Circular RNAs (circRNAs) are an abundant class of mostly non-coding RNAs implicated in gene regulation. One potential mechanism is their ability to hybridize with DNA, forming circular RNA: DNA hybrids (circR-loops); structures thought to impact transcriptional control and genomic maintenance [1]. TDP-43, a multifunctional RNA-binding protein frequently disrupted in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), may regulate circRNA biology and the formation of these RNA:DNA hybrids.
To address this, we developed a computational pipeline to reanalyze publicly available RNA-seq and DNA:RNA hybrid immunoprecipitation (DRIP)-seq data [2] from SH-SY5Y neuronal cells with TDP-43 knockdown. Our analysis identified 966 circR-loops that specifically formed, and 1,596 that were lost, upon TDP-43 depletion. Pathway enrichment analysis revealed that host genes of control-specific circR-loops were highly associated with polycomb repressive complex, nucleocytoplasmic transport, and cell cycle regulation. In contrast, circR-loops unique to TDP-43 knockdown were enriched for homologous recombination, ATP-dependent chromatin remodeling, and mRNA surveillance pathways. Gene ontology analysis showed that host genes of circR-loops in TDP-43-depleted cells were statistically enriched for double-stranded RNA binding and transcriptional coregulator binding functions.
These findings provide the first genome-wide, computationally mapped atlas of circR-loops responsive to TDP-43 loss in neuronal cells. The dynamic, pathway-specific enrichment of circR-loops highlights a potential role for these non-coding RNA:DNA hybrids in regulating cellular functions relevant to neurodegeneration. While functional validation is ongoing, this resource establishes a foundation for targeted mechanistic studies and future biomarker discovery.
This work establishes the first systematic computational mapping of circR-loops in TDP-43-deficient neurons, defining novel non-coding RNA targets and resources for future studies in neurodegenerative disease models.
[1] Conn, Vanessa M., et al. "Circular RNAs drive oncogenic chromosomal translocations within the MLL recombinome in leukemia." Cancer cell 41.7 (2023): 1309-1326.
[2] Hou, Yingzi, et al. "TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk." Cell reports 43.1 (2024).