First Come, First Served: Sui Generis Features of the First Intron

Abstract

Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes undergo alternative splicing (AS), which ostensibly is considered to increase protein diversity as one of the intrinsic mechanisms for fitness to the varying environment or the internal developmental program. In addition, recent findings have prevailed in terms of overlooked intron functions. Here, we review recent progress in the underlying mechanisms of intron function, in particular by focusing on unique features of the first intron that is located in close proximity to the transcription start site. The distinct deposition of epigenetic marks and nucleosome density on the first intronic DNA sequence, the impact of the first intron on determining the transcription start site and elongation of its own expression (called intron-mediated enhancement, IME), translation control in 5′-UTR, and the new mechanism of the trans-acting function of the first intron in regulating gene expression at the post-transcriptional level are summarized.

Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance

“…AS enables regulated production of multiple distinct mRNAs and protein variants from a single gene via differential joining or skipping of exons or portions of exons and removal of introns within a pre-mRNA transcript [ 11 ]. For general mechanisms of AS, the reader is referred to recent reviews [ 12 , 13 , 14 ]. Five major types of AS events include intron retention (IR), exon skipping (ES), alternative 5′ splice sites (A5SS; alternative donor site), alternative 3′ splice sites (A3SS; alternative acceptor site), and mutually exclusive exons (MXE) [ 15 , 16 ].…”

Reading between the Lines: RNA-seq Data Mining Reveals the Alternative Message of the Rice Leaf Transcriptome in Response to Heat Stress

“…This gene shows temperature-dependent DAS-only, altering the relative levels of two isoforms that differ by two AS events: (1) retention or removal of the first intron, which alters the 5′ untranslated region (UTR); and (2) an alternative 3′ splice site of exon 4, which adds or removes, respectively, 3 amino acid residues of the predicted proteins, near the DnaJ domain (PFAM accession PF00226.24) ( Figure 5 A). Post-transcriptional regulation by intron retention (IR) within the 5′-UTR can affect transport, stability and translatability of mRNAs [ 75 ], whereas changes in the protein primary structure can impact its function. These results suggest that AS of LOC_Os01g32870 in response to heat stress might impact its protein levels and function.…”

TheArabidopsis thalianacore splicing factor PORCUPINE/SmE1 requires intron-mediated expression

“…Introns can drive the expression of the gene, affect expression levels and organ-/tissue-specificity, activate transcription, contain cis -regulatory elements, provide miRNA-binding sites, and possibly contain elements that act as riboswitches (Xie and Wu 2002; Meng et al 2013; Meng et al 2021). First introns in particular have been shown to play important roles in these regulatory functions, in some cases turning them into the key regulators of gene expression (Salgueiro et al 2000; Zalabák and Ikeda 2020; Zhu et al 2024). In particular, the phenomenon of the intron-mediated enhancement (IME) has been shown to be strongly linked to the proximity of the given (first) intron to the 5’UTR (Rose 2004; Gallegos and Rose 2015).…”