University of Massachusetts Medical School Faculty Publications
UMMS Affiliation
Department of Biochemistry and Molecular Pharmacology
Publication Date
8-24-2016
Document Type
Article Preprint
Disciplines
Computational Biology | Genetic Phenomena | Genomics | Molecular Biology | Structural Biology | Systems Biology
Abstract
Structural analysis of chromosome folding in vivo has been revolutionized by Chromosome Conformation Capture (3C) and related methods, which use proximity ligation to identify chromosomal loci in physical contact. We recently described a variant 3C technique, Micro-C, in which chromatin is fragmented to mononucleosomes using micrococcal nuclease, enabling nucleosome-resolution folding maps of the genome. Here, we describe an improved Micro-C protocol using long crosslinkers, termed Micro-C XL, which exhibits greatly increased signal to noise, and provides further insight into the folding of the yeast genome. We also find that signal to noise is much improved in Micro-C XL libraries generated from relatively insoluble chromatin as opposed to soluble material, providing a simple method to physically enrich for bona-fide long-range interactions. Micro-C XL maps of the budding and fission yeast genomes reveal both short-range chromosome fiber features such as chromosomally-interacting domains (CIDs), as well as higher-order features such as clustering of centromeres and telomeres, thereby addressing the primary discrepancy between prior Micro-C data and reported 3C and Hi-C analyses. Interestingly, comparison of chromosome folding maps of S. cerevisiae and S. pombe revealed widespread qualitative similarities, yet quantitative differences, between these distantly-related species. Micro-C XL thus provides a single assay suitable for interrogation of chromosome folding at length scales from the nucleosome to the full genome.
Keywords
genomics, Chromosome Conformation Capture, Micro-C XL, chromosome conformation
Rights and Permissions
The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
DOI of Published Version
10.1101/071357
Source
bioRxiv 071357; doi: https://doi.org/10.1101/071357. Link to preprint on bioRxiv service.
Journal/Book/Conference Title
bioRxiv
Repository Citation
Hsieh, Tsung-Han S.; Fudenberg, Geoffrey; Goloborodko, Anton; and Rando, Oliver J., "Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome" (2016). University of Massachusetts Medical School Faculty Publications. 1565.
https://escholarship.umassmed.edu/faculty_pubs/1565
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License
Included in
Computational Biology Commons, Genetic Phenomena Commons, Genomics Commons, Molecular Biology Commons, Structural Biology Commons, Systems Biology Commons