Adiguzel, Y. | Search bioRxiv

bioRxiv2023

Genome related features of introns and exons reveal new properties and pareto fronts

Genome annotations reveal vast amount information, as well as genome related features. We looked at the genome related features of eukaryotes, grouped as primates, rodents, birds, fishes, insects, and plants. Features related to introns and exons reveal distinct assets. Genes mean lengths are positively correlated with the collective data of counts of exons in coding transcripts and both the mean lengths and counts of introns in coding transcripts. Mean lengths of introns in non-coding transcripts are also positively correlated and correlations with the counts-data are excluding the data of plants and fishes. These are valid for the median lengths as well. In addition, certain feature comparisons reveal separation of primates, rodents, birds, fishes, insects, and plants. We also observed pareto fronts in the cumulative data with the max length values of genes and introns in coding transcripts, as well as introns in coding and non-coding transcripts.

evolutionary biology↗

bioRxiv2021

Coronavirus associated molecular mimicry common to SARS-CoV-2 peptide

This study aims to predict autoimmunity-related pathological mechanisms that possess risk for individuals with specific human leukocyte antigen (HLA) serotypes and shared by certain coronaviruses including SARS-CoV-2, based on homology to a SARS-CoV-2 peptide. With the given aim, 1-) coronavirus-associated sequences, which are homologous to the 15mer SARS-CoV-2 peptide CFLGYFCTCYFGLFC, are obtained. 2-) Human peptides that have at least 7 residue matches with those coronavirus sequences, and the SARS-CoV-2 15mer, are found. 3-) Epitope pairs, which are sourced by those aligned coronavirus and human sequences are identified. 4-) Epitope pairs that are predicted to bind strongly not only to the same HLA allele with each other but also to the same HLA allele as those of the respective alignment of the SARS-CoV-2 peptide are selected. Following are the identified proteins or peptides (with HLA-A*02:01 or HLA-A*24:02 epitopes), as described in 1-to-4: Immunoglobulin heavy chain junction regions, CRB1 isoform I precursor, slit homolog 2 protein, hCG1995581, hCG2028737, phospholipid phosphatase-related protein type 2. Among those, CRB1 isoform I precursor sequence with the predicted HLA-A*24:02 epitope aligns with the highest number of different sequences. Results imply autoimmunity risk in COVID-19 patients with HLA-A*02:01 and HLA-A*24:02 serotypes, through molecular mimicry, as a shared pathogenicity risk that can be prevalent upon getting infected with certain coronaviruses. These can pave way to improved risk groups assessment and autoimmunity treatment options, for COVID-19 and its associated diseases. Also, the approach in this study can be used to predict prospective pathologies of the transmissible variants in susceptible humans.

immunology↗