Biology subjects

Formichetti, S.

Publications and source records attributed to Formichetti, S..

3 recordsLinked to original sources

bioRxiv2024

Genetic gradual reduction of OGT activity unveils the essential role of O-GlcNAc in the mouse embryo

The reversible glycosylation of nuclear and cytoplasmic proteins (O-GlcNAcylation) is catalyzed by a single enzyme, namely O-GlcNAc transferase (OGT). The mammalian Ogt gene is X-linked and it is essential for embryonic development and for the viability of proliferating cells. We perturbed OGTs function in vivo by creating a murine allelic series of four single amino acid substitutions reducing OGTs catalytic activity to a range of degrees. The severity of the embryonic lethality was proportional to the degree of impairment of OGTs catalysis, demonstrating that the O-GlcNAc modification itself is required for early development. We identified milder hypomorphic Ogt alleles that perturb O-GlcNAc homeostasis while being compatible with embryogenesis. The analysis of the transcriptomes of the mutant embryos at different stages suggested a sexually-dimorphic developmental delay caused by the decrease in O-GlcNAc. Furthermore, a mild reduction of OGTs enzymatic activity was sufficient to loosen the silencing of endogenous retroviruses in vivo.

developmental biology↗

bioRxiv2024

Perturbing nuclear glycosylation in the mouse preimplantation embryo slows down embryonic growth

The only known form of intracellular protein glycosylation (O-GlcNAc) is reversible and has been mapped on thousands of cytoplasmic and nuclear proteins, including RNA polymerase II, transcription factors and chromatin modifiers. The O-GlcNAc modification is catalyzed by a single enzyme known as O-GlcNAc Transferase (OGT), that is required for mammalian early development. Remarkably, the regulatory function of protein O-GlcNAcylation in the embryo as well as the embryonic O-GlcNAc proteome remain unknown. Here, we devised a new method to enzymatically remove O-GlcNAc from preimplantation embryonic nuclei, where it accumulates coincidently with embryonic genome activation (EGA). Unexpectedly, the depletion of nuclear O-GlcNAc to undetectable levels has no impact on EGA, but dampens the transcriptional activation of the translational machinery, and triggers a spindle checkpoint response. These molecular alterations were phenotypically associated with a developmental delay starting from early cleavage stages and persisting after embryo implantation, establishing a novel link between nuclear glycosylation and embryonic growth.

developmental biology↗

bioRxiv2019

The transcriptome dynamics of single cells during the cell cycle

Despite advances in single-cell data analysis, the dynamics and topology of the cell cycle in high-dimensional gene expression space remains largely unknown. Here, we use a linear analysis of transcriptome data to reveal that cells move along a circular trajectory in transcriptome space during the cell cycle. This movement occurs largely independently from other cellular processes. Non-cycling gene expression (changes in environment or epigenetic state) adds a third dimension and causes helical motion on a hollow cylinder. The circular trajectory shape indicates minimal acceleration of transcription, i.e. the cell cycle has evolved to minimize changes of transcriptional activity and its entailing regulatory effort. Thus, we uncover a general design principle of the cell cycle that may be of relevance to many other cellular differentiation processes. One Sentence SummaryCells traverse high-dimensional gene expression space in a 2D circular motion, thus minimizing changes of expression changes ("Acceleration").

systems biology↗