Post-Transcriptional Regulation

12 Key excerpts on "Post-Transcriptional Regulation"

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  eBook - ePub

  Patterning and Cell Type Specification in the Developing CNS and PNS

  Comprehensive Developmental Neuroscience

  • Bin Chen, Kenneth Y. Kwan(Authors)
  • 2020(Publication Date)
  • Academic Press

    (Publisher)

  Vogel and Marcotte, 2012 ). This suggests that regulatory mechanisms following transcription may significantly influence gene expression in the developing neocortex.

  28.1.2. Posttranscriptional regulation

  How do posttranscriptional mechanisms control gene expression (Fig. 28.2 )? Within the nucleus, alternative splicing (AS) of pre-messenger RNAs generates genetic diversity through production of unique protein-coding isoforms. Precise control of gene expression can also occur via RNA stability mechanisms including nonsense-mediated decay (NMD), as well as translation. Moreover, subcellular mRNA localization and translation enables spatial and temporal control of gene expression. These diverse posttranscriptional mechanisms rely upon cis-elements within RNA, which are dictated by primary and secondary structure, as well as RNA biochemical modifications (epitranscriptome). Posttranscriptional control is also mediated via trans-factors including both RNA-binding proteins (RBPs) and noncoding RNAs. These noncoding RNAs include long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), the latter of which are implicated primarily in translational control. A number of genomic methodologies have been developed to study posttranscriptional regulation (Table 28.1 ) and have propelled our understanding of neurogenesis. We also refer the reader to recent reviews on RBPs, including methods used to investigate their function (Licatalosi and Darnell, 2010 ; Ye and Blelloch, 2014 ; Nussbacher et al., 2015 ; Chen and Hu, 2017 ; Wheeler et al., 2018 ; Corbett, 2018 ; Ramanathan et al., 2019 ).

  Figure 28.2  Posttranscriptional regulatory processes at play within radial glial progenitor cells (RGCs)

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  Gene Control

  • David Latchman(Author)
  • 2020(Publication Date)
  • Garland Science

    (Publisher)

  Section 1.4 ), tissue-specific differences in the levels of the mRNAs encoding actin and tubulin (which are expressed in all cell types) were observed in the absence of differences in transcription rates. Clearly, these and other cases where mRNA levels alter in the absence of changes in transcription rates indicate the existence of post-transcriptional control processes and require an understanding of their mechanisms.

  In principle, such Post-Transcriptional Regulation could operate at any of the many stages between gene transcription and the translation of the corresponding mRNA in the cytoplasm which were described in Chapter 6 . Indeed, the available evidence indicates that in different cases regulation can occur at any one of these levels. Each of these will now be discussed in turn.

  7.1 Alternative RNA Splicing

  RNA splicing can be regulated

  The finding that the protein-coding regions of eukaryotic genes are split by intervening sequences (introns), which must be removed from the initial transcript by RNA splicing of the protein-coding exons (see Chapter 6 , Section 6.3 ), led to much speculation that this process might provide a major site of gene regulation. In theory, an RNA species transcribed in several tissues might be correctly spliced to yield functional RNA in one tissue and remain unspliced in another tissue. An unspliced RNA would either be degraded within the nucleus or if transported to the cytoplasm, would be unable to produce a functional protein due to the interruption of the protein-coding regions (Figure 7.1

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  Complex Physical, Biophysical And Econophysical Systems - Proceedings Of The 22nd Canberra International Physics Summer School

  • Robert L Dewar, Frank Detering(Authors)
  • 2010(Publication Date)
  • World Scientific

    (Publisher)

  15 The mRNA transcript is sub-ject to a complex series of processing steps to prepare it for translation into a protein and export it from the nucleus to the “translational machin-ery”, called ribosomes, located in the cytoplasm of the cell ( Figure 9.1 ). j The reader should be warned that this terminology is non–standard. Complexity, Post-genomic Biology and Gene Expression Programs 333 One example of post–transcriptional control is the phenomenon of alterna-tive splicing , 9 involving the removal of segments of coding sequence from a gene following the initiation of transcription. Alternative splicing ex-pands the diversity of proteins products that can be generated from a sin-gle gene. 9 Recent genome-wide surveys for splicing events have highlighted the widespread presence of this phenomenon in eukaryotic genomes. More recently, the recognition of the widespread role of small regulatory RNA ( e.g. microRNA) has added a new mechanism by which mRNA can be modified, at both post-transcriptional and translational levels. 16,17 The evident transcriptional complexity of the genome, including the seemingly widespread transcription of non-coding regions and the presence of tissue specific transcription start sites, has increased the number and diversity of regulatory elements that need to be taken into account when considering the control of gene expression. 37 Identification of whether a genes’ regulatory regions contains the mo-tif(s) for a transcription factor or regulatory RNA is made extremely diffi-cult by the short length of the motifs themselves. 47 In addition to exper-imental approaches using high–throughput DNA–binding assays, 37 com-parative genomics has an important role to play in identifying regulatory motifs that have been conserved across eukaryotic evolution and several genome–wide maps of transcription factor binding sites have been derived.

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  Biology 2e

  • Mary Ann Clark, Jung Choi, Matthew Douglas(Authors)
  • 2018(Publication Date)
  • Openstax

    (Publisher)

  RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5' UTR or the 3' UTR of the RNA to increase or decrease RNA stability. MicroRNAs associated with RISC complexes may repress translation or lead to mRNA breakdown. 16.6 Eukaryotic Translational and Post-translational Gene Regulation Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein. 16.7 Cancer and Gene Regulation Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer. Chapter 16 | Gene Expression 457 VISUAL CONNECTION QUESTIONS 1. Figure 16.5 In E. coli, the trp operon is on by default, while the lac operon is off. Why do you think that this is the case? 2. Figure 16.7 In females, one of the two X chromosomes is inactivated during embryonic development because of epigenetic changes to the chromatin. What impact do you think these changes would have on nucleosome packing? 3.

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  Biology for AP® Courses

  • Julianne Zedalis, John Eggebrecht(Authors)
  • 2018(Publication Date)
  • Openstax

    (Publisher)

  Depending on the RBP, the stability can be increased or decreased significantly; however, miRNAs always decrease stability and promote decay. 16.6 Eukaryotic Translational and Post-translational Gene Regulation Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein. 16.7 Cancer and Gene Regulation Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer. REVIEW QUESTIONS 1. Control of gene expression in eukaryotic cells occurs at which level(s)? a. only the transcriptional level b. epigenetic and transcriptional levels c. epigenetic and transcriptional and translational levels d. epigenetic and transcriptional, translational, and post-translational levels 2. 666 Chapter 16 | Gene Regulation This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 What do figures X and Y in the graphic illustrate? a. Transcription and translation in a eukaryotic cell (figure X) and a prokaryotic cell (figure Y).

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  Post-transcriptional Gene Regulation in Human Disease

  • Buddhi Prakash Jain, Shyamal K Goswami, Tapan Sharma, Buddhi Prakash Jain, Shyamal K Goswami, Tapan Sharma(Authors)
  • 2022(Publication Date)
  • Academic Press

    (Publisher)

  Chapter 5: Post-Transcriptional Regulation

  a less explored territory in the world of neurodegenerative diseases

  Ayeman Amanullah      University of Twente, Enschede, Netherlands

  Abstract

  Neurodegenerative diseases can be understood broadly as a group of complex disorders characterized by progressive loss of neurons. Alzheimer's disease, amyotrophic lateral sclerosis Parkinson's disease, and Huntington's disease are a few common examples of this group. Decades of studies have improved our understanding of mechanisms and factors associated with the onset and progression of neurodegenerative disorders. Still, estimations suggest neurodegenerative diseases as one of the leading causes of death and disability worldwide. Disrupted protein homeostasis that includes malfunctioned protein folding and degradation machinery, mutations, oxidative damage, mitochondrial dysfunction, DNA damage, and inflammation have extensively been studied and linked with neurodegenerative disorders. However, the role of Post-Transcriptional Regulation is comparatively less explored and understood. This chapter briefly summarizes our current understanding of post-transcriptional gene regulation in a few commonly known neurodegenerative disorders.

  Keywords

  ALS; Alternative splicing; Alzheimer disease; Huntington's disease; Neurodegenerative diseases; Parkinson disease; Post-Transcriptional Regulation

  Introduction

  In an organism, every cell encodes a set of instructions in the form of DNA, which is expressed into proteins by the process of transcription and translation. Unlike prokaryotes, in eukaryotes, the transcription and translation process is not coupled. The transcription site is in the nucleus, whereas the mature RNA translocates into the cytoplasm to get translated into proteins [1 ]. This segregation of transcription from translation permits eukaryotes to integrate an extensive post-transcriptional gene regulation step. This regulatory process involves recruiting numerous RNA binding proteins (RBPs) and other regulatory factors such as micro-RNAs. The interaction of nascent primary transcripts with RBPs and other regulatory factors decides the fate of primary transcripts that whether they would be translated into a protein or not [2 ,3

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  Structure and Function of the Bacterial Genome

  • Charles J. Dorman(Author)
  • 2020(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Messenger RNA will be unable to participate in the process of translation if the requisite signal elements needed for translation initiation are sequestered. This can arise from intramolecular base pairing when the mRNA folds back on itself or it can be due to intermolecular base pairing with another RNA. Either type of base‐pairing reaction can be assisted or impeded by chaperones and these are usually RNA‐binding proteins.

  The binding of small signal molecules can also influence RNA folding and this can provide the basis of a regulatory switch. Typically, the RNA can fold into one of two alternative secondary structures and one of them results in formation of a transcription terminator. The terminator interferes with transcription via a process known as transcription attenuation and blocks the expression of the genetic information that is encoded by the DNA. Many signals can operate RNA‐based switches (or ‘riboswitches’) and include complex molecules (e.g. ATP, sugars, amino acids) and metal ions.

  Non‐coding RNA (ncRNA ) molecules with regulatory roles can operate by binding and sequestering translation signals in target mRNAs and/or by making the target RNA adopt an alternative secondary structure that changes its stability or its proficiency for translation. These ncRNAs are often relatively small (hence ‘sRNA ’ [small RNA ]) and chemically stable and work well in trans. Their production is subject to complex regulation and we are still at an early stage in appreciating the pervasive nature of their influence on the expression of genetic information in bacteria. This chapter will describe the principal types of regulation at the RNA level that have been described in bacteria.

  4.1 Antisense Transcripts and Gene Regulation incis

  The control of gene expression by RNA in modern bacteria is not simply a vestige of an earlier, hypothetical, ‘RNA World’: it plays a central role in governing the flow of genetic information in the cell (Figure 4.1 ) (Wagner and Romby 2015 ). Some of the earliest examples of gene regulation by RNA involved antisense transcripts that base paired with their sense counterparts to affect the expression of the genetic information carried by the latter (Storz et al. 2011 ; Wagner and Simons 1994 ). For example, the 69‐nucleotide RNA‐OUT encoded by the insertion sequence IS10, a component of transposon Tn10, is expressed antisense to the transposase mRNA, also known as RNA‐IN (Figure 2.4) (Simons and Kleckner 1983 ). RNA‐OUT is highly stable and acts efficiently when expressed in trans. Its stability depends on adoption of a simple stem‐loop structure that is resistant to exoribonuclease attack (Pepe et al. 1994 ). RNA‐OUT inhibits the translation of RNA‐IN by base pairing with it to sequester the translation initiation signals of the transposase gene (Kittle et al. 1989 ). The RNA chaperone protein Hfq assists this interaction (Ross et al. 2013 ). Furthermore, RNA‐OUT base‐pairing with RNA‐IN results in destabilisation of the latter, further downregulating expression of transposase (Case et al. 1990 ). Although RNA‐OUT works well in trans, exerting multicopy inhibition of IS10/Tn10 transposition, it is classed as a cis‐encoded sRNA because it is expressed from the DNA strand that is complementary to the strand encoding its RNA target (Dutta and Srivastava 2018 ; Storz et al. 2011

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  Genome Organization And Function In The Cell Nucleus

  • Karsten Rippe(Author)
  • 2012(Publication Date)
  • Wiley-VCH

    (Publisher)

  Activation was also proposed to act by making the DNA accessible to binding proteins, as in the case of intergenic transcription in multigene clusters of the beta-globin and immunoglobulin heavy chain V region [185, 186]. Transcriptional interference seems, however, to be the most common effect of overlapping transcriptional units. For example, the yeast PHO5 locus seems to be regulated by transcription of a ncRNA via changes of local chromatin plasticity [183]. The ncRNA is rapidly degraded by the exosome and its expression in trans does not affect Pho transcription indicating the need of local transcription. Similarly, the yeast SER3 gene is regulated by an upstream transcription [184]. Finally, transcriptional elongation of ncRNAs across regulatory regions or genes can cause changes in histone modifications. For example, continuous ncRNA transcription has been suggested to prevent the silencing of certain Hox genes by PcG proteins [178]. 13.6.2 Non-Coding RNAs Directly Regulating Transcription and RNA Processing In many cases transcription is not sufficient and the non-coding transcript regulates transcription by, for example, modulating RNAP II activity, recruiting transcription factors, inducing changes in chromatin state or directly interacting with the DNA (Figure 13.6b). In addition, ncRNAs have also been shown to regulate alternative splicing and stability of coding mRNAs (Chapter 11). Contrary to transcriptional interference, ncRNA-mediated regulation can also act in trans. A direct interaction of long ncRNAs with RNAP II has been described for repeat-derived sequences. Binding of the murine B2 ncRNA to RNAP II upon heat shock leads to transcriptional inhibition of other mRNAs in trans [189]. B2 is a mouse tRNA-derived small RNA (178 nt) transcribed by RNAP III upon heat shock from the SINE repeat element. It contains a 51-nt core sequence, which binds with high affinity to an RNA docking site in the core of RNAP II

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  Biochemistry of Signal Transduction and Regulation

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

    (Publisher)

  Figure 5.3 Global and specific mRNA control. Global mRNA control is mainly based on the signal-directed modification of translation initiation factor eIF-4E that promotes circularization of mRNAs in cooperation with eIF-4G and the poly(A)-binding protein (PABP). The control of specific mRNAs employs two major approaches. First, the binding of RNA binding proteins to specific structural elements of the RNA can inhibit or activate specific mRNAs. A second mechanism uses RNA interference by miRNAs that bind specifically to sequences in the 3′-control regions of the mRNAs.

  5.2.2.1 mRNA-Specific Control of Translation

  This control is driven by RNA sequences and/or structures that are commonly located in the 5′- or 3′-UTRs of the transcript. These features are usually recognized by regulatory proteins or microRNAs (Section 5.3). Embedded within the UTRs of eukaryotic mRNAs is information specifying the way in which the RNA is to be utilized, and diverse proteins bind specifically to these sequences thus interpreting this information. As a result, the translation of specific mRNAs can be either activated or repressed. The binding of regulatory proteins to mRNA-specific sequence elements often interferes with formation of the cap-binding complex, thus repressing translation in a mRNA-specific manner.

  5.2.2.2 Global Control of Translation

  In response to external or internal signals, the translation of all mRNAs may be either activated or repressed. The treatment of cells with hormones, mitogens or growth factors generally leads to an increase in protein biosynthesis. Conversely a lack of nutrients, or environmental stresses such as heat, UV irradiation or viral infections, generally repress translation. The regulatory mechanisms underlying these controls target, above all, the translation factors eIF-2 and eIF-4E.

  The translational control can be global, with almost all mRNAs being affected. Another translational control is mRNA-specific and regulates the translation of only some mRNAs (Figure 5.3 ).

  Selected examples of the mRNA-specific and global control of translation are presented in the following subsections.

  5.2.3 mRNA-Specific Regulation by 5′-Sequences: Control of Ferritin mRNA Translation by Iron

  There is one well-characterized example illustrating the control of mRNA translation by a specific ion, namely the control of ferritin mRNA by iron. In this system, it is the concentration of iron that regulates protein binding to regulatory sequences at the 5′ end of the ferritin mRNA. This control of ferritin mRNA by iron is an example of translational regulation by protein binding to the 5′ end of the mRNA that interferes with the stable association of the small ribosomal subunit with the mRNA, leading to translational repression and subsequent degradation of the mRNA.

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  RNA-Based Regulation in Human Health and Disease

  • (Author)
  • 2020(Publication Date)
  • Academic Press

    (Publisher)

  Chapter 4: The dynamic aspects of RNA regulation

  Ravi Shankar

  ∗

        Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP, India ∗  Corresponding author 

  Abstract

  With rise of various high throughput approaches and landmark projects like Human Genome Project, ENCODE and FANTOM, our understanding about RNA universe has changed like never before. With hardly 2% of the genome coding for proteins and most of the multicellular eukaryotes displaying almost equal number of protein coding genes, it is clear that regulatory system provided by the so called “junks” of genome is much more critical than the protein coding genes themselves in shaping the fate of cells. Right from their transcription, the RNAs display a high level of coordinated acts of regulation, processing and interactions which in turn become regulatory themselves. RNAs are capable to provide variable regulatory modes just by switching their structures which could be done alone or with help of interacting partners in form of some proteins or RNAs. The present chapter has discussed all these regulatory factors in the life of an RNA where many times the RNA itself is a regulator.

  Keywords

  Regulatory; Functional; Non-coding; Factor; RBP; Interaction

  Introduction

  If the Human Genome discovery was one of the biggest achievements in modern biology, success of projects like ENCODE (Encyclopedia of DNA Elements) is no less which challenged our concept of genes and obsession with proteins [1 ]. It taught us the existence of much bigger world beyond protein coding RNAs. In fact, the process of protein coding itself now appears very much dependent upon various regulatory mechanisms than previously appreciated.

  Today, there are much larger number of various types of RNA molecules than proteins. The degree of variability and control level provided by RNAs has gone much beyond the proteins. Our understanding of RNA universe earlier existed around mRNA and t-RNA duet and orchestra of snoRNAs, snRNAs and various ribosomal RNAs, basically all centered around process of translation and our overt emphasis on the importance of proteins in our life. Yet, the period between the mid of 1990s and beginning of new millennium started making ways for much broader thinking and some remarkable studies, giving emphasis on the noncoding elements and RNA universe. One big reason for this appears to be the Human Genome project itself where one had expected to see a number of protein coding genes, but surprisingly it remained restricted to a number which is almost same in most of other multicellular eukaryotes. It also revealed that just 2%–3% protein coding regions exist, and we are almost 99% similar to Chimpanzee with such protein coding gene set [2 ]. Very shortly it was realized that there is much more than the protein coding regions in our lives. The obsession with proteins prior to HGP started looking more like absurdity. Things which were called “junk” by protein obsessed world were now emerging as the “goldmines” and “king-makers” of genome. Work with repetitive elements in Human Genome had already started proving that. In 2003, with initial target of 1% of non-coding regions of the Human Genome, ENCODE project was launched. The findings of ENCODE project was going to challenge our most fundamental understandings in molecular biology, including the definition of “Gene” itself [3

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  RNA Interference

  • Ibrokhim Y. Abdurakhmonov(Author)
  • 2016(Publication Date)
  • IntechOpen

    (Publisher)

  Keywords: Transcriptional silencing, long noncoding RNA, cancer, neurological disor‐ der, Drosophila 1. Introduction Since the earliest days of molecular biology, RNA-mediated gene regulation was known to the researchers, and it was first suggested that noncoding RNA (ncRNA) might have a role in gene regulation by interacting with promoters [1, 2]. After more than four decades of research, the discovery of RNA interference (RNAi) has revolutionized our perception of the mechanism of © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. gene regulation, organization of chromosomes, and epigenetic regulations. Important clues to ncRNA regulatory mechanisms came from homology-dependent gene silencing in plants, which can be initiated by transgenes and recombinant viruses [3]. Studies on the nematode Caenorhabditis elegans , the fruit fly Drosophila melanogaster [4], fungi mainly yeast, mammalian cells, and plants revealed transcriptional silencing mechanisms involving RNAi, chromatin, and its various modifications [3]. RNAi operates mainly posttranscriptionally; however, its components are associated with transcriptional gene silencing and heterochromatin forma‐ tion, too [5]. Recent findings have made it clear that transcriptional gene silencing (TGS), posttranscrip‐ tional gene silencing (PTGS), and chromatin modifications are utilized by eukaryotic cells to bring about endogenous gene regulation, chromosome organization, and nuclear clustering. The RNA interference mechanisms mainly target the transposable elements, which are abundant and perhaps a defining component of heterochromatin.

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  RNA Regulation, 2 Volumes

  • Robert A. Meyers(Author)
  • 2014(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  cis-Antisense RNAs

  4.1.1 Mode of Action 4.1.2 Specific and Global Antisense-Dependent Regulations

  4.2 trans-Acting Noncoding RNAs

  4.2.1 Gene Expression Inhibition by ncRNAs 4.2.2 Activation of Gene Expression by ncRNAs 5 RNA Changing Protein Activities 5.1 Mimicking DNA Promoters 5.2 Mimicking Ribosome Binding Sequences 6 Concluding Remarks Acknowledgments References

  Regulatory noncoding RNA

  A nonprotein-coding RNA molecule that controls biological processes by directly affecting the transcription, translation, or stability of another RNA, or by binding to proteins.

  trans-Antisense ncRNA

  A regulatory RNA that acts on an RNA molecule (target) that is encoded at a different locus.

  cisI-Antisense ncRNA

  A regulatory RNA that acts on the expression of the gene transcribed from the reverse complementary DNA strand.

  Regulatory 5′ untranslated region

  A noncoding RNA sequence located at the 5′ end of a protein coding sequence within a messenger RNA, and controlling its expression.

  Open reading frame

  A nucleic sequence that starts with a translation initiation codon and ends with a translation stop codon, which can potentially be translated by the ribosome into a specific amino acid chain.

  Shine–Dalgarno sequence

  An RNA sequence recognized and bound by the 16S ribosomal RNA. The sequence is located upstream of the translation initiation codon (4–12 nt) within the ribosome binding site.

  Ribosome binding site

  An RNA sequence recognized and bound by the 30S ribosomal subunit to initiate translation. It generally extends from about − 30 nt to around +16 nt relative to the translation initiation codon.

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