| Literature DB >> 33968994 |
Katherine Dwyer1, Neha Agarwal1, Lori Pile1, Athar Ansari1.
Abstract
Introns impact several vital aspects of eukaryotic organisms like proteomic plasticity, genomic stability, stress response and gene expression. A role for introns in the regulation of gene expression at the level of transcription has been known for more than thirty years. The molecular basis underlying the phenomenon, however, is still not entirely clear. An important clue came from studies performed in budding yeast that indicate that the presence of an intron within a gene results in formation of a multi-looped gene architecture. When looping is defective, these interactions are abolished, and there is no enhancement of transcription despite normal splicing. In this review, we highlight several potential mechanisms through which looping interactions may enhance transcription. The promoter-5' splice site interaction can facilitate initiation of transcription, the terminator-3' splice site interaction can enable efficient termination of transcription, while the promoter-terminator interaction can enhance promoter directionality and expedite reinitiation of transcription. Like yeast, mammalian genes also exhibit an intragenic interaction of the promoter with the gene body, especially exons. Such promoter-exon interactions may be responsible for splicing-dependent transcriptional regulation. Thus, the splicing-facilitated changes in gene architecture may play a critical role in regulation of transcription in yeast as well as in higher eukaryotes.Entities:
Keywords: exon; gene architecture; gene looping; gene regulation; intron; splicing; transcription
Year: 2021 PMID: 33968994 PMCID: PMC8097089 DOI: 10.3389/fmolb.2021.669004
Source DB: PubMed Journal: Front Mol Biosci ISSN: 2296-889X
FIGURE 1Splicing occurs cotranscriptionally and affects different steps of transcription. (A) An intron within the transcribed region is flanked by exon I and exon II. The splice sites are designated as 5′ splice site and 3′ splice site and are the sites for spliceosome assembly during transcription. (B) Splicing factors are recruited cotranscriptionally to the intron with the help of the RNAPII carboxy-terminal domain. Spliceosomal assembly on the splice sites can facilitate the stabilization of general transcription factors (GTFs) at the promoter region of the gene and prime nucleosomes with activation marks (H3-K9 acetylation and H3-K4 trimethylation) for initiation. The splicing factors can also interact with transcription elongation factors and influence nucleosome modifications (H3-K36 trimethylation) to promote elongation. Similarly, splicing factors can contribute to enhanced termination of transcription by facilitating the recruitment of termination factors and removal of elongation marks that block effective termination.
FIGURE 2Intron-dependent gene looping enhances transcription by facilitating initiation, reinitiation and promoter directionality. (A) A gene with an intron (yellow) and exons (blue). (B) During transcription, an elongating RNAPII transcribes the gene and recruits splicing factors (SF) to splice out the intervening intronic sequence. Splicing components (SF) at the 5′ splice site interact with the general transcription factors (GTFs) at the promoter forming a loop between the promoter and 5′ splice site. (C) Once RNAPII has transcribed the intron, splicing components at the 3′ splice site associate with the termination factors near the 3′ end of the gene forming a loop between the 3′ splice site and terminator. Finally, the gene forms an overall three-looped conformation where the promoter and terminator physically interact with one another to assist in reinitiation. The three unique interactions that take place are between the promoter-terminator, promoter-5′ splice site and terminator-3′ splice site. GTFs, general transcription factors; SFs, splicing factors; TF, termination factors.