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Sequence-Dependent Liquid Crystalline Ordering of Gapped DNA.
ACS Macro Lett
January 2025
Department of Physics, Kent State University, Kent, Ohio 44242, United States.
We investigate the impact of poly adenine (poly-A) sequences on the type and stability of liquid crystalline (LC) phases formed by concentrated solutions of gapped DNA (two duplex arms bridged by a flexible single strand) using synchrotron small-angle X-ray scattering and polarizing optical microscopy. While samples with mixed sequence form layered (smectic) phases, poly-A samples demonstrate a columnar phase at lower temperatures (5-35 °C), not previously observed in GDNA samples, and a smectic-B phase of exceptional stability at higher temperatures (35-65 °C). We present a model that connects the formation of these LC phases with the unique characteristics of poly-A sequences, which manifest in various biological contexts, including DNA condensation and nucleosome formation.
View Article and Find Full Text PDFNucleosome dynamics render heterochromatin accessible in living human cells.
bioRxiv
December 2024
Division of Developmental Biology, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda MD 20892, USA.
The eukaryotic genome is packaged into chromatin, which is composed of a nucleosomal filament that coils up to form more compact structures. Chromatin exists in two main forms: euchromatin, which is relatively decondensed and enriched in transcriptionally active genes, and heterochromatin, which is condensed and transcriptionally repressed . It is widely accepted that chromatin architecture modulates DNA accessibility, restricting the access of sequence-specific, gene-regulatory, transcription factors to the genome.
View Article and Find Full Text PDFNucleosome Spacing Can Fine-Tune Higher Order Chromatin Assembly.
bioRxiv
December 2024
Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
Cellular chromatin displays heterogeneous structure and dynamics, properties that control diverse nuclear processes. Models invoke phase separation of conformational ensembles of chromatin fibers as a mechanism regulating chromatin organization . Here we combine biochemistry and molecular dynamics simulations to examine, at single base-pair resolution, how nucleosome spacing controls chromatin phase separation.
View Article and Find Full Text PDFDynamics of nucleosomes and chromatin fibers revealed by single-molecule measurements.
BMB Rep
January 2025
Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea.
The nucleosome is the fundamental structural unit of chromosome fibers. DNA wraps around a histone octamer to form a nucleosome while neighboring nucleosomes interact to form higher-order structures and fit gigabase-long DNAs into a small volume of the nucleus. Nucleosomes interrupt the access of transcription factors to a genomic region and provide regulatory controls of gene expression.
View Article and Find Full Text PDFBeyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion.
Curr Opin Genet Dev
December 2024
Gladstone Institute for Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA. Electronic address:
CCCTC-binding factor (CTCF) is a key regulator of 3D genome organization and transcriptional activity. Beyond its well-characterized role in facilitating cohesin-mediated loop extrusion, CTCF exhibits several cohesin-independent activities relevant to chromatin structure and various nuclear processes. These functions include patterning of nucleosome arrangement and chromatin accessibility through interactions with ATP-dependent chromatin remodelers.
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