RT Journal
A1 Rashmi, Richa
A1 Muruganandham, Abhinaya
A1 Borkar, Pranita
A1 Mallick, Sumana
A1 Hubbs, Taylor
A1 Aviles, Ari
A1 Chung, Daniel
A1 Singh, Irtisha
T1 Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
JF Genome Research 
JO Genome Research 
YR 2026 
FD April 13 
DO 10.1101/gr.281044.125 
SP gr.281044.125 
UL http://genome.cshlp.org/content/early/2026/04/13/gr.281044.125.abstract 
AB Intronic polyadenylation (IPA) is a key mechanism driving transcriptome diversity, yet its detection and functional characterization remain challenging due to complex splicing patterns and complexity of intronic regions. Here, we introduce IPAseek, a dynamic programming-based computational framework that leverages the Pruned Exact Linear Time (PELT) algorithm and Changepoints Over a Range of PenaltieS (CROPS) to enable de novo identification of IPA events from bulk RNA-seq data. IPAseek robustly detects both composite and skipped IPA isoforms. Applying IPAseek to bulk RNA-seq of hematopoietic cell types, reveals lineage and stage-specific IPA signatures, with lymphoid cells exhibiting higher IPA site usage than myeloid cells. Temporal profiling during megakaryocyte differentiation uncovers dynamic, gene-specific IPA regulation linked to functional pathways including peroxisomal metabolism and autophagy which are known to play a crucial role in megakaryocytic differentiation, impacting the development and maturation of megakaryocytes. Further, integrative analysis demonstrates that IPA site usage is associated with lower DNA methylation within introns, supporting a regulatory axis connecting epigenetic state and IPA. This finding aligns with emerging evidence that DNA methylation modulates alternative polyadenylation via CTCF-mediated chromatin looping. Thus, IPAseek provides a platform to characterize IPA across physiological systems and disease contexts using widely available bulk RNA-seq data. These IPA events can be further integrated with other regulatory datasets to elucidate their interplay and functional significance.