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Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy

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cris.lastimport.scopus2024-02-12T19:49:56Z
dc.abstract.enThe three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33 kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2–22 nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorJodkowska, Karolina
dc.contributor.authorPlewczyński, Dariusz
dc.contributor.authorRuan, Yijun
dc.contributor.authorBanecki, Krzysztof
dc.contributor.authorChew, Teng-Leong
dc.contributor.authorAaron, Jesse
dc.contributor.authorWang, Ping
dc.contributor.authorLee, Byoungkoo
dc.contributor.authorZhu, Jacqueline Jufen
dc.contributor.authorParteka-Tojek, Zofia
dc.date.accessioned2024-01-26T09:24:27Z
dc.date.available2024-01-26T09:24:27Z
dc.date.issued2022
dc.description.financePublikacja bezkosztowa
dc.description.number1
dc.description.volume12
dc.identifier.doi10.1038/S41598-022-12568-9
dc.identifier.issn2045-2322
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/121142
dc.identifier.weblinkhttps://www.nature.com/articles/s41598-022-12568-9.pdf
dc.languageeng
dc.pbn.affiliationbiological sciences
dc.relation.ispartofScientific Reports
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.titleSuper-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
dc.typeJournalArticle
dspace.entity.typePublication