Article Figures & Data
Figures
- Figure 1. Schematic overview of the complete cycle through all stages of the spliceosome machinery and corresponding molecules involved in each cycle.
(A) In the first step of splicing, known as “branching,” a 2′ hydroxyl region of conserved adenosine (BS) of the pre-mRNA attacks a phosphate at the 5′ss and results in the release of exon 5′ and formation of a lariat intermediate intron. The second step, called “exon ligation,” allows the binding between the 5′ and 3′ exons of the transcript through the attack carried out by the hydroxyl group of the 5′ exon to the 3′ss, which causes the release of the intron and binding of the exons, generating a mature mRNA. (B) 10 conformational states of the spliceosome are named as E, A, pre–B, B, Bact, B*, C, C*, P, and ILS complexes. Transitions between these states are regulated by helicases or ATPases and several other families of molecules. (C) List of molecules involved in spliceosome machinery and their classification into subgroups of complexes.
- Figure 2. During spliceosome assembly, the snRNPs U1 and U2 interact respectively with the 5′ splice site and the branching site of the intron, forming the spliceosome A complex.
The initial and still unstable coupling of tri-snRNP (U4/U6.U5) to complex A forms the pre–B complex; at this time, U1 snRNA is still paired to the 5′ splice site, and the U2/U6 helix forms.
- Figure 3. In B complex, the transcript undergoes conformational changes, which is characterized by the formation of the stable binding of tri-snRNP with the transcript, the transcript positioning mediated by the DDX23 helicase of U6 in the 5′ss replacing U1, and the unwinding through SNRNP200 of the U4/U6 helices, which are extensively paired in the tri-snRNP complex, and with U4 dissociation, which triggers in a highly structured RNA network between the pre-mRNA and the snRNAs U2, U6, and U5, generating the spliceosome catalytic RNA core (Bact complex).
At this process, some proteins including the RES complex, NTC, and NTR proteins are recruited. By the activity and release of the DHX16, some splicing factors, SF3A, SF3B, and RES complexes, are dissociated. For the B* complex to occur, the vacant space likely allows the recruitment of DHX38 and the stage I–specific factors CWC25 and YJU2, the NTC proteins SFY2 and ISY1, the exon junction complex, and the PPIs PPWD1 and PPIG, allowing the branching reaction, generating a 5′ exon and an intron lariat-3′ exon intermediate (C complex).
- Figure 4. During the transition from C to C*, the PRKRIP1 protein is recruited into the C* complex to stabilize the new position of the U2 snRNP, SNRNP200 is translocated, DHX38 is dissociated in the transition allowing the binding of the DHX8 helicase, and second-stage factors SLU7, PRP18, and DHX8 are required to allow the juxtaposition of the 3′ OH of exon 5′ and the splice site 3′ (C* complex), producing the ligated exons and the lariat intron (P complex).
- Figure 5. Transition from the P complex to the ILS is driven by DHX8; the bound exon is released, causing an efflux of protein components and generating voids for subsequent spliceosome reorganization.
Notably, CWF19L2 was recruited into the ILS1 complex and contributed to the stabilization of ILS1; its structural characteristics support the idea that it assists in the debranching of the intron lariat of the RNA, in the BPS/U2 translocation, and in the disassembly of the spliceosome. ATPase/helicase DHX15 is loaded into the human ILS2 complex and mediates the disassembly of spliceosomes, which are recycled for the next round of splicing.
- Figure 6. Website of the detailed and curated atlas of spliceosome-related molecules, IARA.
The website is composed of three sections. The first section has the menu items to access the website functionalities; the second section has the search field to locate specific words or molecules within the entire website; the third section has the table that displays gene Symbol, gene Name, Details button, and quick Links for external databases.
Tables
- Table 1.
URL path with parameters and description to the API function. URL patterns are prefixed by “https://string-db.org”
URL pattern Parameters used Description /api/[output-format]/network [output-format] [identifiers] [optional_parameters] Retrieves an image of a STRING network of a neighborhood surrounding one or more proteins Parameter Description Value [output-format] Output format: image (PNG image with alpha-channel), highres_image (high-resolution PNG image with alpha-channel), or SVG (Scalable Vector Graphics) SVG [identifiers] Identifiers to gene or protein Gene symbol [optional_parameters] None: loads default parameters (required_score = [depends on the network]; network_flavor = confidence; network type = functional; hide_node_labels = 0; hide_disconnected_nodes = 0; how_query_node_labels = 0; block_structure_pics_in_bubbles = 0) None - Table 3.
URL path with parameters and description to the API function. All URL patterns are prefixed by “https://gtexportal.org/rest/v1/”
URL pattern Parameters used Description /reference/transcript [datasetId] [gencodeId] This service returns information about transcripts of the given versioned GENCODE ID /reference/exon [datasetId] [gencodeId] This service returns exons from all known transcripts of the given gene /expression/geneExpression [datasetId] [gencodeId] [tissueSiteDetailId] [format] This service returns normalized gene expression in tissues at the sample level /expression/medianExonExpression [datasetId] [hcluster] [gencodeId] [tissueSiteDetailId] [format] This service returns median exon read counts by tissues of a given gene from all known transcripts /expression/medianJunctionExpression [datasetId] [hcluster] [gencodeId] [tissueSiteDetailId] [format] This service returns median junction read counts by tissues of a given gene from all known transcripts /expression/medianTranscriptExpression [datasetId] [hcluster] [gencodeId] [tissueSiteDetailId] [format] This service returns median normalized expression in tissues of all known transcripts of a given gene Parameter Description Value [datasetId] Unique identifier of a dataset. Usually includes a data source and data release gtex_v8 [gencodeId] Versioned GENCODE ID of a gene Ensembl code (from the selected row of the table) [tissueSiteDetailId] Tissue ID of the tissue of interest None: all tissues [hcluster] Specifies whether or not to perform hierarchical clustering true [format] Format of result JSON
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