During nuclear maturation of most eukaryotic pre-messenger RNAs and long non-coding RNAs, introns are removed through the process of RNA splicing. Different classes of introns are excised by the U2-type or the U12-type spliceosomes, large complexes of small nuclear ribonucleoprotein particles and associated proteins. We created intronIC, a program for assigning intron class to all introns in a given genome, and used it on 24 eukaryotic genomes to create the Intron Annotation and Orthology Database (IAOD). We then used the data in the IAOD to revisit several hypotheses concerning the evolution of the two classes of spliceosomal introns, finding support for the class conversion model explaining the low abundance of U12-type introns in modern genomes.

Myeloid neoplasms are characterized by frequent mutations in at least seven components of the spliceosome that have distinct roles in the process of pre-mRNA splicing. Hotspot mutations in SF3B1 , SRSF2 , U2AF1 and loss of function mutations in ZRSR2 have revealed widely different aberrant splicing signatures with little overlap. However, previous studies lacked the power necessary to identify commonly mis-spliced transcripts in heterogeneous patient cohorts. By performing RNA-Seq on bone marrow samples from 1,258 myeloid neoplasm patients and 63 healthy bone marrow donors, we identified transcripts frequently mis-spliced by mutated splicing factors (SF), rare SF mutations with common alternative splicing (AS) signatures, and SF-dependent neojunctions. We characterized 17,300 dysregulated AS events using a pipeline designed to predict the impact of mis-splicing on protein function. Meta-splicing analysis revealed a pattern of reduced levels of retained introns among disease samples that was exacerbated in patients with splicing factor mutations. These introns share characteristics with “detained introns,” a class of introns that have been shown to promote differentiation by detaining pro-proliferative transcripts in the nucleus. In this study, we have functionally characterized 17,300 targets of mis-splicing by the SF mutations, identifying a common pathway by which AS may promote maintenance of a proliferative state.

During nuclear maturation of most eukaryotic pre-messenger RNAs and long non-coding RNAs, introns are removed through the process of RNA splicing. Different classes of introns are excised by the U2-type or the U12-type spliceosomes, large complexes of small nuclear ribonucleoprotein particles and associated proteins. We created intronIC, a program for assigning intron class to all introns in a given genome, and used it on 24 eukaryotic genomes to create the Intron Annotation and Orthology Database (IAOD). We then used the data in the IAOD to revisit several hypotheses concerning the evolution of the two classes of spliceosomal introns, finding support for the class conversion model explaining the low abundance of U12-type introns in modern genomes. INTRODUCTIONThe process of RNA splicing is a necessary step in the maturation of nearly all eukaryotic pre-messenger RNAs and many long non-coding RNAs. During this process, introns are excised from primary RNA transcripts, and the flanking exonic sequences are joined together to form functional, mature messenger RNAs (1, 2) . In most organisms, introns can be excised through two distinct pathways: by the major (greater than 99% of introns in most organisms) or minor (less than 1% in most organisms, with some organisms lacking minor class introns altogether) spliceosome. Despite the existence of eukaryotic species lacking the minor spliceosome, many reconstructions have shown that all eukaryotes descended from ancestors that contained minor class introns in their genomes, all the way back to the last eukaryotic common ancestor (3, 4) . The minor class introns have consensus splice site and branch point sequences distinct from the major class introns (5, 6) . It was originally thought that the two classes of introns were distinguished by their terminal dinucleotides, with introns recognized by the major spliceosome beginning with GT and ending with AG, and introns recognized by the minor spliceosome beginning with AT and ending with AC. However, it was later shown that introns in both classes can have either sets of terminal dinucleotides and that longer sequence motifs recognized by the snRNA components unique to each spliceosome distinguish the two classes of introns, hence the designations of "U2-type" for the major and "U12-type" for the minor spliceosomes (7) .The large-scale and well-organized online databases of genomic data, like Ensembl (8) , UCSC (9) , and RefSeq (10) , do not provide extensive annotation information of intronic sequence in particular. Many databases focusing primarily on intron annotation information were created in the early 2000s, but most are no longer accessible (11)(12)(13)(14)(15)(16) , and the ones that remain accessible have not been updated in many years (17,18) . The Exon-Intron Database (EID) (14) was one of the most comprehensive and robust databases in this group, and served as a basis for many further investigations into the peculiarities of introns (19-21) , including other, more niche intron annotation databases (15,22) . EID ...