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Multiple intron motifs have redundant functions in trans-splicing of the mod(mdg4) locus

ABSTRACT: In contrast to canonical cis-splicing, trans-splicing combines exons from two distinct transcripts, yielding chimeric mRNAs. One striking example is the ubiquitously expressed modifier of mdg4 (mod(mdg4)) locus in Drosophila, where all mRNAs spanning over 30 isoforms are generated exclusively by trans-splicing. This process combines common constitutive exons with one of many alternative 3′ variable exons transcribed from independent promoters. Here, we demonstrate that trans-splicing is determined by an approximately 600-bp region located in the proximal part of the last common intron. Deletion analysis in a model system and directly within the endogenous mod(mdg4) locus revealed that this intronic region contains multiple redundant motifs for RNA-binding proteins (RBPs), which collectively determine the level of trans-splicing. By affinity purification of the in vitro transcribed proximal part of the intronic RNA, we identified specific binding of a large group of spliceosome-associated RBPs, some of which were found to have binding motifs in the intronic region of mod(mdg4) RNA, which is critical for trans-splicing.

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ORGANISM(S): Drosophila Melanogaster (fruit Fly)

TISSUE(S): Cell Culture

SUBMITTER: Georgij Arapidi

LAB HEAD: Georgij Arapidi

PROVIDER: PXD079014 | Pride | 2026-05-28

REPOSITORIES: Pride

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Project description:Whole genome profiling of 4 histone modifications (H3K27me1, H3K27me3,H3K36me1 and H3K36me3) using ChIP-on-chip. It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons ("exon-intron marking"), linking chromatin structure and function to co- transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.

			Action	DRS
	Sh-129.dat	Other
	Sh-129.mgf	Mgf
	Sh-129.mzid	Mzid
	Sh-129.mzid_Sh-129.MGF	Mzid
	Sh-129.raw	Raw

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Multiple intron motifs have redundant functions in trans-splicing of the mod(mdg4) locus

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