Splicing and synthesis of mRNA precursors are functionally coupled
Almost all protein-coding genes and many long non-coding RNA genes are transcribed by RNA polymerase II (Pol II; see Glossary) to generate precursors containing non-coding intron sequences that are spliced out and the flanking exons ligated with exquisite accuracy. The average human gene contains ~10 introns that make up ~90% of its length. Splicing of precursors in alternative ways generates multiple mRNAs from >95% of human genes . Alternative splicing entails the inclusion or skipping of
Heterogeneous pathways of cotranscriptional splicing
Spliceosome assembly and activation (Box 1) are highly regulated and vary greatly in efficiency between introns in different biological contexts. In addition to SS and branch point (BP) sequences that are recognized by the core spliceosome [19,20], splicing is modulated by diverse RBPs including serine and arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs). These factors exert context-dependent positive and negative effects on spliceosome function through
The U1 snRNP–Pol II connection and spatial coupling
Functional coupling of splicing with transcription likely involves a physical interaction between Pol II and splicing factors including U2AF, Prp19 , and SR proteins [43,44]. Such interactions involve contacts with both the Pol II body and its C-terminal domain (CTD) – a unique feature of Pol II that is not found on other RNA polymerases. The CTD is an intrinsically disordered region (IDR) composed of conserved heptad repeats (Y1S2P3T4S5P6S7) that are reversibly phosphorylated at multiple
Determinants of cotranscriptional splicing
Transcription imposes an order and timing on the synthesis of SS and RBP binding sites, whereas on a full-length transcript they are all presented simultaneously. This distinction means that different regulatory mechanisms may operate on cotranscriptional and post-transcriptional splicing. An important challenge is to uncover how cotranscriptional splicing efficiency [i.e., the fraction of transcripts where splicing of a particular intron is completed before release from the polymerase by
The influence of cotranscriptional RNA folding on splicing
Folding of a growing RNA chain is a highly dynamic process that has recently been revealed in vivo by chemical probing methods . Nascent RNA folding is sensitive to transcription speed: slow transcription favors base-pairing of more proximal elements whereas fast transcription favors pairing of more distal elements to form more open structures . The alternative RNA conformations assumed by a growing transcript are most accurately described as ensembles of multiple local energy minima
Splicing and cotranscriptional RNA modifications
Splicing is one of several interdependent cotranscriptional pre-mRNA processing steps that include 5′ capping, covalent nucleotide modification, and cleavage/polyadenylation (CPA). The 5′ cap is added shortly after the 5′ end emerges from the RNA exit channel by capping enzymes that directly contact Pol II [91., 92., 93.]. The cap is recognized by nuclear cap-binding complex (CBC, Figure 2) which promotes recognition of the exon 1 5′ SS by U1 snRNP and subsequent handoff to U6 [94., 95., 96.,
Connections between splicing and cleavage/polyadenylation
There is a complex relationship between cotranscriptional splicing and 3′-end processing by CPA. Splicing of the last intron and processing at the poly(A) site are mutually interdependent, although the mechanisms responsible for this coupling are not well understood. Poly(A) site recognition facilitates splicing of the last intron, probably because it defines the 3′ end of the last exon, and mutation of the poly(A) site inhibits terminal intron splicing [107,108]. Conversely, recognition of the
Splicing connections with transcription initiation, elongation, and chromatin modification
The average speed of transcript elongation by Pol II varies from <0.5 kb/minute to >5.0 kb/minute both between genes and within genes . Transcript elongation comprises short intervals of relatively rapid growth punctuated by frequent pauses where the polymerase may even backtrack. Pausing is more frequent, and transcription is slower, in exons that have higher GC content than introns [124,125]. Slower elongation in exons, or pausing at specific positions in the vicinity of SSs, could affect
Concluding remarks and future perspectives
Our understanding of cotranscriptional splicing has advanced significantly in recent years through the development of sophisticated methods to capture and sequence nascent pre-mRNAs as they are being synthesized and processed by the spliceosome. These studies suggest some new rules that apply specifically to cotranscriptional splicing of nascent RNAs which were not revealed by work on splicing uncoupled from transcription, or by analysis of mature mRNAs. The relative importance of exon
We thank R. Zhao, R. Luhrmann, E. Makeyev, and T. Blumenthal for helpful discussions. Figures were created with BioRender.com. Our work is supported by the University of Colorado Denver RNA Bioscience Initiative and National Institutes of Health (NIH) grants R35GM118051 and R01HD100935 to D.L.B.
Declaration of Interests
The authors declare no conflicts of interest.
- Branch point (BP)
- a short sequence usually containing an A base located 15–50 nt upstream of the 3′ SS that is recognized by base-pairing with U2 snRNA. The 2'-OH of the BP A base attacks the 5′ SS in step 1 to create an intronic lariat intermediate.
- 5′ Cap
- the 5′-triphosphate end of the primary transcript is converted cotranscriptionally to an N7-meG(5′)ppp(5′)-2'-O-meN cap structure by removing the terminal phosphate, GMP transfer, N7-methylation (me) of the terminal G, and 2'-O-methylation of
Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis
The American Journal of Human Genetics, Volume 110, Issue 4, 2023, pp. 663-680
The vast majority of human genes encode multiple isoforms through alternative splicing, and the temporal and spatial regulation of those isoforms is critical for organismal development and function. The spliceosome, which regulates and executes splicing reactions, is primarily composed of small nuclear ribonucleoproteins (snRNPs) that consist of small nuclear RNAs (snRNAs) and protein subunits. snRNA gene transcription is initiated by the snRNA-activating protein complex (SNAPc). Here, we report ten individuals, from eight families, with bi-allelic, deleterious SNAPC4 variants. SNAPC4 encoded one of the five SNAPc subunits that is critical for DNA binding. Most affected individuals presented with delayed motor development and developmental regression after the first year of life, followed by progressive spasticity that led to gait alterations, paraparesis, and oromotor dysfunction. Most individuals had cerebral, cerebellar, or basal ganglia volume loss by brain MRI. In the available cells from affected individuals, SNAPC4 abundance was decreased compared to unaffected controls, suggesting that the bi-allelic variants affect SNAPC4 accumulation. The depletion of SNAPC4 levels in HeLa cell lines via genomic editing led to decreased snRNA expression and global dysregulation of alternative splicing. Analysis of available fibroblasts from affected individuals showed decreased snRNA expression and global dysregulation of alternative splicing compared to unaffected cells. Altogether, these data suggest that these bi-allelic SNAPC4 variants result in loss of function and underlie the neuroregression and progressive spasticity in these affected individuals.(Video) Structure of a Spliceosome: Molecular Framework for Understanding Pre-mRNA Splicing
Cms1 coordinates stepwise local 90S pre-ribosome assembly with timely snR83 release
Cell Reports, Volume 41, Issue 8, 2022, Article 111684
Ribosome synthesis begins in the nucleolus with 90S pre-ribosome construction, but little is known about how the many different snoRNAs that modify the pre-rRNA are timely guided to their target sites. Here, we report a role for Cms1 in such a process. Initially, we discovered CMS1 as a null suppressor of a nop14 mutant impaired in Rrp12-Enp1 factor recruitment to the 90S. Further investigations detected Cms1 at the 18S rRNA 3′ major domain of an early 90S that carried H/ACA snR83, which is known to guide pseudouridylation at two target sites within the same subdomain. Cms1 co-precipitates with many 90S factors, but Rrp12-Enp1 encircling the 3′ major domain in the mature 90S is decreased. We suggest that Cms1 associates with the 3′ major domain during early 90S biogenesis to restrict premature Rrp12-Enp1 binding but allows snR83 to timely perform its modification role before the next 90S assembly steps coupled with Cms1 release take place.
Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing
Molecular Cell, Volume 82, Issue 24, 2022, pp. 4681-4699.e8
Long introns with short exons in vertebrate genes are thought to require spliceosome assembly across exons (exon definition), rather than introns, thereby requiring transcription of an exon to splice an upstream intron. Here, we developed CoLa-seq (co-transcriptional lariat sequencing) to investigate the timing and determinants of co-transcriptional splicing genome wide. Unexpectedly, 90% of all introns, including long introns, can splice before transcription of a downstream exon, indicating that exon definition is not obligatory for most human introns. Still, splicing timing varies dramatically across introns, and various genetic elements determine this variation. Strong U2AF2 binding to the polypyrimidine tract predicts early splicing, explaining exon definition-independent splicing. Together, our findings question the essentiality of exon definition and reveal features beyond intron and exon length that are determinative for splicing timing.(Video) mRNA Splicing - mRNA post-transcriptional processing/modifications - What is alternative splicing?
Integrator is a global promoter-proximal termination complex
Molecular Cell, Volume 83, Issue 3, 2023, pp. 416-427
Integrator is a metazoan-specific protein complex capable of inducing termination at all RNAPII-transcribed loci. Integrator recognizes paused, promoter-proximal RNAPII and drives premature termination using dual enzymatic activities: an endonuclease that cleaves nascent RNA and a protein phosphatase that removes stimulatory phosphorylation associated with RNAPII pause release and productive elongation. Recent breakthroughs in structural biology have revealed the overall architecture of Integrator and provided insights into how multiple Integrator modules are coordinated to elicit termination effectively. Furthermore, functional genomics and biochemical studies have unraveled how Integrator-mediated termination impacts protein-coding and noncoding loci. Here, we review the current knowledge about the assembly and activity of Integrator and describe the role of Integrator in gene regulation, highlighting the importance of this complex for humanhealth.
Involvement of S. cerevisiae Rpb4 in subset of pathways related to transcription elongation
Gene, Volume 545, Issue 1, 2014, pp. 126-131
Yeast Rpb4, a subunit of RNA pol II is not essential for viability but is involved in multiple cellular phenotypes such as temperature sensitivity, enhanced pseudohyphal morphology, and decreased sporulation. Both in vivo and in vitro studies strongly support involvement of Rpb4 in transcription initiation, while its role in transcription elongation is not entirely consistent. Here we show that Rpb4 is not required for recruitment of RNA pol II on the coding region of YLR454w, a representative long gene. Yet we find strong genetic interaction of rpb4∆ with mutants in many transcription elongation factors such as Paf1, Spt4, Dst1, Elp3 and Rpb9. We demonstrate that, Rpb4 interacts functionally with Paf1 to affect the transcription elongation of the FKS1 gene. Our results suggest that while Rpb4 is not required for general transcription elongation, it could support transcription elongation for specific of class of genes by interaction with other elongation factors.(Video) mRNA Processing
Utility of Intraflap Perfusion Procedure for Abdominal Free Flap in Unilateral Breast Reconstruction
Journal of Plastic, Reconstructive & Aesthetic Surgery, 2023
Heparin prophylaxis for venous thromboembolism can be used in microsurgery. If the vein anastomosis was performed before the artery, heparin irrigation into the artery could be performed locally without systematic effect. The purpose of this study was to introduce this “intraflap perfusion procedure” in autologous breast reconstruction.
In the 220 unilateral breast cancer patients performed free abdominal flap, we retrospectively compared the group that had the intraflap perfusion procedure and the group that did not (108 patients with intraflap perfusion vs. 112 patients without). 10mL of a heparinized physiological saline solution (100 units/mL) was injected into deep inferior epigastric artery. Before, during, and after vein anastomosis, intraflap perfusion was performed without the vessel clip of vein. The artery anastomosis was performed without the use of a vein clamp. The vein anastomosis was performed tightly to prevent leakage from the vein anastomosis site during the artery anastomosis.
The rates of superficial inferior epigastric vein (SIEV) superdrainage (18.5% vs. 42.0%, P < 0.001) and intraoperative flap congestion (0.9% vs. 8.0%, P = 0.01) were significantly lower in patients undergoing this procedure. There were no significant differences regarding other factors (age, BMI, laterality, comorbidities and other operative details).
This procedure prevented long-term stasis at the venous anastomosis site and capillary level. It could reduce flap congestion. Because flap congestion occurred, SIEV superdrainage was performed, particularly in patients not undergoing this procedure. Consequently, this procedure could be concluded to reduce the superdrainage rate.(Video) Lecture 16 mRNA splicing Part1
© 2023 Elsevier Ltd. All rights reserved.
RNA splicing is the process by which the newly synthesized pre-mRNA, also known as hnRNA, (heterogeneous nuclear RNA) is processed and forms the mature mRNA. hnRNA is processed in the nucleus and converted to mRNA, which then comes to the cytoplasm and undergoes translation or protein synthesis.What happens in the splicing reaction of pre-mRNA? ›
Splicing of a pre-mRNA molecule occurs in several steps that are catalyzed by small nuclear ribonucleoproteins (snRNPs). After the U1 snRNP binds to the 5′ splice site, the 5′ end of the intron base pairs with the downstream branch sequence, forming a lariat.What is the purpose of pre-mRNA splicing? ›
Precursor mRNA (pre-mRNA) splicing is a critical step in gene expression that results in the removal of intronic sequences from immature mRNA, leading to the production of mature mRNA that can be translated into protein.What occurs if splicing of the pre-mRNA molecule is not done precisely and the sequence of rejoined exons is shifted? ›
All of a pre-mRNA's introns must be completely and precisely removed before protein synthesis. If the process errs by even a single nucleotide, the reading frame of the rejoined exons would shift, and the resulting protein would be dysfunctional.
Three major events constitute pre-mRNA processing: (a) 5′-end capping, (b) splicing, and (c) 3′-end polyadenylation. In 5′-capping, the 5′-triphosphate of the nascent transcript is hydrolyzed to a diphosphate and a guanosine monophosphate is added in a reverse 5′-5′ orientation.What is the pre-mRNA to mRNA process called? ›
Pre-mRNA splicing is one of the fundamental processes in the intrinsic and regulated gene expression in eukaryotes. It is a highly precise process that involves the removal of noncoding intronic sequences from the pre-mature RNA transcript (pre-mRNA) to produce the mature form of protein-coding messenger RNA (mRNA).What does the process of pre-mRNA splicing remove in eukaryotic cells? ›
Pre-mRNA splicing is one of the fundamental processes in the intrinsic and regulated gene expression in eukaryotes. It is a highly precise process that involves the removal of noncoding intronic sequences from the pre-mature RNA transcript (pre-mRNA) to produce the mature form of protein-coding messenger RNA (mRNA).What happens to mRNA during splicing? ›
During splicing, coding-regions of mRNA (exons?) are kept and non-coding regions of mRNA (introns?) are cut out and removed. mRNA Splicing is an important step in the transcription process, as without removing the introns the correct protein cannot be formed.What happens from DNA to pre-mRNA? ›
During transcription, the enzyme RNA polymerase (green) uses DNA as a template to produce a pre-mRNA transcript (pink). The pre-mRNA is processed to form a mature mRNA molecule that can be translated to build the protein molecule (polypeptide) encoded by the original gene.Which pre-mRNA processing step is important for? ›
'7-methylguanosine cap' is the option (d). Every mRNA molecule has a 7-methylguanosine cap, which shields the molecule from exonucleases that breakdown it. The cap is recognized by protein synthesis factors that aid in the initiation of the translation process in ribosomes. As a result, this choice is right.
Gene splicing is a post-transcriptional modification in which a single gene can code for multiple proteins. Gene Splicing is done in eukaryotes, prior to mRNA translation, by the differential inclusion or exclusion of regions of pre-mRNA. Gene splicing is an important source of protein diversity.What is splicing and why is it necessary? ›
It occurs during protein synthesis. It involves the removal of non-coding sequences known as introns and then, joining the coding regions known as exons. The splicing helps to make genes more modular and helps to make new combinations of exons during evolution.What do you think would happen if the mRNA was not sequenced correctly? ›
If an error was made during transcription so that the mRNA has the sequence AUA, this would result in a different amino acid being encoded. As seen in Genetic Code table below, AUG is the codon for the amino acid methionine and AUA encodes the amino acid isoleucine.What happens if RNA splicing does not occur? ›
Splicing removes interrupting segments called introns from the raw, unedited RNA copy of a gene, leaving only the exons, or protein-coding regions. There are over 200,000 introns in the human genome, and if they are spliced out imprecisely, cells will generate faulty proteins.What would be the consequences if mutations happen in the splice sites of pre-mRNA? ›
A genetic alteration in the DNA sequence that occurs at the boundary of an exon and an intron (splice site). This change can disrupt RNA splicing resulting in the loss of exons or the inclusion of introns and an altered protein-coding sequence.How is pre-mRNA processed before translation? ›
The vast majority of precursor mRNAs (pre-mRNAs) undergo 5′ capping, splicing and 3′ polyadenylation before export to the cytoplasm for subsequent translation on ribosomes.What are the stages of transcription in pre-mRNA production? ›
- Step 1: Initiation. Initiation is the beginning of transcription. ...
- Step 2: Elongation. Elongation is the addition of nucleotides to the mRNA strand. ...
- Step 3: Termination. Termination is the ending of transcription, and occurs when RNA polymerase crosses a stop (termination) sequence in the gene.
For most pre‐mRNA, these steps include three main processes: addition and modification of a 5′ cap, removal of introns by RNA splicing, and formation of mature 3′ ends by cleavage and polyadenylation.What is the difference between pre-mRNA and mRNA? ›
The key difference between pre-mRNA and mRNA is that pre-mRNA is the first product of the transcribed gene and contains both non-coding sequences (introns) and coding sequences (exons) while mRNA is the second product of a transcribed gene which contains only coding sequences. Gene is the functional unit of heredity.What is the difference between pre-mRNA and mRNA quizlet? ›
Pre-mRNA contains introns and exons, mRNA contains only exons. Introns are present in gene, mRNA only contains exons. As there are still introns is DNA. mRNA is a long strand, tRNA is a short strand.
The term hnRNA is often used as a synonym for pre-mRNA, although, in the strict sense, hnRNA may include nuclear RNA transcripts that do not end up as cytoplasmic mRNA. There are several steps contributing to the production of primary transcripts.What does the process of pre mRNA splicing remove ______? ›
RNA splicing removes the introns from pre mRNA to produce the final set of instructions for the protein.What can be removed from pre-mRNA during alternative splicing? ›
Sequences called introns are the portions of the pre-mRNA that are removed during splicing. In alternative splicing, some sequences serve as exons under some conditions and are included in the final mRNA.What is the processes of removing the from pre-mRNA and joining the remaining together to form a mature mRNA molecule? ›
The process of removing the introns and rejoining the coding sections or exons, of the mRNA, is called splicing. Once the mRNA has been capped, spliced and had a polyA tail added, it is sent from the nucleus into the cytoplasm for translation.What happens during the process of mRNA splicing quizlet? ›
What happens during the process of mRNA splicing? Introns are removed from the transcript. Exons are joined together. Due to , mature mRNAs of eukaryotes have a modified guanosine covalently attached at the 5' end.What causes mRNA splicing? ›
Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated.What is removed during splicing? ›
Introns are the non-coding regions that are removed from the mRNA during splicing. Only the exons, which actually code for genes, are retained.Where does mRNA splicing occur? ›
Splicing occurs in the nucleus before the RNA migrates to the cytoplasm. Once splicing is complete, the mature mRNA (containing uninterrupted coding information), is transported to the cytoplasm where ribosomes translate the mRNA into protein. The pre-mRNA transcript contains both introns and exons.What is gene splicing in simple words? ›
(SPLY-sing) The process by which introns, the noncoding regions of genes, are excised out of the primary messenger RNA transcript, and the exons (i.e., coding regions) are joined together to generate mature messenger RNA. The latter serves as the template for synthesis of a specific protein.How is gene splicing used by humans? ›
Splicing is an intermediate step in the process when our genes are decoded into proteins, the workhorses of the cell. In this process, the DNA of our genes are transcribed into “messenger” RNA, a molecule similar to DNA that serves as the blueprint for constructing proteins.
|Disease||Gene||Type of splicing mutation|
|Cystic fibrosis (CF)||CFTR||Acceptor splice site mutation|
|Duchenne muscular dystrophy (DMD)||DMD||Donor splice site mutation|
|X-linked spondyloepiphyseal dysplasia tarda||TRAPPC2|
Connectors and splices link the ends of two fibers both optically and mechanically. The two are not interchangeable. A connector is mounted on the end of a cable or optical device so it can be attached to other cables or devices.What happens during splicing? ›
In splicing, some sections of the RNA transcript (introns) are removed, and the remaining sections (exons) are stuck back together. Some genes can be alternatively spliced, leading to the production of different mature mRNA molecules from the same initial transcript.What is the basics of splicing? ›
Splicing is used to concatenate fibers when joining two cables or terminating cables with factory made pigtails (a cable with a connector on one end.) Mechanical splicing uses a small alignment device and index matching gel. Fusion splicing welds fibers together in an electrical arc.What is the possible danger with mRNA vaccines? ›
Anaphylaxis, antibody-dependent enhancements, and deaths, comprise the most serious side-effects, albeit occurring in sparing numbers.What is the main problem with mRNA vaccines against covid 19? ›
A Vaccine Safety Datalink (VSD) analysis indicated that both Pfizer-BioNTech and Moderna vaccines were associated with the risk of myocarditis and pericarditis in individuals aged 18-39 years (an estimated 22.4 excess cases per million doses and 31.2 excess cases per million doses, respectively) (Goddard, August 2022).What happens to the mRNA from a vaccine after it has been used? ›
After vaccination, the mRNA will enter the muscle cells. Once inside, they use the cells' machinery to produce a harmless piece of what is called the spike protein.Does splicing always occur? ›
Splicing occurs in all the kingdoms or domains of life, however, the extent and types of splicing can be very different between the major divisions. Eukaryotes splice many protein-coding messenger RNAs and some non-coding RNAs.Why is splicing of pre-mRNA necessary? ›
Pre-mRNA splicing is essential for gene expression in mammalian cells in which most protein-coding genes are disrupted by intervening sequences (introns). The process to remove introns is efficient and precise, thus constituting the vast majority of constitutive splicing events in the cell.Can RNA splicing errors cause disease? ›
Disrupting the relative abundance of alternatively spliced RNA isoforms can lead to disease. Frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17) arises when mutations occur in the gene MAPT.
Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the processing or the translation of the mRNA, with similar disastrous effects.Does mRNA splicing change the genetic code? ›
The process of splicing fundamentally changes the information content of the RNA transcript, which directly impacts translation of that genetic information into protein.What happens if there is a mutation in mRNA? ›
The mutation may convert a codon that specifies an amino acid into a termination codon. This is a nonsense mutation and it results in a shortened protein because translation of the mRNA stops at this new termination codon rather than proceeding to the correct termination codon further downstream.What is the process of splicing in mRNA? ›
During the process of splicing, introns are removed from the pre-mRNA by the spliceosome and exons are spliced back together. If the introns are not removed, the RNA would be translated into a nonfunctional protein. Splicing occurs in the nucleus before the RNA migrates to the cytoplasm.What is the process from DNA to pre-mRNA? ›
During transcription, the enzyme RNA polymerase (green) uses DNA as a template to produce a pre-mRNA transcript (pink). The pre-mRNA is processed to form a mature mRNA molecule that can be translated to build the protein molecule (polypeptide) encoded by the original gene.What is the processing of RNA splicing? ›
RNA splicing is a process that removes the intervening, non-coding sequences of genes (introns) from pre-mRNA and joins the protein-coding sequences (exons) together in order to enable translation of mRNA into a protein.