Biology subjects

Nosella, M. L.

Publications and source records attributed to Nosella, M. L..

4 recordsLinked to original sources

bioRxiv2026

An expanded evolutionary landscape of H3 histones with variants that destabilize nucleosomes and promote chromatin accessibility

Histones are among the most conserved proteins in eukaryotes, yet many animal lineages have evolved divergent histone variants with specialized functions. Some broadly conserved variants (e.g., H3.3) have been linked to the regulation of chromatin accessibility in stem cells, but whether highly divergent variants function similarly remains unclear. Here, we characterize the histone repertoire of the acoel Hofstenia miamia, an animal that can undergo whole-body regeneration using adult pluripotent stem cells (aPSCs). We identify two novel histone H3 paralogs, H3-a and H3-b, that are expressed in aPSCs and form a lineage-specific sister clade to H3.2 and H3.3. Despite substantial sequence divergence and reduced compatibility with canonical chaperone machinery, both variants assemble bona fide nucleosomes in vitro. These nucleosomes exhibit reduced stability and incomplete DNA wrapping, and a cryo-EM structure of the H3-b nucleosome reveals the disruption of conserved histone-DNA contacts. In vivo, H3-a and H3-b are upregulated following injury, and their depletion reduces genome-wide chromatin accessibility, suggesting a role in the maintenance of accessible chromatin during regeneration. A survey of H3 sequences across animal phyla shows that H3-a and H3-b belong to a broader landscape of highly divergent H3 proteins, some of which exhibit sequence differences across both the N-terminal tail and histone-fold domain. Together, these findings link histone sequence diversification to chromatin regulation in aPSCs and highlight the underappreciated evolutionary diversity and functional potential of divergent animal H3 proteins.

evolutionary biology↗

bioRxiv2024

PARP1 condensates differentially partition DNA repair proteins and enhance DNA ligation

Poly(ADP-ribose) polymerase 1 (PARP1) is one of the first responders to DNA damage and plays crucial roles in recruiting DNA repair proteins through its activity - poly(ADP-ribosyl)ation (PARylation). The enrichment of DNA repair proteins at sites of DNA damage has been described as the formation of a biomolecular condensate. However, it is not understood how PARP1 and PARylation contribute to the formation and organization of DNA repair condensates. Using recombinant human PARP1 in vitro, we find that PARP1 readily forms viscous biomolecular condensates in a DNA-dependent manner and that this depends on its three zinc finger (ZnF) domains. PARylation enhances PARP1 condensation in a PAR chain-length dependent manner and increases the internal dynamics of PARP1 condensates. DNA and single-strand break repair proteins XRCC1, LigIII, Pol{beta}, and FUS partition in PARP1 condensates, although in different patterns. While Pol{beta} and FUS are both homogeneously mixed within PARP1 condensates, FUS enrichment is greatly enhanced upon PARylation whereas Pol{beta} partitioning is not. XRCC1 and LigIII display an inhomogeneous organization within PARP1 condensates; their enrichment in these multiphase condensates is enhanced by PARylation. Functionally, PARP1 condensates concentrate short DNA fragments and facilitate compaction of long DNA and bridge DNA ends. Furthermore, the presence of PARP1 condensates significantly promotes DNA ligation upon PARylation. These findings provide insight into how PARP1 condensation and PARylation regulate the assembly and biochemical activities in DNA repair foci, which may inform on how PARPs function in other PAR-driven condensates.

biochemistry↗

bioRxiv2022

Exploration of O-GlcNAc-transferase (OGT) glycosylation sites reveals a target sequence compositional bias

O-GlcNAc transferase (OGT) is an essential glycosylating enzyme that catalyzes the addition of N-acetylglucosamine to serine or threonine residues of nuclear and cytoplasmic proteins. The enzyme glycosylates a broad range of peptide sequences and prediction of glycosylation sites has proven challenging. The lack of an experimentally verified set of polypeptide sequences that are not glycosylated by OGT has made prediction of legitimate glycosylation sites more difficult. Here, we tested a number of intrinsically disordered protein regions as substrates of OGT to establish a set of sequences that are not glycosylated by OGT. The negative data set suggests an amino acid compositional bias for OGT targets. This compositional bias was validated by modifying the amino acid composition of the protein Fused in sarcoma (FUS) to enhance glycosylation. NMR experiments demonstrate that the tetratricopeptide repeat (TPR) region of OGT can bind FUS and that glycosylation-promoting mutations enhance binding. These results provide evidence that the TPR recognizes disordered segments of substrates with particular compositions to promote glycosylation, providing insight into the broad specificity of OGT.

biochemistry↗

bioRxiv2021

O-GlcNAcylation reduces phase separation and aggregation of the EWS N-terminal low complexity region

Many membraneless organelles are thought to be biomolecular condensates formed by phase separation of proteins and other biopolymers. Post-translational modifications (PTMs) can impact protein phase separation behavior, although for many PTMs this aspect of their function is unknown. O-linked {beta}-D-N-acetylglucosaminylation (O-GlcNAcylation) is an abundant form of intracellular glycosylation whose roles in regulating biomolecular condensate assembly and dynamics have not been delineated. Using an in vitro approach, we found that O-GlcNAcylation reduces the phase separation propensity of the EWS N-terminal low complexity region (LCRN) under different conditions, including in the presence of the arginine-and glycine-rich RNA-binding domains (RBD). O-GlcNAcylation enhances fluorescence recovery after photobleaching (FRAP) within EWS LCRN condensates and causes the droplets to exhibit more liquid-like relaxation following fusion. Following extended incubation times, EWS LCRN+RBD condensates exhibit diminished FRAP, indicating a loss of fluidity, while condensates containing the O-GlcNAcylated LCRN do not. In HeLa cells, EWS is less O-GlcNAcylated following OGT knockdown and more prone to aggregation based on a filter retardation assay. Relative to the human proteome, O-GlcNAcylated proteins are enriched with regions that are predicted to phase separate, suggesting a general role of O-GlcNAcylation in regulation of biomolecular condensates. Insert Table of Contents artwork here O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/443654v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@a09fb6org.highwire.dtl.DTLVardef@1556f47org.highwire.dtl.DTLVardef@1fcd76borg.highwire.dtl.DTLVardef@a2dbda_HPS_FORMAT_FIGEXP M_FIG C_FIG For Table of Contents only.

biochemistry↗