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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
Published on: September 10, 2013
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CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning.
Marlies E Oomen1, Anders S Hansen2, Yu Liu1
1Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
Genome Research
|January 19, 2019
Summary
CCCTC-binding factor (CTCF) binding is lost during prometaphase, leading to the absence of topologically associating domains (TADs) and CTCF loops. This dynamic loss of CTCF binding and nucleosome rearrangement reveals cell cycle-dependent chromatin organization.
Area of Science:
- Cell Biology
- Genomics
- Chromatin Biology
Background:
- Topologically associating domains (TADs) and CTCF loops are crucial for interphase genome organization.
- The dynamic regulation of TADs and CTCF loops during mitosis remains poorly understood.
- Contradictory findings exist regarding CCCTC-binding factor (CTCF) binding to mitotic chromatin.
Purpose of the Study:
- To investigate the dynamic changes in CTCF binding and chromatin organization during the cell cycle, specifically during mitosis.
- To resolve conflicting observations on CTCF binding to mitotic chromatin.
- To elucidate the mechanisms underlying the loss of TADs and CTCF loops during mitosis.
Main Methods:
- 5C (Chromosome Conformation Capture Carbon Copy) to analyze TADs and loops.
- ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) to assess chromatin accessibility.
- CUT&RUN (Cleavage Under Targets and Release Using Nuclease) for site-specific CTCF binding analysis.
- Live-cell imaging, FRAP (Fluorescence Recovery After Photobleaching), and single-molecule tracking for CTCF dynamics.
Main Results:
- TADs and CTCF loops are present in interphase but absent in prometaphase.
- CTCF sites show reduced accessibility and lose CTCF footprints in prometaphase, indicating loss of binding and nucleosome rearrangement.
- Transcription start sites remain accessible, but adjacent nucleosomes reposition during mitosis.
- CUT&RUN confirms loss of site-specific CTCF binding in prometaphase.
- Live-cell imaging demonstrates a significant loss of CTCF chromatin binding during prometaphase.
Conclusions:
- CTCF binding to its sites is lost during prometaphase.
- Chromatin landscape around CTCF motifs is rearranged during prometaphase.
- Loss of CTCF binding and cohesin contributes to the absence of TADs and CTCF loops in mitosis.
- CTCF sites exhibit cell cycle-dependent dynamics in factor binding and nucleosome positioning.
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