Biology subjects

Banka, A.

Publications and source records attributed to Banka, A..

3 recordsLinked to original sources

bioRxiv2026

RNA-binding proteins activate transcription through defined molecular grammars

Transcription factors (TFs) regulate gene expression through interactions with DNA, RNA, and proteins. RNA-binding proteins (RBPs) also assemble near regulatory elements and mediate RNA processing, yet their perturbation causes transcriptional defects. Here, we find select RBPs activate transcription through latent activation domains akin to TFs. RBP activators regulate distinct genes and interact with transcriptional condensates. Their activation domains are enriched in aromatic and polar residues but depleted of basic residues - essential features that are conserved and partially mimic TF activation domains. We validated additional RBP activators across the human proteome based on this molecular grammar, including the C-terminal domain (CTD) of RPB1, the catalytic subunit of RNA polymerase II. RPB1-CTD activates transcription by recruiting coactivators, demonstrating a non-enzymatic function in transcriptional regulation. These findings position RBPs and RPB1 as transcriptional regulators, explain coupling between transcription and RNA processing, and reveal RNA-RBP regulatory networks that parallel DNA-TF networks.

molecular biology↗

bioRxiv2026

Adaptive and Spandrel-like Constraints at Functional Sites in Protein Folds

How new molecular functions emerge during protein evolution remains a fundamental question in molecular biology. The energy landscape theory states that proteins are minimally frustrated, i.e. they have minimized their internal conflicts, to allow robust folding. Yet, not all energetic conflicts are eliminated, with functional regions such as catalytic residues and ligand-binding sites being often enriched in frustrated interactions, trading localized stability for biological activity. However, it is still uncertain whether this functional frustration is an evolutionary adaptation, positively selected despite its energetic cost or an inevitable physical byproduct of the fold architecture. Here, we combine reverse folding, structure prediction, and sequence analysis with local frustration profiling to address this long-standing question. Unexpectedly, we found that reverse folding algorithms are unable to energetically minimize evolutionary conserved frustration at specific residues, even when detrimental to overall structural stability. We propose that these frustration hotspots act as architectural spandrels, inherent physical constraints of the fold that evolution subsequently co-opts for function. Our findings connect biophysical constraints and evolutionary selection, providing a new framework to understand how functional specificity emerges in protein landscapes.

bioinformatics↗

bioRxiv2024

PRMT1 Modulates Alternative Splicing to Enhance HPV18 mRNA Stability and Promote the Establishment of Infection

Only persistent HPV infections lead to the development of cancer. Thus, understanding the virus-host interplay that influences the establishment of viral infection has important implications for HPV biology and human cancers. The ability of papillomaviruses to establish in cells requires the strict temporal regulation of viral gene expression in sync with cellular differentiation. This control primarily happens at the level of RNA splicing and polyadenylation. However, the details of how this spatio-temporal regulation is achieved still need to be fully understood. Until recently, it has been challenging to study the early events of the HPV lifecycle following infection. We used a single-cell genomics approach to identify cellular factors involved in viral infection and establishment. We identify protein arginine N-methyltransferase 1 (PRMT1) as an important factor in viral infection of primary human cervical cells. PRMT1 is the main cellular enzyme responsible for asymmetric dimethylation of cellular proteins. PRMT1 is an enzyme responsible for catalyzing the methylation of arginine residues on various proteins, which influences processes such as RNA processing, transcriptional regulation, and signal transduction. In this study, we show that HPV18 infection leads to increased PRMT1 levels across the viral lifecycle. PRMT1 is critical for the establishment of a persistent infection in primary cells. Mechanistically, PRMT1 inhibition leads to a highly dysregulated viral splicing pattern. Specifically, reduced PRMT1 activity leads to intron retention and a change in the E6 and E7 expression ratio. In the absence of PRMT1, viral transcripts are destabilized and subject to degradation via the nonsense-mediated decay (NMD) pathway. These findings highlight PRMT1 as a critical regulator of the HPV18 lifecycle, particularly in RNA processing, and position it as a potential therapeutic target for persistent HPV18 infections.

microbiology↗