Biology subjects

Sakkas, E. D.

Publications and source records attributed to Sakkas, E. D..

3 recordsLinked to original sources

bioRxiv2025

The landscape of allele-specific expression in human kidneys

Allele-specific expression (ASE), the preferential expression of one gene copy, is a key mechanism of genomic regulation. However, its role in human kidney disease remains poorly understood. In this study, we generated a high-quality, genome-wide ASE map using paired whole-genome sequencing and RNA-seq from microdissected glomerular (GLOM) and tubulointerstitial (TUBE) compartments of patients with proteinuric kidney disease. We showed that the majority of common ASE events were deterministic and sequence-mediated. We also found that diseased kidneys exhibited significantly more ASE in GLOM than TUBE, compared to controls. Unexpectedly, higher ASE in GLOM than TUBE was significantly associated with improved kidney disease outcomes in the disease cohort. Differential gene expression analysis suggested this was the result of an active, protective transcriptional response, including ribosome and ATP synthesis upregulation, rather than pathogenic dysregulation. Our work reveals glomerular ASE as a marker of adaptive transcriptional activity in proteinuric kidney disease.

genomics↗

bioRxiv2025

StACKER, A TOOL FOR SYSTEMS LEVEL ANALYSIS OF BASE STACKING IN NUCLEOTIDE-RICH STRUCTURES

Nucleic acid macromolecules can undergo significant structural changes--often mediated by nucleotide modification or molecular interactions. These alterations can be critical to their function. An ongoing challenge is to develop useful tools to quantify system-wide changes in nucleic acid-rich structures. We introduce StACKER, a robust Python package for observing conformational changes in a nucleic acid structure through its pi-stacking of base rings. StACKER creates System Stacking Fingerprints (SSFs) which highlight the landscape of pi-stacking throughout a molecule and can be used to show widespread conformational adjustments. Additionally, StACKERs Pairwise Stacking Fingerprint (PSF) can further characterize pi-stacking in a select residue pair, showing how the effects of localized residue changes spread through a nucleic acid system. We apply StACKER to molecular dynamics (MD) simulations of a subsystem of the ribosome to reveal that alternative codons at the ribosome A-site and 3 adjacent +1 codon position induce allosteric structure changes in the decoding center neighborhood, leading to a toggle between two conformational states. Through previous analysis of ribosome profiling data, we link these states to an observed fast/slow translation phenotype (Sun et al. 2024). We benchmark StACKER alongside other lenses for observing allostery to demonstrate its use in assessing allosteric shifts and its relevance to future structure-to-function studies.

bioinformatics↗

bioRxiv2024

GNN codon adjacency regulates protein translation

The central dogma treats the ribosome as a molecular machine that reads one mRNA codon at a time as it adds each amino acid to its growing peptide chain. However, this and previous studies suggest that ribosomes actually perceive pairs of adjacent codons as they take three-nucleotide steps along the mRNA. We examined GNN codons which we find are surprisingly overrepresented in eukaryote protein-coding open reading frames (ORFs), especially immediately after NNU codons. Ribosome profiling experiments in yeast revealed that ribosomes with NNU at their aminoacyl (A) site have particularly elevated densities when NNU is immediately followed (3) by a GNN codon, indicating slower mRNA threading of the NNU codon from the ribosomes A to peptidyl (P) sites. Moreover, if the assessment was limited to ribosomes that have only recently arrived at the next codon, by examining 21-nucleotide ribosome footprints (21-nt RFPs), elevated densities were observed for multiple codon classes when followed by GNN. This striking translation slowdown at adjacent 5-NNN GNN codon pairs is likely mediated in part by the ribosomes CAR surface which acts as an extension of the A-site tRNA anticodon during ribosome translocation and interacts through hydrogen bonding and pi stacking with the GNN codon. The functional consequences of 5-NNN GNN codon adjacency are expected to influence the evolution of protein coding sequences. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/583757v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@d29087org.highwire.dtl.DTLVardef@e8f7dorg.highwire.dtl.DTLVardef@1ee5792org.highwire.dtl.DTLVardef@b750fb_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

molecular biology↗