Pachter, L. S. | bioRxiv Science

bioRxiv2025

Differential Analysis Reveals Isoform Switching Following Pneumococcal Vaccination

Advances in RNA-sequencing (RNA-seq) technology have enabled scalable and accessible transcriptomics studies. Longitudinal RNA sequencing studies have been used to track gene expression over time, revealing biological pathways and expression patterns. Traditional approaches for such studies rely on pairwise comparisons or linear regression models, but these methods face challenges when dealing with many time points or modeling complex, non-linear expression patterns. Spline regression offers a robust alternative by efficiently capturing temporal patterns. In this study, we apply spline regression to analyze longitudinal RNA-seq data and demonstrate its advantages in isoform-level differential expression analysis. By modeling transcript-level expression, our method captures isoform switching events that can be obscured in traditional gene-level analyses.

bioinformatics↗

bioRxiv2019

Odd-paired is a late-acting pioneer factor coordinating with Zelda to broadly regulate gene expression in early embryos

Pioneer factors such as Zelda help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates late expression through enhancer sog_Distal, along the dorso-ventral axis, we hypothesized that Opa acts as a general timing factor. Chromatin-immunoprecipitation (ChIP-seq) confirmed Opa in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zelda. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zelda, influences chromatin accessibility genome-wide, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa, a general timing factor and likely a late-acting pioneer factor, heralds in a secondary wave of zygotic gene expression.

developmental biology↗