Disruption of the minor spliceosome causes primordial dwarfism in microcephalic osteodysplastic primordial dwarfism type 1. Similarly, primordial dwarfism in domesticated animals is linked to positive selection in minor spliceosome components. Despite the importance of minor intron splicing in limb size regulation, its role in limb development remains unexplored. Here we show that loss of U11 small nuclear RNA, an essential minor spliceosome component, results in stunted limbs that maintain patterning. Notably, earlier loss of U11 corresponded to increased severity. We find that limb size is reduced due to elevated minor intron retention in minor intron-containing genes that regulate cell cycle. Limb progenitor cells experience delayed prometaphase to metaphase transition and prolonged S-phase, resulting in death of rapidly dividing, distally located progenitors. Consequently, crucial limb patterning genes are upregulated and their expression is maintained spatially to achieve basic patterning. Overall, these findings reveal a potential mechanism shared in disease and domestication.The minor spliceosome, which consists of five small nuclear RNAs (snRNAs) U11, U12, U4atac, U5, and U6atac and associated proteins, splices <0.5% of introns, termed minor introns, found in <2% of genes, termed minor intron-containing genes (MIGs) 1-3 . In metazoans, the minor spliceosome, MIGs, and the position of minor introns within MIGs are all highly conserved 4-6 . This conservation could be explained by the enrichment of MIGs in essential functions required for cell survival 7 , which is consistent with embryonic lethality observed in multiple animal models with constitutive loss of minor spliceosome function [8][9][10] . Consequently, it is unsurprising that human diseases with minor spliceosome loss-of-function mutations have not been discovered. However, mutations that result in partial loss of minor spliceosome function have been reported [11][12][13][14][15][16] .For example, microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1), Roifman syndrome (RS), and Lowry-Wood syndrome (LWS) are linked to partial inhibition of the minor spliceosome 11,12,14,16 . Here, individuals harbor disparate mutations in RNU4ATAC, which encodes the U4atac snRNA, and display symptoms including microcephaly, micrognathia, vertebral deficits, and primordial dwarfism 16,17 . The severity of primordial dwarfism observed in MOPD1, RS, and LWS is observed along a gradation, with MOPD1 being the most severe, RS moderate, and LWS mild 16,17 . Nonetheless, in all cases, the basic patterning of the limb skeletal elements, including the presence of a stylopod (humerus; femur), zeugopod (radius/ulna; tibia/fibula), and autopod (hand; foot), is maintained 16,17 .Since unique mutations in RNU4ATAC have been linked to MOPD1, RS, and LWS, the gradation of primordial dwarfism might be due to differential inhibition of the minor spliceosome 16,17 . This suggests that the activity of the minor spliceosome might serve as a rheostat for tissue size cont...