Biology subjects

Cai, S.

Publications and source records attributed to Cai, S..

5 recordsLinked to original sources

bioRxiv2018

High stretchability, strength and toughness of living cells enabled by hyperelastic vimentin network

In many normal and abnormal physiological processes, including cellular migration during normal development and invasion in cancer metastasis, cells are required to withstand severe deformations. The structural integrity of eukaryotic cells under small deformations has been known to depend on the cytoskeleton including actin filaments (F-actin), microtubules and intermediate filaments (IFs). However, it remains unclear how cells resist severe deformations since both F-actin and microtubules fluidize or disassemble under moderate strains. Here, we demonstrate that vimentin intermediate filaments (VIFs), a marker of mesenchymal cells, dominate cytoplasmic mechanics at large deformations. Our results show that cytoskeletal VIFs form a stretchable, hyperelastic network. This network works synergistically with other dissipative cytoplasmic components, substantially enhancing the strength, stretchability, resilience and toughness of the living cytoplasm.

biophysics↗

bioRxiv2018

The in situ structures of mono-, di-, and tri-nucleosomes in human heterochromatin

The in situ 3-D organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography (cryo-ET) to determine the in situ structures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.

cell biology↗

bioRxiv2018

A cosine similarity-based method to infer variability of chromatin accessibility at the single-cell level

Cellular identity between generations of developing cells is propagated through the epigenome particularly via the accessible parts of the chromatin. It is now possible to measure chromatin accessibility at single-cell resolution using single-cell assay for transposase accessible chromatin (scATAC-seq), which can reveal the regulatory variation behind the phenotypic variation. However, single-cell chromatin accessibility data are sparse, binary, and high dimensional, leading to unique computational challenges. To overcome these difficulties, we developed PRISM a computational workflow and R package (https://github.com/stanleycai123/PRISM) that quantifies cell-to-cell chromatin accessibility variation while controlling for technical biases. Using data generated in our lab or publically available, we show that PRISM outperforms an existing algorithm, which relies on the aggregate of signal across a set of genomic regions. PRISM shows robustness to noise in low accessibility cells and reveals previously masked accessibility variation where accessible sites differ between cells but total number of accessible sites is constant. We also show that PRISM, but not an existing algorithm, finds suppressed heterogeneity of accessibility at CTCF binding sites. PRISM is a novel multidimensional scaling-based method using angular cosine distance metrics coupled with distance from the spatial centroid. PRISM takes differences in accessibility at each genomic region between single cells into account. This updated approach uncovers new biological results with profound implications on the cellular heterogeneity of chromatin architecture.

genomics↗

bioRxiv2017

Cryo-ET reveals nucleosome reorganization in condensed mitotic chromosomes in vivo

Chromosomes condense during mitosis in most eukaryotes. This transformation involves rearrangements at the nucleosome level and has consequences for transcription, but the details remain unclear. Here, we use cryo-electron tomography to determine the 3-D arrangement of nucleosomes and other large nuclear features in frozen-hydrated fission-yeast cells. Nucleosomes can form irregular clusters in both interphase and mitotic cells, but they are smaller than expected for Hi-C domains. The nucleosomes are co-mingled with two features: nucleosome-free pockets and megadalton-sized \"megacomplexes\". Compared to interphase, the nucleosomes in mitotic chromosomes pack into slightly larger clusters. However, nearest-neighbor distance analysis reveals that mitotic nucleosome clusters have the same internal packing density as in interphase. Furthermore, mitotic chromosomes contain fewer megacomplexes. This uneven chromosome condensation helps explain a longstanding enigma of mitosis: most genes are repressed but a subset is upregulated.

cell biology↗

bioRxiv2017

Natural Chromatin Is Heterogeneous And Self Associates In Vitro

The 30-nm fiber is commonly found in oligonucleosome arrays in vitro but rarely found in chromatin within nuclei. To determine how chromatin high-order structure is controlled, we used cryo-ET to study the undigested natural chromatin released from cells that do not have evidence of 30-nm fibers in vivo: picoplankton and yeast. In the presence of divalent cations, most of the chromatin from both organisms is compacted into a large mass. Rare irregular 30-nm fibers do form at the periphery of this mass, some of which include face-to-face interactions. In the absence of divalent cations, picoplankton chromatin decondenses into open zigzags. By contrast, yeast chromatin mostly remains compact with looser nucleosome packing, even after treatment with histone-deacetylase inhibitor. The 3-D configuration of natural chromatin is therefore sensitive to the local environment, but generally nonpermissive of regular motifs, even at the level of oligonucleosomes.

cell biology↗