescence between the active and inactive X chromosomes in cells that specifically express the X-linked gene FoxP3. This finding may lead to transvection based silencing of FoxP3 and the increase in autoimmunity observed in females.

Collectively, this body of work furthers the understanding of how lineage specific nuclear topologies emerge as a function of gene expression and greatly expands the current understanding of how these topologies exert influence over the expression of genes.

Indexing (document details)
Advisor: Kosak, Steven
Commitee: Adam, Stephen, Harris, Ann, Huang, Sui, McNally, Elizabeth
School: Northwestern University
Department: Life Sciences
School Location: United States -- Illinois
Source: DAI-B 77/08(E), Dissertation Abstracts International
Subjects: Biology
Keywords: Cell differentation, Gene expression/regulation, Gene loci/chromosome territory positioning, Oligonucleotide array sequence anaylsis, Transcriptional noise abstract:
Publication Number: 10044036
ISBN: 978-1-339-55489-1
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