Biology subjects

Bisaria, N.

Publications and source records attributed to Bisaria, N..

5 recordsLinked to original sources

bioRxiv2026

An RNA Language Model trained on sequence alone reveals the structural logic of Internal Ribosome Entry Sites

Millions of RNA sequences are readily available, but the structures that determine their function are not. Picornaviruses initiate translation through Internal Ribosome Entry Sites (IRESes), RNA elements that recruit ribosomes independent of the 5` cap. These elements are large and highly divergent, and structural understanding remains limited to a handful of cases. We address this bottleneck by introducing an RNA language model (Albatross), trained purely on sequence, that predicts high-quality IRES structures at scale. We collect in cellulo chemical probing data for 96 full-length IRESes from divergent viruses and show that Albatross achieves far higher precision (0.80) than state-of-the-art predictions (0.47). Analyzing 75,000 IRES structures, we discover a novel Type II structural subclass and validate it experimentally. We demonstrate the pipeline broadly generalizes to identify functional structures, including tertiary contacts and alternative riboswitch structures. These findings establish Albatross as a scalable framework that accelerates RNA structure discovery and antiviral targeting.

molecular biology↗

bioRxiv2023

RNA binding proteins and glycoRNAs form domains on the cell surface for cell penetrating peptide entry

The composition and organization of the cell surface determine how cells interact with their environment. Traditionally, glycosylated transmembrane proteins were thought to be the major constituents of the external surface of the plasma membrane. Here, we provide evidence that a group of RNA binding proteins (RBPs) are present on the surface of living cells. These cell surface RBPs (csRBPs) precisely organize into well-defined nanoclusters that are enriched for multiple RBPs, glycoRNAs, and their clustering can be disrupted by extracellular RNase addition. These glycoRNA-csRBP clusters further serve as sites of cell surface interaction for the cell penetrating peptide TAT. Removal of RNA from the cell surface, or loss of RNA binding activity by TAT, causes defects in TAT cell internalization. Together, we provide evidence of an expanded view of the cell surface by positioning glycoRNA-csRBP clusters as a regulator of communication between cells and the extracellular environment.

cell biology↗

bioRxiv2021

Pairing to the microRNA 3' region occurs through two alternative binding modes, with affinity shaped by nucleotide identity as well as pairing position

MicroRNAs (miRNAs), in association with Argonaute (AGO) proteins, direct repression by pairing to sites within mRNAs. Compared to pairing preferences of the miRNA seed region (nucleotides 2-8), preferences of the miRNA 3' region are poorly understood, due to the sparsity of measured affinities for the many pairing possibilities. We used RNA bind-n-seq with purified AGO2-miRNA complexes to measure relative affinities of >1,000 3'-pairing architectures for each miRNA. In some cases, optimal 3' pairing increased affinity by >500-fold. Some miRNAs had two high-affinity 3'-pairing modes--one of which included additional nucleotides bridging seed and 3' pairing to enable high-affinity pairing to miRNA nucleotide 11. The affinity of binding and the position of optimal pairing both tracked with the occurrence of G or oligo(G/C) nucleotides within the miRNA. These and other results advance understanding of miRNA targeting, providing insight into how optimal 3' pairing is determined for each miRNA. HIGHLIGHTSO_LIRNA bind-n-seq reveals relative affinities of >1,000 3'-pairing architectures C_LIO_LITwo distinct 3'-binding modes can enhance affinity, by >500-fold in some instances C_LIO_LIG and oligo(G/C) residues help define the miRNA 3' segment most critical for pairing C_LIO_LISeed mismatch identity can influence the contribution of compensatory 3' pairing C_LI

biochemistry↗

bioRxiv2018

The biochemical basis of microRNA targeting efficacy

MicroRNAs (miRNAs) act within Argonaute proteins to guide repression of mRNA targets. Although various approaches have provided insight into target recognition, the sparsity of miRNA-target affinity measurements has limited understanding and prediction of targeting efficacy. Here, we adapted RNA bind-n-seq to enable measurement of relative binding affinities between Argonaute-miRNA complexes and all [≤]12-nucleotide sequences. This approach revealed noncanonical target sites unique to each miRNA, miRNA-specific differences in canonical target-site affinities, and a 100-fold impact of dinucleotides flanking each site. These data enabled construction of a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network. This model substantially improved prediction of cellular repression, thereby providing a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks.

biochemistry↗

bioRxiv2018

RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix

Over 50% of residues within functional structured RNAs are base-paired in Watson-Crick helices, but it is not fully understood how these helices geometric preferences and flexibility might influence RNA tertiary structure. Here, we show experimentally and computationally that the ensemble fluctuations of RNA helices substantially impact RNA tertiary structure stability. We updated a model for the conformational ensemble of the RNA helix using crystallographic structures of Watson-Crick base pair steps. To test this model, we made blind predictions of the thermodynamic stability of >1500 tertiary assemblies with differing helical sequences and compared calculations to independent measurements from a high-throughput experimental platform. The blind predictions accounted for thermodynamic effects from changing helix sequence and length with unexpectedly tight accuracies (RMSD of 0.34 and 0.77 kcal/mol, respectively). These comparisons lead to a detailed picture of how RNA base pair steps fluctuate within complex assemblies and suggest a new route toward predicting RNA tertiary structure formation and energetics.

biophysics↗