TY  - JOUR
AU  - Baeza-Centurión, Pablo
AU  - Miñana, Belén
AU  - Faure, Andre J
AU  - Thompson, Mike
AU  - Bonnal, Sophie
AU  - Quarantani, Gioia
AU  - Clarke, Joseph
AU  - Lehner, Ben
AU  - Valcárcel, Juan
TI  - Deep indel mutagenesis reveals the regulatory and modulatory architecture of alternative exon splicing.
JO  - Nature Communications
VL  - 16
IS  - 1
SN  - 2041-1723
CY  - [London]
PB  - Springer Nature
M1  - DKFZ-2025-01812
SP  - 8117
PY  - 2025
N1  - Pablo Baeza-Centurión
AB  - While altered pre-mRNA splicing is a frequent mechanism by which genetic variants cause disease, the regulatory architecture of human exons remains poorly understood. Antisense oligonucleotides (AONs) that target pre-mRNA splicing have been approved as therapeutics for various pathologies including patient-customised treatments for rare diseases, but AON discovery is currently slow and expensive, limiting the wider adoption of the approach. Here we show that deep indel mutagenesis (DIM) -which can be made experimentally at very low cost - provides an efficient strategy to chart the regulatory landscape of human exons and rapidly identify candidate splicing-modulating oligonucleotides. DIM reveals autonomous effects of insertions, while systematic deletion scans delineate the checkerboard architecture of sequential enhancers and silencers in a model alternative exon. The results also suggest a mechanism for repression of transmembrane domain-encoding exons and for the generation of microexons. Leveraging deep learning tools, we provide a resource, DANGO, that predicts the splicing regulatory landscape of all human exons and can help to identify effective splicing-modulating antisense oligonucleotides.
KW  - Exons: genetics
KW  - Humans
KW  - Alternative Splicing: genetics
KW  - INDEL Mutation: genetics
KW  - Oligonucleotides, Antisense: genetics
KW  - Mutagenesis
KW  - Deep Learning
KW  - RNA Precursors: genetics
KW  - Oligonucleotides, Antisense (NLM Chemicals)
KW  - RNA Precursors (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:40885722
DO  - DOI:10.1038/s41467-025-62957-7
UR  - https://inrepo02.dkfz.de/record/304271
ER  -