Biology subjects

Mali, S.

Publications and source records attributed to Mali, S..

4 recordsLinked to original sources

bioRxiv2025

USP15: the fourth Proteasome-associated DUB

The human genome encodes approximately 100 deubiquitinating enzymes (DUBs), but only three are considered proteasome-associated DUBs (pDUBs): PSMD14/Rpn11, USP14, and UCHL5. Among these, only PSMD14 is an integral 19S subunit, whereas USP14 and UCHL5 bind transiently to specific proteasomal subunits. Given the dynamic nature of proteasome composition, we searched for additional pDUBs. USP15 was found to be associated with 26S proteasomes purified from cultured cells. In proteasome preparations from erythrocytes, USP15 was identified as the most abundant transient pDUB. It was even feasible to separate proteasomes containing USP15 from those containing USP14. Although USP15 utilizes an internal ubiquitin-like (UBL) domain for positioning itself at the proteasome, it did not compete with the UBL-containing USP14. USP15 facilitated substrate selection at the proteasome by efficiently disassembling short polyubiquitin (polyUb) chains, while sparing K48-linked tetra-ubiquitin conjugates from deubiquitination. This feature may aid the proteasome in differentiating between substrates to be rescued from those committed to proteolysis. Identification of a fourth pDUB encourages the continued search for additional proteasome-interacting proteins that modulate its substrate specificity in a context-specific manner.

biochemistry↗

bioRxiv2025

Quantifying Conformational Heterogeneity of 3D Genome Organization in Fruit Fly

The three-dimensional (3D) organization of interphase chromatin in eukaryotes is complex; details of the corresponding genome structures vary stochastically from cell to cell. Here, we propose a metric to quantify the cell-to-cell heterogeneity of the 3D chromatin conformations in ensembles of single cells: Conformational Heterogeneity (C.H.) is defined as the standard deviation of the ensemble distribution of the per cell average Euclidean inter-loci distances [<]Rs[>], for a given genomic separation s between the loci. We have used the metric to examine and quantify in detail the cell-to-cell heterogeneity of conformations of the interphase X chromosome in fruit fly generated via three distinctly different modeling approaches, which take experimental Hi-C data as input. Two of the approaches use bulk Hi-C and lamina-DamID data, while the third relies on single-cell Hi-C maps. An algorithm is proposed to facilitate comparison of C.H. of models constructed at different resolutions, and to examine the behavior of conformational heterogeneity with increasing model resolution. Higher resolution models show a greater C.H., in general. The impact of the model resolution is strongest near the genomic distance s corresponding to the resolution limit of the model, and diminishes for larger genomic distances: extrapolating the resolution from approximately 14 kb to 2 kb has little effect on the C.H. beyond [~]100 kb. All chromatin models examined in this work show a very similar trend of monotonically increasing structural heterogeneity with s, up to the genomic TAD size; beyond that, significant differences arise, with the model based on single-cell Hi-C showing nearly opposite trend compared to the two models that use bulk Hi-C data. We attribute these major differences to relatively subtle differences in the modeling approaches, which we discuss. Based on the analysis, we propose to explore the possibility of inclusion of bulk Hi-C data into training of chromatin models that are based on necessarily limited single-cell Hi-C data. Within our computational approach, depletion of nuclear lamins leads to increased structural heterogeneity at nearly all genomic separations, with the potential implication that cell functions that depend on chromatin structure might be more variable within lamins depleted nuclei compared to the wild type.

genomics↗

bioRxiv2022

Drosophila epidermal cells are intrinsically mechanosensitive and drive nociceptive behavioral outputs

Somatosensory neurons (SSNs) that detect and transduce mechanical, thermal, and chemical stimuli densely innervate an animals skin. However, although epidermal cells provide the first point of contact for sensory stimuli. our understanding of roles that epidermal cells play in SSN function, particularly nociception, remains limited. Here, we show that stimulating Drosophila epidermal cells elicits activation of SSNs including nociceptors and triggers a variety of behavior outputs, including avoidance and escape. Further, we find that epidermal cells are intrinsically mechanosensitive and that epidermal mechanically evoked calcium responses require the store-operated calcium channel Orai. Epidermal cell stimulation augments larval responses to acute nociceptive stimuli and promotes prolonged hypersensitivity to subsequent mechanical stimuli. Hence, epidermal cells are key determinants of nociceptive sensitivity and sensitization, acting as primary sensors of noxious stimuli that tune nociceptor output and drive protective behaviors.

neuroscience↗

bioRxiv2021

Variation in upstream open reading frames contributes to allelic diversity in protein abundance

The 5 untranslated region (UTR) sequence of eukaryotic mRNAs may contain upstream open reading frames (uORFs), which can regulate translation of the main open reading frame (mORF). The current model of translational regulation by uORFs posits that when a ribosome scans an mRNA and encounters a uORF, translation of that uORF can prevent ribosomes from reaching the mORF and cause decreased mORF translation. In this study, we first observed that rare variants in the 5 UTR dysregulate protein abundance. Upon further investigation, we found that rare variants near the start codon of uORFs can repress or derepress mORF translation, causing allelic changes in protein abundance. This finding holds for common variants as well, and common variants that modify uORF start codons also contribute disproportionately to metabolic and whole-plant phenotypes, suggesting that translational regulation by uORFs serves an adaptive function. These results provide evidence for the mechanisms by which natural sequence variation modulates gene expression, and ultimately, phenotype.

genomics↗