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Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1
The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited by PARP1/PARP2 and their co-factor HPF1. ALC1 has emerged...
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Skeletal muscle differentiation induces wide-ranging nucleosome repositioning in muscle gene promoters
In a previous report, we demonstrated that Cbx1, PurB and Sp3 inhibited cardiac muscle differentiation by increasing nucleosome density around...
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Structures of transcription preinitiation complex engaged with the +1 nucleosome
The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation....
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Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler
Nearly all essential nuclear processes act on DNA packaged into arrays of nucleosomes. However, our understanding of how these processes (for...
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Structure of nucleosome-bound human PBAF complex
BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create...
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Structure of histone deacetylase complex Rpd3S bound to nucleosome
Crosstalk between histone modifications represents a fundamental epigenetic mechanism in gene regulation. During the transcription elongation...
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DNA damage and repair in the nucleosome: insights from computational methods
Cellular DNA is constantly exposed to endogenous or exogenous factors that can induce lesions. Several types of lesions have been described that can...
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General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex
BackgroundChromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors...
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Refinement of Nucleosome Positions within Individual Genes Using Molecular Modeling Methods and MNase Sequencing Data
AbstractChromatin organization plays an important role in regulating the genetic machinery of the cell. A nucleosome is a basic unit of chromatin...
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Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking
Single-particle cryo-EM is widely used to determine enzyme-nucleosome complex structures. However, cryo-EM sample preparation remains challenging and...
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Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition
Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed...
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Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex
Acetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase...
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Quantifying ATP-Independent Nucleosome Chaperone Activity with Single-Molecule Methods
The dynamics of histone-DNA interactions govern chromosome organization and regulates the processes of transcription, replication, and repair....
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ISWI catalyzes nucleosome sliding in condensed nucleosome arrays
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. Here we investigated these...
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Structural basis of paralog-specific KDM2A/B nucleosome recognition
The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted...
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Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome
The engagement of a DNA glycosylase with a damaged DNA base marks the initiation of base excision repair. Nucleosome-based packaging of eukaryotic...
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Structural basis for APE1 processing DNA damage in the nucleosome
Genomic DNA is continually exposed to endogenous and exogenous factors that promote DNA damage. Eukaryotic genomic DNA is packaged into nucleosomes,...
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Genome-wide map** and cryo-EM structural analyses of the overlap** tri-nucleosome composed of hexasome-hexasome-octasome moieties
The nucleosome is a fundamental unit of chromatin in which about 150 base pairs of DNA are wrapped around a histone octamer. The overlap**...
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In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization
Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms driving the formation of these domains are difficult to dissect in...
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Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility
Nucleosomes, containing histone variants H2A.Z, are important for gene transcription initiation and termination, chromosome segregation and DNA...
