Biology subjects

Grigoryev, S. A.

Publications and source records attributed to Grigoryev, S. A..

5 recordsLinked to original sources

bioRxiv2025

Molecular Dynamics-Guided All-Atom Reconstruction of Cryo-ET Maps Reveals Mechanisms of Histone Tail-Mediated Chromatin Compaction

Dynamics and physical state of chromatin are crucial in regulating gene expression, DNA replication, and repair. Intrinsically disordered histone tails were previously recognized as key modulators of chromatin states. However, detailed atomistic mechanisms by which histone tail dynamics are associated with chromatin compaction and higher-order chromatin organization remain poorly understood. In this work, we combine extensive all-atom molecular dynamics simulations of tri-nucleosomes with cryo-electron tomography (Cryo-ET) of native nucleosome arrays to investigate histone tail-mediated chromatin folding. Our approach offers distinct advantages as it elucidates realistic inter- and intra-nucleosomal interactions and DNA conformations derived from physics-based MD simulations, enabling a more accurate and physically grounded interpretation of Cryo-ET data. The results reveal that histone tails promote chromatin compaction and constrain tri-nucleosome unfolding via three major patterns: through histone-DNA interactions, histone H2A-H4 and H3-H4 tail-tail interactions. Notably, the distributions of MD-generated structural parameters of tri-nucleosomes with truncated histone tails were found to be in strong agreement with those of experimental open chromatin arrays with widely spaced nucleosomes, whereas the system with histone tails resembled more condensed chromatin. These findings provide mechanistic insights into how histone tails may mediate chromatin folding at the atomistic scale and underscore the dual role of histone tails in both structural compaction and inter-nucleosomal communication.

biophysics↗

bioRxiv2022

Cryo-electron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination

Nucleosome chains fold and self-associate to form higher order structures whose internal organization is unknown. Here, cryo-electron tomography (cryo-ET) of native human chromatin reveals novel folding motifs such as 1) non-uniform nucleosome stacking, 2) intermittent parallel and perpendicular orientations of adjacent nucleosome planes, and 3) an inverse zigzag nucleosome chain path, which deviates from the direct zigzag topology seen in reconstituted nucleosomal arrays. By examining these self-associated structures, we observed prominent nucleosome stacking in-cis and anti-parallel nucleosome interactions in-trans, which are consistent with partial nucleosome interdigitation. Histone citrullination strongly inhibits nucleosome stacking and self-association with a modest effect on chromatin folding, while the reconstituted arrays showed a zigzag topology which undergoes a dramatic unfolding induced by histone citrullination. This study sheds light on the internal structure of compact chromatin nanoparticles and suggests a novel mechanism for how epigenetic changes in chromatin are retained across both open and condensed forms of chromatin.

molecular biology↗

bioRxiv2019

CENP-C stabilizes the conformation of CENP-A nucleosomes within the inner kinetochore at human centromere

The centromere is the chromosomal locus that seeds the kinetochore, allowing for a physical connection between the chromosome and the mitotic spindle. At the heart of the centromere is the centromere-specific histone H3 variant CENP-A/CENH3. Throughout the cell cycle the constitutive centromere associated network is bound to CENP-A chromatin, but how this protein network modifies CENP-A nucleosome dynamics in vivo is unknown. Here, we purify kinetochore associated native centromeric chromatin and analyze its biochemical features using a combinatorial approach. We report that kinetochore bound chromatin has strongly reduced DNA accessibility and a distinct stabilized nucleosomal configuration. Disrupting the balance between CENP-A and CENP-C result in reduced centromeric occupancy of RNA polymerase 2 and impaired de novo CENP-A loading on the centromeric chromatin fiber, correlating with significant mitotic defects. CENP-A mutants that restore the ratio rescue the mitotic defects. These data support a model in which CENP-C bound centromeric nucleosomes behave as a barrier to the transcriptional machinery and suggest that maintaining the correct ratio between CENP-A and CENP-C levels is critical for centromere homeostasis.

biochemistry↗

bioRxiv2018

Elastic and Rigidified CENP-A Nucleosomes govern Centromeric Chromatin Plasticity

Histone variants fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether and how nucleosome variants encode unique mechanical properties to their cognate chromatin structures remains elusive. Here, using novel in silico and in vitro nanoindentation methods, extending to in vivo dissections, we report that histone variant nucleosomes are intrinsically more elastic than their canonical counterparts. Furthermore, binding proteins which discriminate between histone variant nucleosomes suppress this innate elasticity and also compact chromatin. Interestingly, when we overexpress the binding proteins in vivo, we also observe increased compaction of chromatin enriched for histone variant nucleosomes, correlating with diminished access. Together, these data suggest a plausible link between innate mechanical properties possessed by histone variant nucleosomes, the adaptability of chromatin states in vivo, and the epigenetic plasticity of the underlying locus.\n\nSignificanceNucleosomes are the base unit which organize eukaryotic genomes. Besides the canonical histone, histone variants create unique local chromatin domains that fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. We developed computational and single-molecule nanoindentation tools to determine mechanical properties of histone variant nucleosomes. We found that the CENP-A nucleosome variant is more elastic than the canonical H3 nucleosome but becomes stiffer when bound to its partner CENP-C. In addition, CENP-C induces cross-array clustering, creating a chromatin state that less accessible. These data suggest that innate material properties of nucleosomes can influence the ultimate chromatin state, thereby influence biological outcomes.

biochemistry↗

bioRxiv2017

DNA topology in chromatin is defined by nucleosome spacing

In eukaryotic chromatin, DNA makes about 1.7 left superhelical turns around an octamer of core histones implying that formation of nucleosomes would alter the overall topology of DNA by a comparable difference of the DNA linking number ({Delta}Lk) per nucleosome. However, earlier experiments have documented a significantly (about 50%) lower absolute value |{Delta}Lk| than expected from the nucleosome geometry. Recently, using computer modeling, we have predicted two families of energetically stable conformations of the arrays with precisely positioned nucleosomes, one with an integer number of DNA turns in the linker DNA {L = 10n} and the other with extra five base pairs in the linker {L = 10n + 5}, to be topologically different. Here, using arrays of precisely positioned clone 601 nucleosomes, topological electrophoretic assays, and electron microscopy we experimentally tested these predictions. First, for small 12-mer nucleosome circular arrays we observed that dLk per nucleosome changes from -1.4 to -0.9 for the linkers {L = 10n} and {L = 10n + 5}, respectively. Second, for larger hybrid arrays containing a mixture of positioned and non-positioned nucleosomes we found that changing the DNA linker length within the positioned arrays was sufficient to significantly alter the overall DNA topology fully consistent with our prediction. The observed topological polymorphism of the circular nucleosome arrays provides a simple explanation for the DNA topology in native chromatin with variable DNA linker length. Furthermore, our results may reflect a more general tendency of chromosomal domains containing active or repressed genes to acquire different nucleosome spacing to retain topologically distinct higher-order structures.

molecular biology↗