Insan, J. | bioRxiv Science

bioRxiv2026

Genome-wide annotation and analyses of bifunctional genes in the human genome

Conventional gene annotation pipelines classify eukaryotic genes into protein-coding and non-coding. Alternative splicing may generate non-coding transcript variants from protein-coding genes, that are expressed in tissue- or disease- specific manner. We and others have described the genes which transcribe both coding and non-coding transcripts as bifunctional genes. Here we present a genome-wide analyses of bifunctional genes and reannotate the genes in the human genome reference assembly into coding, non-coding and bifunctional. We identify over 4000 bifunctional genes in the human genome, constituting approximately 10% of the transcribed genes, and present evidence that these genes are conserved in evolution and their number correlate well with genome size and complexity. These genes are enriched in gene sets involved in vesicular transport, autophagy, RNA/DNA binding, glycosylation and splicing. By monitoring the expression of non-coding exons in long-read sequencing datasets and by quantitative RT-PCR, we provide evidence for the expression of non-coding variants from bifunctional genes. The ncRNA transcripts from these genes might have similar or different roles from their cognate mRNA counterparts. They may act as miRNA sponges or harbour non-canonical open-reading frames that encode microproteins, while also competing for binding with RNA-binding proteins. We present evidence for establishing potential biological functions of bifunctional genes and summarise the findings in a searchable database. Further studies and functional characterization focused on this special group of genes may reveal interesting gene regulatory mechanisms relevant to physiology and pathology.

genomics↗

bioRxiv2023

Kinase inhibitor-induced cell-type specific vacuole formation in the absence of canonical ATG5-dependent autophagy

Pyridinyl imidazole class p38 MAPK/{beta} (MAPK14/MAPK11) inhibitors including SB202190 have been shown to induce a cell-type specific defective autophagy response resulting in micron-scale vacuole formation, autophagy-dependent death, and tumor growth suppression in vivo. We had earlier shown that this is an off-target effect of SB202190. Here we provide evidence that the cell-type specific vacuole formation is independent of canonical autophagy pathway. While SB202190 seems to interfere with autophagic flux in many cell lines in parallel to vacuolation, autophagy-deficient DU-145 cells and CRISPR/Cas9 gene-edited ATG5 knockout A549 cells also undergo vacuolation upon SB202190 treatment. Late-endosomal GTPase RAB7 colocalizes with these compartments and RAB7 GTP-binding seems to be essential for SB202190-induced vacuolation. RAB7 is a driver of tumor progression and interfering with RAB7-positive endo/lysosomal compartments may enhance cytotoxicity. A screen for modulators of SB202190-induced vacuolation revealed molecules including multi-kinase inhibitor Sorafenib as inhibitor of vacuolation and sorafenib co-treatment enhanced the cytotoxicity of SB202190. Moreover VE-821, an ATR kinase inhibitor was found to phenocopy the cell-type specific vacuolation response of SB202190. To identify the factors determining the cell-type specificity of the vacuolation response induced by SB-compounds and VE-821, we compared the transcriptomics data from vacuole forming and non-vacuole forming cancer cell lines and identified a gene expression signature which may define sensitivity of cancer cells to these small-molecule kinase inhibitors. Further analyses using the small molecule tools and the gene signature discovered here, could reveal novel mechanisms regulating this interesting phenotype relevant to anti-cancer therapy.

cell biology↗