Aleksandra A. Galitsyna

Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation

Xiangru Huo, Denis L. Lafontaine, Thomas M. Reimonn, Liyan Yang et autres

Abstract Nuclear organization is a fundamental feature of cell identity and cell fate determination. Compared with differentiated cells, pluripotent stem cells exhibit markedly distinct nuclear architecture at multiple levels, including chromosome folding, lamina association, histone modification landscapes and nuclear body organization. Although …

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Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation

Aleksandra A. Galitsyna, Sergey V. Ulianov, Mariia Bazarevich, Nikolai S. Bykov et autres

The initiation of gene expression during development, known as zygotic genome activation (ZGA), is accompanied by massive changes in chromosome organization. However, the earliest events of chromosome folding and their functional roles remain unclear. Using Hi-C on zebrafish embryos, we discovered that …

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Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells

Nicholas M. Adams, Aleksandra A. Galitsyna, Ioanna Tiniakou, Eduardo Esteva et autres

The cohesin complex extrudes chromatin loops, stopping at sites bound by CCCTC-binding factor (CTCF) and organizing chromosomes into topologically associated domains, yet biological implications of this process remain obscure. We show that cohesin controls the in vivo differentiation and function of murine …

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Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells

Nicholas M. Adams, Aleksandra A. Galitsyna, Ioanna Tiniakou, Eduardo Esteva et autres

Type I interferons (IFN-I), including IFN-β and multiple IFN-α subtypes, are key antiviral proteins encoded within a single large locus. Here, we studied how the chromatin organization of this locus controls cell-type-specific IFN-I responses. The professional IFN-I-producing plasmacytoid dendritic cells (pDCs) simultaneously …

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Generalized discovery of chromatin structural patterns across developmental and evolutionary scales

Aleksandra A. Galitsyna

Chromatin in the eukaryotic nucleus is organized into regulatory structures that are visible in chromosomeconformation maps, including domains, loops, and other patterns that remain less systematically characterized. Although 3D genome organization is closely linked to gene regulation, development, and disease-associated misregulation, current …

Deciphering the 3D genome organization across species from Hi-C data

Aleksei Shkolikov, Aleksandra A. Galitsyna, Mikhail Sergeevich Gelfand

3D genome organization is essential for gene regulation, yet in various species it is driven by different biological mechanisms. Species-specific factors and DNA sequences influence chromatin folding, complicating cross-species comparisons. Leveraging Hi-C data and machine learning, we introduce Chimaera-a convolutional neural network …

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Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation

Leonid A. Mirny, Aleksandra A. Galitsyna, Sergey V. Ulianov, Nikolai S. Bykov et autres

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Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum

Irina V. Zhegalova, Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya A Pletenev et autres

Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome …

ru (code pays fourni par la source)

Deciphering the 3D genome organization across species from Hi-C data

Aleksei Shkolikov, Aleksandra A. Galitsyna, Mikhail Sergeevich Gelfand

ABSTRACT Three-dimensional genome organization is essential for gene regulation, yet in various species it is driven by different biological mechanisms. Species-specific factors and DNA sequences influence chromatin folding, complicating cross-species comparisons. Leveraging Hi-C data and machine learning, we introduce Chimaera — a …

ru, fr (code pays fourni par la source)

Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells

Nicholas M. Adams, Aleksandra A. Galitsyna, Ioanna Tiniakou, Eduardo Esteva et autres

Abstract The cohesin protein complex extrudes chromatin loops, stopping at CTCF-bound sites, to organize chromosomes into topologically associated domains, yet the biological implications of this process are poorly understood. We show that cohesin is required for the post-mitotic differentiation and function of …

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Single-Cell Hi-C Analysis Workflow with Pairtools

Aleksandra A. Galitsyna

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Convergent gene pairs restrict chromatin looping in Dictyostelium discoideum, acting as directional barriers for extrusion

Irina V. Zhegalova, Sergey V. Ulianov, Aleksandra A. Galitsyna, Ilya A Pletenev et autres

Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome …

ru (code pays fourni par la source)