Mrna utr region. Despite its name, the 5′ UTR, or a portion of it is .
Mrna utr region. The 3′ untranslated regions (3′UTRs) of the mRNA serve pivotal roles in post-transcriptional gene expression, regulating mRNA stability, translation, and localization. The 3' untranslated region (UTR) is a section of mRNA that follows the coding sequence and precedes the poly(A) tail. Figure 1 shows these and other features of mRNAs. The mRNA is then translated into a protein. Exosomes can contain DNA, mRNA Download scientific diagram | mRNA processing generates 3'-UTR variants. Sequences in 3′ UTRs confer alterations in mRNA stability, direct mRNA localization Mar 7, 2025 · 3’ Untranslated Region (3’ UTR) Description: Sequence between the stop codon and poly (A) tail. This suggests an important role for 3′-UTRs in the biology of higher Sep 9, 2025 · Synthetic mRNA has the same primary structure as mature mRNA molecules, typically consisting of five elements (from 5′ to 3′): a cap structure, a 5′ untranslated region (5′ UTR), a coding sequence, a 3′ UTR, and the poly (A) tail. 8% in endogenous 5′ UTRs, surpassing existing models. Feb 25, 2025 · The 5′ untranslated region (5′ UTR) of mRNA plays a key role in this process, often exhibiting a complicated and structured landscape. Sep 9, 2025 · The translation initiation efficiency of mRNA is affected by the sequence and structure of the 5′ UTR region. The UTRs are the non-coding regions of a gene that flank the coding sequence and are responsible for regulating gene expression Jul 27, 2020 · Massively parallel reporter assays from a synthetic mRNA library identify sequence features of 5′ UTRs that control mRNA translatability and reveal ribosome-dependent and ribosome-independent Oct 28, 2024 · Abstract Messenger RNA (mRNA) vaccines and therapeutics are emerging as powerful tools against a variety of diseases, including infectious diseases and cancer. Variants within the UTR can lead to changes associated with human traits and diseases; however, computational prediction of UTR variant effect is challenging. Precise control of protein synthesis by engineering sequence elements in 5' untranslated regions (5' UTRs) remains a fundamental challenge. This regulation is performed mainly by RNA binding proteins (RBPs) and miRNAs, which primarily target the 3’ untranslated region (3’UTR) of transcripts. In this review, we summarize the information known to date about 3'end processing, sequence characteristics including related binding proteins and the role of 3'UTRs in several selected signaling pathways to delineate their importance A systematic survey shows increased levels of secondary structure in the 5′ UTR near the 5′ cap in mRNAs that are regulated by miRNA in animals, but not in plants. (See Central dogma of molecular biology). Many mRNAs have polymorphic 3′UTR regions. These sequences encode regulatory structures and sequences often referred to as cis -regulatory, or cis -acting elements. Current noncoding variant prediction mainly focuses on Aug 5, 2020 · UTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. In bacteria, mRNAs comprise two UTRs that flank the coding sequences (CDS), referred to as 5′ and the 3′ UTRs (Menendez-Gil and Toledo-Arana, 2020). A common feature found in the 5´ UTR is the poly-adenine (poly(A)) tract. Keywords: RNA structure, 5′ untranslated region, microRNA, gene regulation Apr 29, 2024 · Untranslated regions (UTRs) are the regions flanking the protein-coding sequence of genes that form part of the mRNA, but are not translated into protein. 5 While UTRs are not translated, they contain regulatory elements that control mRNA half-life, intracellular localization, and translation rate by interacting with translation factors, mRNA-binding proteins, and microRNAs (miRNAs). However, the effect of 5´ UTR poly(A) on protein production remains controversial. The length of 5′ untranslated regions (UTRs) has increased in eukaryotes during evolution, with median lengths ranging between 53–218 nucleotides (nt). The protein-coding region of a gene contains nucleotides that codes for amino acids. In addition, 3′ UTRs can establish 3′ UTR-mediated protein–protein interactions (PPIs), and thus can transmit genetic information encoded in 3′ UTRs to proteins. These structures may regulate cap-dependent translation Jan 10, 2024 · Untranslated regions (UTRs) are noncoding portions of the sequence of mRNA located upstream (5′UTR) and downstream (3′UTR) of the coding region of mRNA. The mRNA sequence consists of five key structural elements: the 5' cap structure (Cap), 5' untranslated region (UTR), coding sequence (CDS), 3' untranslated region (UTR), and poly (A) tail. The 5′ and a 3′ UTR sequences do not code for amino acids but contain regulatory sequences that influence gene expression. The violin plots Dec 20, 2023 · UTR Mutations and Genetic Disorders Genetics play a crucial role in the development and functioning of organisms. 1% of the mean ribosome load (MRL) variation in random 5′ UTRs and 82. SUMMARY 3′ untranslated regions (3′ UTRs) of messenger RNAs (mRNAs) are best known to regulate mRNA-based processes, such as mRNA localization, mRNA stability, and translation. The review describes various applications and challenges of UTR design in the development of gene therapy and mRNA-based therapeutics. The current Jan 3, 2012 · 5′-UTR of mRNA and associated diseases In this section, we describe how various cis -regulatory elements located in the 5′-UTRs of mRNAs influence translation and cause diseases under altered conditions. Alignments of Expressed sequence tags (ESTs) are shown in purple, and the messenger RNA (mRNA) and complementary DNA (cDNA) evidence alignment is shown in brown. 3′-untranslated regions (3′-UTRs) are the noncoding parts of mRNAs. Nov 15, 2024 · How to improve gene expression by optimizing mRNA structures is a crucial question for various medical and biotechnological applications. The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly upstream from the initiation codon. (A) Schematic depictions of pre-mRNA and mature mRNA. The current May 21, 2025 · The 5′ untranslated region (UTR) of mRNAs has a central role in translation initiation: for example, the 5′ cap promotes initiation, whereas upstream open reading frames suppress initiation May 1, 2012 · Abstract The untranslated regions (UTRs) at the 3'end of mRNA transcripts contain important sequences that influence the fate of mRNA and thus proteosynthesis. Sep 26, 2024 · In this review, we outline four key principles for optimal mRNA sequence design: enhancing ribosome loading and translation efficiency through untranslated region (UTR) optimization, improving translation efficiency via codon optimization, increasing structural stability by refining global RNA sequence and extending in-cell lifetime and Aug 16, 2024 · This paper proposes a novel contextual language model (LM)-based embedding method: mRNA2vec. (A) Long 3′UTRs and transcriptional read-through can produce overlapping 3′UTRs that modulate the expression of convergent genes. UTRs … See full list on academic. Its features include binding sites for regulatory proteins and microRNAs that can modulate gene expression after transcription has occurred. UTR (untranslated region), CDS (protein coding sequence), UC-PAS The 5′ untranslated region (5′ UTR) is a region at the beginning of an mRNA that precedes the coding sequence of the protein. By comparing the expression levels of reporter genes with different 5'UTRs, we identified the 5'UTR associated with the Nov 27, 2017 · 3'-untranslated regions (3'-UTRs) are the noncoding parts of mRNAs. While its roles in the 3’ untranslated regions (3’ UTR) are well-studied, its role in the 5' UTR and its relationship with histone modifications remain underexplored. Untranslated regions (UTRs) are segments of mRNA that are located at the 5' and 3' ends of the coding sequence but do not encode for proteins. Similar to DNA mutations producing aberrant proteins, RNA alterations expand the transcriptome landscape and change the cellular Jan 8, 2021 · Figure 1. mRNA structure, approximately to scale for a human mRNA, where the median length of 3′UTR is 700 nucleotides In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that The 5’ and 3’ untranslated regions (UTRs) are mRNA domains that control critical post-transcriptional gene regulation processes. The length of the 5′-UTR of an mRNA, its thermal stability and GC content, as well as the locations of secondary structures, multiple uORFs (upstream ORFs) and IRES influence its overall Jun 10, 2025 · In summary, we proposed a novel strategy to enhance mRNA stability and protein translation efficiency by introducing AU-rich elements in the 3′ UTR region of mRNA. One important area of study in genetics is the role of mutations in the untranslated regions (UTRs) of genes and their association with genetic disorders. Most eukaryotic protein-coding genes express 3’UTR isoforms owing to alternative cleavage and polyadenylation (APA). Chu, Yu and colleagues develop a language model for analysing Feb 28, 2002 · The resultant mature mRNA, in eukaryotes, has a tripartite structure consisting of a 5' untranslated region (5' UTR), a coding region made up of triplet codons that each encode an amino acid and a 3' untranslated region (3' UTR). Numerous eukaryotic mRNAs possess long 5′ UTRs that contain diverse regulatory elements, including RNA secondary structures, specific nucleotide motifs, and chemical modifications. coli reporter increases translation The 5' UTR is an important region as it contains a site which the ribosome can assemble in order to initiate the scanning process for the AUG start codon in the coding region. In mRNA, translation start is AUG and translation stop can be UAA, UAG, and UGA. Considerations for therapies: As with the 5’ UTR, sequences from the alpha and beta globins are widely used for the 3’ UTR of therapeutic mRNAs. The 3’UTR of mRNA is transcribed from DNA, but is not translated into protein. 3′ UTRs are believed to harbor recognition sites for a diverse set of Aug 1, 2003 · Although other regions of an mRNA can regulate its activity, this review focuses on how elements that are located in the 3′ UTR control translation. In contrast to existing mRNA embedding approaches, our method is based on the self-supervised teacher-student learning framework of data2vec. , 2015). mRNA structure is highly unstable and prone to degradation, and rational sequence design is a highly effective strategy for enhancing mRNA stability. This study adopted a combinatorial screening strategy to enhance exogenous mRNA translation efficiency by de novo designing 5′UTRs and combining them with multiple potential 3′UTRs. Cap analysis of gene expression (CAGE), a method for the detection of capped 5′ ends of mRNAs, additionally reveals a large number of apparently 5′ capped RNAs derived from locations within the body of the transcript, including 3′UTRs. 93 Jan 24, 2019 · The coding sequence (CDS) of an mRNA is flanked by 5′- and 3′-untranslated regions (UTR). 6,7 A significant amount of research explored the Sep 16, 2024 · Post-transcriptional regulatory sequences often reside within messenger RNA (mRNA) 3’-untranslated regions (UTRs). UTRs are known to vary substantially across genes, both in size, and in the composition Jan 1, 2023 · Genomic information stored in the DNA is transcribed to the mRNA and translated to proteins. Mar 12, 2025 · Background N6-methyladenosine (m6A) is a prevalent and conserved RNA modification in eukaryotes. Despite its name, the 5′ UTR, or a portion of it is Apr 5, 2024 · The 5′ untranslated region is a critical regulatory region of mRNA, influencing gene expression regulation and translation. We have successfully Mar 20, 2025 · The untranslated regions (UTRs) influence important parameters like mRNA stability and translation efficiency. Here, we provide Additionally, quantification of AUF1 mRNA 3′UTR splice variants during murine embryonic development showed that the expression of NMD-sensitive AUF1 mRNAs is specifically enhanced as development proceeds, contributing to dynamic changes in AUF1 3′UTR structures during embryogenesis. In animals, miRNAs • 3’UTR – The three prime untranslated region is the part of messenger RNA that procedes the translation termination codon. Generally, the 3′ UTR encompasses the transcription termination site and plays a pivotal role in ensuring the stability of the The 3′ untranslated regions (3′ UTRs) of mRNAs serve as hubs for post-transcriptional control as the targets of microRNAs (miRNAs) and RNA-binding proteins (RBPs). Untranslated region (UTR) refers to the segments of mRNA located at the 5′ and 3′ ends that are not translated into protein, playing crucial roles in regulating gene expression through interactions with specific factors that influence the translation process. These overlapping double-stranded RNA regions are processed by RNase III, which ultimately decreases protein expression. The linkage between methylated G residue and a 5' to 5' triphosphate bridge is known as the cap structure, which is essential for efficient initiation of protein synthesis. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. Feb 4, 2025 · The 5′ UTR is critical for mRNA stability and translation efficiency in therapeutics. Compared to yeast, in humans, median 3'-UTR length has expanded approximately tenfold alongside an increased generation of alternative 3'-UTR isoforms. The ribosomal initiation The 5′ untranslated region (5′ UTR) of mRNA plays a key role in this process, often exhibiting a complicated and structured landscape. Abstract RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. The production of synthetic mRNA by in vitro transcription (IVT) is simple, fast, and cost-effective at any scale. To accelerate our understanding of the cis-regulatory code embedded in 5' UTRs, we devised massively parallel reporter assays from a synthetic messenger RNA lib … Messenger RNAs (mRNAs) contain prominent untranslated regions (UTRs) that are increasingly recognized to play roles in mRNA processing, transport, stability, and translation. ) mRNA structure, approximately to scale for a human mRNA In molecular genetics, an untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. Controlling 3′UTR This protocol focuses on probing the function of RNA-binding proteins (RBPs) through their interactions with the 3' untranslated region (UTR), thus examining gene expression regulation on the mRNA level. In contrast, the number of coding genes, as well as coding region length, has re … Jan 3, 2024 · Background The 5´ untranslated region (5´ UTR) plays a key role in regulating translation efficiency and mRNA stability, making it a favored target in genetic engineering and synthetic biology. The 3’UTR isoform The 5'-untranslated region (5'-UTR) of mRNA contains structural elements, which are recognized by cell-specific RNA-binding proteins, thereby affecting the translation of the molecule. Sep 16, 2024 · Post-transcriptional regulatory sequences often reside within messenger RNA (mRNA) 3’-untranslated regions (UTRs). Despite its name, the 5′ UTR, or a portion of it is Mar 3, 2002 · The resultant mature mRNA, in eukaryotes, has a tripartite structure consisting of a 5' untranslated region (5' UTR), a coding region made up of triplet codons that each encode an amino acid and a 3' untranslated region (3' UTR). Machine-learning models are powerful The 3’ untranslated region (3’UTR) of mRNA plays a key role in post-transcriptional regulation of gene expression. Aug 27, 2024 · To investigate the impact of different 5ʹ untranslated regions (UTRs) on mRNA vaccine translation efficiency, five dual-reporter gene expression plasmids with different 5ʹUTRs were constructed The untranslated regions (UTRs) of messenger RNAs (mRNAs) play a crucial role in regulating translational efficiency, stability, and tissue-specific expression. This The 5’ UTR, a regulatory region at the beginning of an mRNA molecule, plays a crucial role in regulating the translation process and impacts the protein expression level. • Exosomes – are large vesicles between 30–100 nm which are released by cells and found in many biological fluids such as blood, urine, salvia. In the current update, the UTR entries have Untranslated regions (UTRs) are noncoding portions of the sequence of mRNA located upstream (5′UTR) and downstream (3′UTR) of the coding region of mRNA. The starting point for IVT mRNA . Using UTR-Insight, we performed high-throughput in Aug 17, 2018 · The transcript models are shown on the left labelled ‘Ensembl’, with 3’ UTR regions highlighted in pink. The flow of information within a cell. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. This function has been shown to regulate Jun 17, 2016 · The eukaryotic 5′ untranslated region (UTR) is critical for ribosome recruitment to the messenger RNA (mRNA) and start codon choice and plays a major role in the control of translation efficiency and shaping the cellular proteome. Language models have showcased their effectiveness in decoding the functions This paper concerns 3′-untranslated regions (3′UTRs) of mRNAs, which are non-coding regulatory platforms that control stability, fate and the correct spatiotemporal translation of mRNAs. Compared to yeast, in humans, median 3′-UTR length has expanded approximately tenfold alongside an increased generation of alternative 3′-UTR isoforms. (See Central dogma of molecular biology. Experimentally validated functional motifs are annotated and also collated at the UTRsite database where more specific information on the functional motifs and cross-links to interacting regulatory protein are provided. Image by Walter Suza. The activation of an innate immune response upon transfection of mRNA into cells is reduced when the mRNA comprises … May 10, 2024 · In eukaryotes, G-quadruplex in mRNA (RG4) 5′ UTR inhibit translation initiation. As regions that are transcribed, but seldom translated, the 5’ and 3’UTRs contain a myriad of regulatory elements involved in pre-mRNA processing, mRNA stability, and translation initiation. It is known that UTRs are associated with processes of mRNA translation, and by interacting with RNA-binding proteins (RBPs) and microRNAs, UTRs can influence mRNA’s translation Mar 26, 2018 · ABSTRACT mRNA based therapies hold great promise for the treatment of genetic diseases. Modulation of untranslated regions (UTR) represents one approach to enhance both mRNA stability and translation efficiency. We developed UTR-Insight, a model integrating a pretrained language model with a CNN-Transformer architecture, explaining 89. Therefore, to better understand the control of IE1 and IE2 mRNA translation, we examined the role of the shared 5′ UTR of the IE1 and IE2 mRNAs (MIE 5′ UTR) in regulating translation. By comparing the expression levels of reporter genes with different 5'UTRs, we identified the 5'UTR associated with the Oct 28, 2024 · Messenger RNA (mRNA) vaccines and therapeutics are emerging as powerful tools against a variety of diseases, including infectious diseases and cancer. In this study, the authors characterize 5’UTR-regulated translation in cell types relevant for mRNA therapies and with fully Nov 7, 2024 · The 3′ untranslated region (3′UTR) plays a crucial role in determining mRNA stability, localisation, translation and degradation. This region plays a critical role in post-transcriptional regulation, influencing mRNA stability, localization, and translation efficiency. Sequences of 5′ and 3′ untranslated regions (UTRs) are responsible for Figure 3. Additionally, the 5'-most nucleotide is the 5' cap, which mediates mRNA stability as well as facilitates translation. However, this therapeutic approach suffers from multiple challenges including the short half-life of exogenously administered mRNA and subsequent protein production. AI generated definition based on: Current Opinion in Genetics & Development, 2013 Jun 10, 2025 · In summary, we proposed a novel strategy to enhance mRNA stability and protein translation efficiency by introducing AU-rich elements in the 3′ UTR region of mRNA. oup. ABSTRACT mRNA based therapies hold great promise for the treatment of genetic diseases. We compared RefSeq-annotated 5′ UTR lengths of reviewed and validated transcripts (n) between species for which at least 100 5′ UTRs are annotated. The design of mRNA molecules, particularly the untranslated region (UTR) and coding sequence (CDS) is crucial for optimizing translation efficiency and stability. In this study, we present a rational strategy that enhances mRNA stability and translation by engineering both the 5′ and 3′ UTR sequences. The untranslated region (UTR) refers to the segments of mRNA that are not translated into protein, specifically including the 5’-untranslated region (5’-UTR), which is located between the transcription initiation site and the translation initiation codon, playing a crucial role in mRNA stability and translation efficiency. Different 3′UTR-mediated regulatory mechanisms in bacteria. The corresponding mRNA transcripts were transcribed and capped in vitro. May 23, 2024 · Abstract The untranslated region (UTR) of messenger ribonucleic acid (mRNA), including the 5′UTR and 3′UTR, plays a critical role in regulating gene expression and translation. UTRs are thought to be particularly important in the context of unregulated Nov 20, 2023 · mRNA-based therapeutics have been found to be a promising treatment strategy in immunotherapy, gene therapy, and cancer treatments. (B) 3′UTRs can interact with the 5′UTR of the same mRNA to Apr 1, 2018 · The mRNA 5′ untranslated region (5′ UTR) plays an important role in regulating mRNA translation. In contrast, the number of coding genes, as well as coding region length, has remained similar. Open in a new tab Jun 20, 2024 · mRNA therapeutics are revolutionizing the pharmaceutical industry. Aug 27, 2024 · Abstract To investigate the impact of different 5' untranslated regions (UTRs) on mRNA vaccine translation efficiency, five dual-reporter gene expression plasmids with different 5'UTRs were constructed. Jan 1, 2025 · The untranslated regions (UTR) play a central role in bacterial post-transcriptional control (Duval et al. Previous efforts focus largely on investigation of the 5′ UTR hairpin structures. The current studies describe and validate screening methods using a diverse set of 5'UTR and 3'UTR combinations for improved expression of the Arginase 1 (ARG1) protein, a potential therapeutic mRNA target. Jan 8, 2021 · Figure 1. We jointly use the 5' untranslated region (UTR) and coding sequence (CDS) region as the input sequences. Current design approaches generally focus solely on either the 5' UTR or the CDS D Untranslated regions (UTR) The 5' untranslated region (5' UTR) is the region of the mRNA transcript that is located between the cap site and the initiation codon. Language models have showcased their effectiveness in decoding the functions May 1, 2025 · Results and discussion β-Catenin 5′UTR contains two structurally distinct domains Human β-catenin mRNA contains a 214-nucleotides long 5′UTR, featuring a GC-rich region and a short stretch of AU nucleotides just upstream of the AUG start codon. Function in the cytosol: The 3’ UTR influences the stability of the transcript. Here the authors employ single molecule assay to show that RG4 in E. Genomic information stored in the DNA is transcribed to the mRNA and translated to proteins. It plays a critical role in regulating the translation from mRNA May 1, 2025 · Results and discussion β-Catenin 5′UTR contains two structurally distinct domains Human β-catenin mRNA contains a 214-nucleotides long 5′UTR, featuring a GC-rich region and a short stretch of AU nucleotides just upstream of the AUG start codon. Results We demonstrate that m6A methylation in the 5’ UTR of mRNA triggers a downstream shift in H3K4me3 modification. Open in a new tab Mar 3, 2002 · The resultant mature mRNA, in eukaryotes, has a tripartite structure consisting of a 5' untranslated region (5' UTR), a coding region made up of triplet codons that each encode an amino acid and a 3' untranslated region (3' UTR). DNA is first transcribed into RNA, which is subsequently translated into protein. Effectiveness of mRNA therapeutics depends on the level and duration of a desired protein’s expression, which is determined by various cis- and trans-regulatory elements of the mRNA. UTRs are important mediators of post-transcriptional regulation, controlling mRNA stability, cellular localisation and the rate of protein synthesis [1]. Jun 29, 2022 · The 5' untranslated region (5' UTR) is a sequence present in messenger RNA (mRNA), which serves as the point of entry for the ribosome during translation. Figure 1. For yeast, we used the 5′ UTR lengths as annotated in REFS 34, 35. com Mar 20, 2025 · The untranslated regions (UTRs) influence important parameters like mRNA stability and translation efficiency. We would like to show you a description here but the site won’t allow us. The 3′ untranslated regions (3′UTRs) of the mRNA serve pivotal roles in post-transcriptional gene expression, regulating mRNA stability, translation, and Modulation of untranslated regions (UTR) represents one approach to enhance both mRNA stability and translation efficiency. Assessment of 3' UTR sequence requirements, as well as single and co-regulatory roles of RBPs in regulation of mRNAs will be discussed. These regions play crucial roles in the regulation of gene expression, particularly at the translational level, influencing how efficiently a protein is produced from the mRNA. UTRs contain important sequences that can affect mRNA stability Apr 14, 2017 · Introduction Post-transcriptional regulation is the set of mechanisms and processes that control gene expression at the RNA level and affect the properties and the amount of RNA transcribed and translated into proteins. rwego br3gg0 q8h 6rruv i1ux7p 4xial bzk hhyge j0rg 9meff