Genomic and microscopic dissection of large-scale chromatin compaction

Large-scale chromatin compaction varies across the human genome, and these variations correlate with differences in transcriptional activity in a limited number of model systems. However, without validated genome-wide methods directly measuring large-scale chromatin compaction, the degree to which this level of chromatin organization correlates with defined features of genome organization remains unknown. Existing methods assess chromatin compaction indirectly, based on, for example, the accessibility of DNA to enzymes or susceptibility to mechanical shear, and probe lower--level chromatin organization, primarily at the nucleosome level. Therefore, these existing measures of chromatin compaction may not translate to measurements of large-scale chromatin compaction. In this dissertation I explore new methods for measuring large-scale chromatin compaction using genomic and microcopic tools. I have developed a new genomic method, based on TSA-seq, to measure chromatin compaction. TSA-Seq is a genomic method that directly probes the average physical distances of chromosome loci relative to different nuclear structures. Here I use the first derivative, or slope, of the TSA-Seq signal to identify unusually decondensed large-scale chromatin domains (DLCDs). These DLCDs have an average size of ~70 kb and correlate with nearby enrichment of active chromatin marks, enhancers and especially super-enhancers, and cohesin and CTCF binding sites. They map closely to a large fraction of genome organization domain boundaries identified by Hi-C, LAD/innerLAD boundaries defined by lamin B1 DamID, and rapid transitions in the Hi-C principal eigenvector signal. Moreover, cluster analysis reveals DLCDs map most frequently to divisions between chromatin domains of varying epigenetic marks. To validate the existence of DLCDs, I have created a digital image processing package, Angler, for analyzing DNA--FISH experiments with minimal supervision using established computer vision algorithms. Angler can measure spatial properties of FISH loci in a high throughput manner. In conclusion, my results demonstrate the non-random placement of large-scale chromatin decondensed regions, which may contribute to the functional division of the genome into discrete and independently-regulated chromatin domains.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Cell and Developmental Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Gholamalamdari, Omid

Contributors dc:contributor

• Belmont, Andrew S
• Brieher, William M
• Freeman, Brian C
• Sinha, Saurabh

• chromatin structure
• compaction
• genome organization

Statement dc:rights

• Copyright 2021 Omid Gholamalamdari

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/113207

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/113207