RNA Processing

12 Key excerpts on "RNA Processing"

• 

  eBook - ePub

  Advanced Molecular Biology

  A Concise Reference

  • Richard Twyman(Author)
  • 2018(Publication Date)
  • Garland Science

    (Publisher)

  Chapter 27

  RNA Processing

  Fundamental concepts and definitions

  • RNA Processing describes the structural and chemical maturation of newly synthesized RNA molecules. The modifications occur during transcription (cotranscriptional modification) and afterwards (posttranscriptional modification); they may be essential for RNA function or may represent a mechanism of gene regulation. Such reactions fall into ten categories, as shown in Table 27.1 .
  • An RNA molecule copied from a DNA template is a transcript. During transcription, it is a nascent transcript, and when transcription is complete it is a primary transcript — an exact copy of the DNA from which it was transcribed. After any modification, the product is a mature transcript and may no longer be an exact copy of the DNA.
  • Not all RNA is modified: bacterial mRNAs are rarely processed (indeed protein synthesis usually initiates before transcription is complete), and eukaryotic 5S rRNA is transcribed as a molecule with mature ends. The precursor of fully processed and functional RNA is termed pre-RNA. Eukaryotic pre-mRNA is also described as heterogeneous nuclear RNA (hnRNA) because, unlike the other forms of nuclear RNA, it has a great size diversity, reflecting varying gene sizes and the presence of partially processed molecules.
  • In eukaryotes, transcription and RNA Processing do not occur ‘free’ in the nucleus, but are localized at discrete foci in the nuclear matrix. Certain mRNA Processing factors (specifically the spliceosome and polyadenylation enzymes) are attached to the C-terminal tail of RNA polymerase II in the elongation complex, so that transcription and processing are directly linked. The localization of mRNA Processing complexes in the nuclear matrix may facilitate export. RNA is associated with proteins in the nucleus and (if appropriate) the cytoplasm, to form ribonucleoprotein particles.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Processing of RNA (1983)

  • David Apirion(Author)
  • 2017(Publication Date)
  • CRC Press

    (Publisher)

  The discovery of such splicing reactions has clarified considerably our conception of posttranscriptional processing of mRNA precursors, not least because many questions can now be framed in specific terms and be addressed by direct experimentation. This is not, however, to imply that RNA Processing is fully appreciated: a more precise outline can certainly be drawn, but the discovery of splicing reactions, like all seminal discoveries, has raised more questions than it has answered. And the answers to these questions may well lie in realms even more remote than, for example, the enzymatic reactions that fashion a mature mRNA species from its primary transcript.

  II. Enzymatic Processing Reactions

  The biogenesis of mature mRNA species from primary products of transcription in eukaryotic cells can be described as an ordered sequence of discrete enzymatic reactions that alter the chemical properties of the RNA: novel 5′ and 3′ termini are made and internal sequences may be modified or removed. These reactions can be distinguished from a second class of processing events during which the chemical nature of sequence of the RNA is not altered, examples of which include association of mRNA precursors with proteins to form ribonucleoproteins, and movement of the RNA from its sites of synthesis, cellular chromatin, to the cytoplasm where it can be translated. Such a distinction, made here for descriptive convenience, is of course artificial and it is important to keep in mind that the substrates of the various processing reactions are not naked RNA molecules but rather ribonucleoproteins. Possible implications of this frequently ignored fact are discussed in Section III; the processing reactions to which an eukaryotic mRNA precursor may be subjected are described in subsequent parts of this section.

  A. Capping, Internal Methylation, and Polyadenylation of mRNA Precursors

  The posttranscriptional modification of presumed precursors to mRNA by addition of 5′ blocking groups (capping), methylation of 5′ terminal and internal residues, and addition of poly (A) to 3′ termini have been recognized for a decade or more. Indeed, capping and polyadenylation have been well studied and are the subjects of Chapters 5 and 6 in this volume. In the general context of synthesis of mature mRNAs, it is, however, worth recapitulating that capping is both ubiquitous among cellular mRNA species and the first of the enzymatic processing reactions to which pre-mRNA species are subject. Addition of poly (A) is a later event and some mature mRNA species are devoid of poly (A) tracts. By contrast, relatively little is known of the mechanism, or significance, of internal methylation.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Fundamentals of Molecular Structural Biology

  • Subrata Pal(Author)
  • 2019(Publication Date)
  • Academic Press

    (Publisher)

  Chapter 10

  RNA Processing

  Abstract

  In eukaryotic cells, before RNA polymerase II-generated transcripts could be translated into protein products, these transcripts (pre-mRNAs) need to be suitably processed to form messenger RNA (mRNA). 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. Subsequently, the GpppN- cap is methylated to form m7 GpppN-. In splicing, the noncoding sequences (introns) that separate the coding sequences (exons) are removed and the exons are joined together. 3′-Polyadenylation involves cleavage of the transcript at a specific site and addition of a poly(A) tail. In addition, there is a fourth mechanism of RNA Processing, known as RNA editing, in which instead of stretches of the transcript, individual bases are inserted, deleted, or altered posttranscriptionally.

  Keywords

  RNA Processing; Capping; Polyadenylation; Splicing; Spliceosome; RNA editing

  The previous chapter has described how a gene is transcribed to produce RNA and the manner in which the process of transcription is regulated. We have also seen that, in eukaryotic cells, the protein-coding genes are transcribed by RNA polymerase II (RNAP II). However, before RNAP II-generated transcripts could be translated into protein products (a phenomenon to be described in the next chapter), these transcripts need to be suitably “formatted” or processed to acquire a form known as messenger RNA (mRNA). The primary transcription product of the protein-coding genes is called the precursor messenger RNA (pre-mRNA).

  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. Subsequently, the GpppN- cap is methylated to form m7

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Cell Biology A Comprehensive Treatise V3

  Gene Expression: The Production of RNA's

  • David M. Prescott(Author)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  This review will focus upon a limited aspect of RNA metabolism, namely, the posttranscriptional processes involved in the biosynthesis and degradation of tRNA and rRNA. The discovery that RNAs are syn-thesized via precursor RNA's that are larger than the mature species has raised several questions related to the process by which these molecules are converted into mature RNA species. Of special interest are the iden-tities of the participating enzymes (processing enzymes) and the nu-cleotide sequences of the initial precursor RNA's and all precursor RNA intermediates generated in the production of mature RNA's. An apprecia-tion of these details should provide a framework for asking how a precur-sor RNA is enzymatically recognized and handled so that its conversion to functional RNA is guaranteed. Perhaps the most intriguing question re-lates to the biological significance of this process: Why has nature chosen to utilize precursor RNA's in the production of RNA? Similarly, in the study of RNA degradation, it is of interest to determine the enzymes involved and the manner in which the degradation process is controlled by the cell. Little is as yet known about this subject, and it will be treated only briefly in this chapter. II. APPROACHES TO THE STUDY OF RNA Processing Complete elucidation of the biosynthetic steps involved in RNA pro-cessing requires identification of both the enzymes involved and the nu-cleotide sequences of the precursor RNA intermediates generated in the production of mature RNA's. Although the involvement of precursor RNA's in the synthesis of stable RNA's was first demonstrated in mamma-lian cells (Burdon et al., 1967), characterization of these has been difficult because with mammalian cells it is difficult to obtain highly labeled, radiochemically pure preparations of an RNA. Thus, in most cases, se-quence analysis of these precursor RNA's has been precluded.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  RNA: Catalysis, Splicing, Evolution

  • M. Belfort, D.A. Shub(Authors)
  • 2012(Publication Date)
  • Elsevier Science

    (Publisher)

  BIOLOGICAL DIVERSITY OF RNA Processing This page intentionally left blank 155 RNA editing: the creation of nucleotide sequences in mRNA — a minireview* (RNA Processing; mitochondrion; gene regulation; editosome) Kenneth Stuart, Jean £. Feagin and John M. Abraham Seattle Biomedical Research Institute, Seattle, WA 98109-1651 (U.S.A.) Received by M. Belfort: 25 October 1988 Accepted: 13 December 1988 SUMMARY RNA editing changes the nucleotide sequence of mRNAs that are encoded in genes which contain the sequences in an abbreviated form. Editing adds uridines that are not encoded in the gene to the transcripts and less frequently removes encoded uridines. The process appears to be posttranscriptional and to proceed in the 3'-to-5' direction. Some sites may undergo multiple editings until the final sequence is produced; in some cases uridines may be added and subsequently removed. A general hypothesis is proposed that predicts a series of reactions that may occur in association with a macromolecular complex, the editosome, which interacts with a multinucleotide region. INTRODUCTION The understanding of how genetic information can be stored has been expanded by the discoveries of overlapping open reading frames, frameshifts and alternate genetic codes. These complexities are accommodated at the level of translation while introns and separated genes are accommodated at the RNA level by splicing and trans-splicing, respec-Correspondence to: Dr. K. Stuart, Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109-1651 (U.S.A.) Tel. (206)284-8846; Fax (206)284-0313. * Presented at the Albany Conference on 'RNA: Catalysis, Splicing, Evolution', Rensselaerville, NY (U.S.A.) 22-25 September 1988.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Biochemistry of Signal Transduction and Regulation

  • Gerhard Krauss(Author)
  • 2014(Publication Date)
  • Wiley-VCH

    (Publisher)

  5 RNA Processing, Translational Regulation, and RNA Interference

  5.1 Pre-mRNA Processing

  Summary

  The information encoded in the primary product of transcription, the pre-mRNA can, by alternative splicing, be used to generate multiple mRNAs from a single pre-mRNA. Alternative splicing vastly expands the repertoire of proteins in a cell, and the subtypes generated by the alternative splicing of a pre-mRNA may have quite different functional and regulatory properties. Splice site selection and splicing itself are intimately linked to transcription by RNA polymerase II and to processes upstream and downstream of transcription, including translation and mRNA decay. The features of alternative splicing important for splice-site selection have been only partially characterized. The structure of the primary transcript, the components of the spliceosome, chromatin structure and proteins involved in transcription elongation, have been all found to cooperate in splice site selection.

  Transcription and translation are spatially separated events in eukaryotes. The primary product of nuclear transcription is pre-mRNA, that is characterized by three structural features: (i) capping at the 5′-end; (ii) polyadenylation at the 3′-end; and (iii) the presence of introns interspersed between the coding regions of the pre-mRNA, the exons. The introns are removed in the process of splicing to yield the mature RNA that is transported out of the nucleus for translation. How much protein, and which protein is formed by translation, depend heavily on the identity and quantity of processed, mature RNA. Capping, polyadenylation and splicing are highly regulated and coordinated events that have been shown to be intimately linked to the transcribing RNA polymerase complex.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Receptors and Hormone Action

  • Bert O'Malley, Lutz Birnbaumer, Bert W. O'Malley(Authors)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  The importance of processing of RNA as a site of gene regulation has been recently reviewed by Robertson and Dickson (1975). Several of the potential functions ascribed to RNA Processing are the following: (1) Precursor RNA's may allow for the coordinated synthesis of multiple components, as in the case of ribosomal RNA synthesis or poliovirus RNA. (2) RNA precursors may act as potential storage forms or zymogens for specific RNA sequences. (3) Processing of RNA may regulate the effective lifetime of a given RNA if the last step in processing represents the first step of breakdown. (4) Extra RNA fragments could play a role in the coor-dination of gene expression following their removal from the precursor. (5) Noncoding regions may be important in inducing the correct conformation necessary for proper processing or be involved in RNA transport. Although precedents for some of these functions of RNA Processing have been obtained from the analysis of rRNA (Perry, 1976), tRNA (Perry, 1976; Altman, 1975), or viral RNA synthesis (Flint and Sharp, 1975), their roles in the regulation of mRNA synthesis are still essentially unknown. B. Hormonal Regulation of Gene Expression The multiple effects of steroid hormones on the synthesis of RNA in their respective target tissues have been conclusively documented (O'Malley, 1969; O'Malley and Means, 1974). Most steroid hormones appear to act in the cell nucleus to regulate the synthesis of all types of RNA (O'Malley and Means, 1974). However, in addition to their direct and rate limiting action on gene transcription (Schwartz et al., 1976), hormones may exert pleio-trope effects at several levels within the cell (Tomkins, 1974).

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Molecular Biology

  Academic Cell Update Edition

  • David P. Clark(Author)
  • 2012(Publication Date)
  • Academic Cell

    (Publisher)

  12 Processing of RNA

  Summary

  Before a protein can be translated, the mRNA needs to be modified and processed in many ways. In bacteria, there is some processing, but in eukaryotes, the primary transcript undergoes many modifications before translation. Three different modifications occur in all species, base modification, cleavage, and splicing which removes intervening sequences that do not have any protein coding information. Some intervening sequences or introns are self-splicing, therefore, that particular RNA is labeled a ribo-zyme. In eukaryotes, the primary transcript must also be capped at the 5′ end and a poly-adenine (poly(A)) tail added to the 3′ end to make the transcript competent for export out of the nucleus.

  The numbers and types of RNA vary greatly in prokaryotes and eukaryotes. Many bacteria have non-coding RNA that includes tRNA, rRNA, and other transcripts in addition to the traditional mRNAs. In eukaryotes, a combination of coding and non-coding RNAs also creates the proteins and cellular components needed to function. The non-coding RNAs include tRNA, rRNA, and a variety of small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and small cytoplasmic RNA (scRNA). The small transcripts in the nucleus (snRNA and snoRNA) are called U-RNA also because they are rich in uridine. Even these small transcripts undergo modifications and processing.

  Ribosomal RNA and transfer RNA are processed from a primary transcript into a mature transcript even though they are not translated into a protein. Ribosomal RNA starts as one transcript in prokaryotes, and must be cut by ribonucleases P to form three, 16S rRNA, 23S rRNA, and 5S rRNA. In eukaryotes, the 18S rRNA, 28S rRNA, and 5.8S rRNA start as one transcript that is processed like in bacteria. Transfer RNA also begins as longer precursor molecules that are cleaved by ribonuclease P. Interestingly, ribonuclease P is a complex of RNA and protein, but since it is the RNA component that catalyzes ribosomal RNA cleavage, this is considered a ribozyme. In addition to cleavage of primary transcripts, non-coding RNAs are subjected to base modifications and editing. Transfer RNA and rRNA have modified bases. The snoRNA from the nucleolus is a type of guide RNA that locates the correct nucleotide for processing. Each snoRNA recognizes a specific site for modification, and then directs the enzyme to the site for modification. Some nucleotides are modified by methylation of the 2’OH group or converting uridine to pseudouridine. Many eukaryotes have the coding region for snoRNAs within introns of other genes.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Computational Biology and Bioinformatics

  Gene Regulation

  • Ka-Chun Wong(Author)
  • 2016(Publication Date)
  • CRC Press

    (Publisher)

  In 92 Computational Biology and Bioinformatics prokaryotes, especially bacterial, mature 16S rRNAs, 23S rRNAs, 5S rRNAs and some tRNAs, are originated from a single 30S rRNA precursor sequence by base specific methylation and enzymetic cleavage carried out by the enzymes RNase III, RNase P, and RNase E. Similarly, in eukaryotes, mature 18S rRNAs, 28S rRNAs, and 5.8S rRNAs are originated from a single 45S pre-rRNA transcript by excessive methylation and a series of enzymatic cleavages processed in the nucleolus. Most eukaryotic cytoplasm have at least a pool of the 20 distinct mature tRNAs charged with 20 different amino acids, for example - tRNA Tyr , - tRNA Ala ,- tRNA Met . Some abundantly present amino acids have multiple copies of the respective tRNA genes. These mature tRNAs are derived from longer RNA precursors by base modification and enzymatic removal of nucleotides from the 5’ and 3’ ends and addition of CCA to the 3’ end. Therefore, any precursor RNA (pre-mRNA, pre-rRNA, pre-tRNA) which are the immediate product of transcription are modified and edited before they are translated. The most important RNA Processing and modification steps are involved in the pre-mRNAs found in nucleus of eukaryotes, which are edited before they are translated into the cytoplasm. Post-transcriptional Regulation of mRNA by 5’ Capping, PolyAdenylation, RNA splicing and RNA Editing The 5’-capping is a unique feature of eukaryotic mRNA Processing in which a residue of 7-methylguanosine (7mGppp cap) is linked to the 5’-terminal nucleotide through an unusual 5’, 5’-triphosphate linkage providing protection and stability to 5’ end. The synthesis of 7mGppp cap is carried out by enzymes tethered to the CTD of Pol II. The cap remains tethered to the CTD through an association with the cap-binding complex (CBC). Similarly, the 3’ end of primary transcript or precursor mRNA is cleaved, and 80-250 adenine (A) residues are added to create a poly-A tail.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Molecular Biology

  Structure and Dynamics of Genomes and Proteomes

  • Jordanka Zlatanova(Author)
  • 2023(Publication Date)
  • Garland Science

    (Publisher)

  Figure 14.23. It is clear that the cell has evolved a set of highly complex mRNA Processing events that are intimately connected to transcription. Practically all individual steps are subject to regulation, the result being the production of the right type of mRNA in the right amount, at the right place, at the right time.

  Figure 14.23

  Overview of co-transcriptional RNA Processing. Pre-mRNA is represented by a green line: thicker at the exon portions and thinner at the introns. The three adjacent boxes represent the composition of protein complexes bound to either the polymerase, mainly through its CTD, or the nascent transcript. The complexes perform specific RNA Processing functions during specific stages of polymerase movement along the gene. Dashed arrows denote interactions that stabilize the complexes or perform the respective enzymatic function. (Left box) 5′-End capping. Capping occurs as soon as the 5′-end of the RNA transcript emerges from the RNA polymerase Pol II; the capping enzymes are recruited via Ser5 phosphorylation of the CTD. Once the cap structure is on, the cap-binding complex, CBC, binds to it and recruits the transcription-export complex, TREX. Splicing factors, SFs, and some of the CPA (cleavage and polyadenylation) components also join the complex at this stage. (Middle box) Spliceosome assembly. Assembly at the first intron is enhanced by protein factors that bind to both the CTD and the nascent RNA, thus bringing the first and second exons into close proximity. The exon-junction complex (EJC) is recruited by the splicing machinery and is deposited just upstream of the exon–exon junction. The TREX complex is now stably associated with nascent RNA through interactions with the CBC, SFs, and/or the EJC. (Right box) Splicing of the 3′-terminal exon and formation of the 3′-end of the mRNA. These two processes occur when transcription approaches the end of the gene, after the final intron and 3′-end exons have been transcribed. Recruitment of the CPA machinery occurs on the CPA signal. The schematic on the far right shows the proteins bound to the processed mRNA when exported to the cytoplasm. Note that many of the proteins still remain bound and might affect subsequent processes. [Adapted from Pawlicki JM & Steitz JA (2010) Trends Cell Biol

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Biochemistry

  An Integrative Approach with Expanded Topics

  • John T. Tansey(Author)
  • 2022(Publication Date)
  • Wiley

    (Publisher)

  Conversely, eukaryotic organisms modify their RNA molecules, often while they are being transcribed. Modifications to mRNA include capping, polyadenylation, and splicing; modifications to tRNA and rRNA generally involve other types of chemical modification of bases (Figure 15.7). FIGURE 15.7 Messenger RNA Processing in eukaryotes. Messenger RNAs undergo the addition of a 7-methylguanine cap to the 5′ end of the message, addition of a poly(A) tail to the 3′ end, and splicing to remove introns prior to export from the nucleus. (Source: Wessner, Microbiology, 2e, copyright 2017, John Wiley & Sons. This material is reproduced with permission of John Wiley & Sons, Inc.) Given that prokaryotes do not modify RNA in any significant way, why have these processes evolved in eukaryotes? The function of some modifications is unclear, but capping is known to assist in the export of RNA from the nucleus and polyadenylation to increase the stability of RNA. This section discusses the different modifications made to RNA and their effects. 15.2.1 Messenger RNA molecules receive a 5′-methylguanine cap Messenger RNA molecules are modified before transcription has been completed. Following synthesis of the first 25 to 30 nucleotides of the nascent mRNA, a 5 ′ -methylguanine cap is added in three separate steps (Figure 15.8). First, RNA triphosphatase removes the γ-phosphate from the 5′ nucleotide. Next, guanylyltransferase transesterifies a molecule of GMP to the terminal phosphate, leaving a structure with the sequence GpppN, in which N is the first nucleotide of the message. The donor molecule in this step is GTP, and pyrophosphate is lost and degraded in the course of the reaction. In mammals, these first two steps are catalyzed by a multifunctional enzyme complex. Finally, the cap is methylated on the 7 position of the ring by guanine-7-methyltransferase

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Karp's Cell Biology

  • Gerald Karp, Janet Iwasa, Wallace Marshall(Authors)
  • 2018(Publication Date)
  • Wiley

    (Publisher)

  The pattern of phosphorylated serine residues changes as the polymerase proceeds from the beginning to the end of the gene being transcribed (compare to Figure 5.18). The phosphate groups linked to the #5 residues are largely lost by the time the polymerase has transcribed the 3′ end of the RNA. SOURCE: After E. J. Steinmetz, Cell 89:493, 1997; by permission of Cell Press. of other genes. The movement of genetic “modules” among unrelated genes—a process called exon shuffling—is greatly facilitated by the presence of introns, which act like inert spacer elements between exons. Genetic rearrangements require breaks in DNA molecules, which can occur within introns without introducing mutations that might impair the organism. Over time, exons can be shuffled independently in various ways, allowing a nearly infinite number of combina- tions in search for new and useful coding sequences. As a result of exon shuffling, evolution need not occur only by the slow accumulation of point mutations but might also move ahead by “quantum leaps” with new proteins appearing in a single generation. 5.10 • Small Regulatory RNAs and RNA Silencing Pathway 191 5.9 Creating New Ribozymes in the Laboratory The main sticking point in the minds of many biologists con- cerning the feasibility of an RNA world in which RNA acted as the sole catalyst is that, to date, only a few reactions have been found to be catalyzed by naturally occurring RNAs. These include the cleavage and ligation of phosphodiester bonds required for RNA splicing and the formation of peptide bonds during protein synthesis. Are these the only types of reactions that RNA mole- cules are capable of catalyzing, or has their catalytic repertoire been sharply restricted by the evolution of more efficient protein enzymes? Several groups of researchers have explored the cata- lytic potential of RNA by creating new RNA molecules in the laboratory.

  Sign up to read

  Learn more about book