rRNA, tRNA and mRNA

12 Key excerpts on "rRNA, tRNA and mRNA"

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  Fundamental Molecular Biology

  • Lizabeth A. Allison(Author)
  • 2021(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Not drawn to scale. 3.2 RNA is involved in a wide range of cellular processes 49 Messenger RNA (mRNA): a copy of the DNA sequence that encodes a protein and binds to ribosomes in the cytoplasm. Transfer RNA (tRNA): small RNA that is “charged” with a specific amino acid , the building block of proteins. tRNA delivers to the ribosome the appropriate amino acid via specific base-pairing interactions of the tRNA with the mRNA. Small nuclear RNA (snRNA): plays a role in pre-mRNA splicing , a process that pre-pares the mRNA for translation. Small nucleolar RNA (snoRNA): plays a role in rRNA processing, to prepare the rRNA for function. MicroRNA (miRNA): involved in post-transcriptional gene regulation; each miRNA binds to a complementary sequence in a target mRNA, usually resulting in gene silenc-ing, by triggering degradation of mRNA or by blocking translation by the ribosome. PIWI-interacting RNAs (piRNAs): small RNAs present in germline cells that are 24–31 nucleotides in length. They associate with PIWI proteins to form piRNA-induced silencing complexes, which repress transposable elements via transcriptional or post-transcriptional mechanisms. Long noncoding RNA (lncRNA): a large and diverse class of RNA molecules that do not encode proteins; they play a role in several cellular functions, including the regula-tion of gene transcription. Contributing to the versatility of RNA function is the ability of RNA to form comple-mentary base pairs with other RNA molecules and with single-stranded DNA. The ability of RNA to make specific base pairs is a key to understanding its role in everything from post-transcriptional gene silencing to translation. RNA–protein interactions are also of cen-tral importance. Most of the RNA in a eukaryotic cell is associated with protein as part of RNA–protein complexes termed ribonucleoproteins (RNPs) . In addition, most, if not all, RNA-based catalytic reactions are thought to take place in conjunction with proteins.

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  Introduction to Molecular Biology

  • S Bresler(Author)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  Such RNA molecules apparently act as a template which directs the assembly of polypeptide chains. Messenger RNA is rapidly meta-bolized in bacterial cells throughout exponential growth ; its synthesis requires 20 to 30 seconds and it is generally degraded in the course of a few minutes. The steady-state concentration of mRNA in the cell is on the order of 3 to 8 % of the total cellular RNA. The number of mRNA molecules corresponding to a given protein is variable, depending on the requirements of the cell and on the rate at which each protein must be made. 2. Transfer RNA and the Activation of Amino Acids 451 Besides high-molecular-weight rRNA and mRNA, there is a low-molecular-weight RNA called transfer RNA (tRNA) present in the cell. This third type of RNA has a special function completely distinct from those of either previous class. It cova-lently binds amino acids and transports them to the sites of protein synthesis. Its role as an adaptor molecule in the actual assembly of the polypeptide chain was considered in the preceding chapter. Transfer RNA comprises between 10 and 20% of the total cellular RNA. Finally, monoribonucleotides and their phosphorylated derivatives such as ATP, GTP, and others play an important role in the cellular economy. They are widely distributed and often behave as coenzymes in addition to their participation in energy metabolism. We shall not be concerned with monoribonucleotides in this chapter since the reader can find a detailed exposition on this topic in any textbook of biochemistry. 2. Transfer RNA and the Activation of Amino Acids Since all types of RNA are implicated in protein synthesis, let us begin our discus-sion with transfer RNA (tRNA), actually a class of similar compounds that transport different amino acids to the sites of protein synthesis and there participate in the very first stages of polypeptide chain formation (1).

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  Cell Biology A Comprehensive Treatise V3

  Gene Expression: The Production of RNA's

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

    (Publisher)

  Each RNA type occurs in multiple molecular species: rRNA consists of three or four major species, tRNA includes about 60 different species, and mRNA may exist in hundreds or thousands 5 END 0 = Ρ -0 -C H 2 BASE 0 = Ρ- 0 - CHo BASE 0 = P -0 -C H 2 BASE Ύ OH Ο = Ρ- 0 - C H 2 I I BASE o-I -o . OH 3 END Fig. 1. The structure of RNA. 9. Maturation Events Leading to tRNA and rRNA 441 of species. (For a detailed classification of cellular RNA see Chapter 10 of this volume.) Messenger RNA serves as a template for the sequential ordering of amino acids during protein synthesis. Triplets of nucleotides (codons) along the mRNA specify the linear amino acid sequence. Although mRNA composes only about 2 to 5% of the mass of cellular RNA, it consists of many species of various molecular weights and base sequences, since each of the proteins synthesized by cells is coded by a specific mRNA or segment of an mRNA molecule. Molecules of mRNA are generally meta-bolically unstable, with an average half-life of several minutes in pro-karyotic organisms. However, in eukaryotes the half-life of mRNA species may be as long as 24 hours (Brawerman, 1974). The other two classes of RNA are metabolically stable, with half-lives that may be expressed in terms of days. Although these do not serve as templates, they nevertheless play vital roles in protein synthesis. Transfer RNA's are small, about 25,000 daltons, and act as carriers of specific amino acids during protein synthesis. Each of the 20 amino acids has at least one corresponding tRNA species, and some have multiple tRNA species. These tRNA species differ in nucleotide sequence, but all share certain identifying features which are described in Section III,A. About 80% of the mass of cellular RNA is ribosomal RNA, which is a structural component of the ribosomes on which protein synthesis occurs.

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  Protein Synthesis: Methods and Protocols

  • Bhupendra Pushkar(Author)
  • 2020(Publication Date)
  • Delve Publishing

    (Publisher)

  t-RNA and Aminoacyl-tRNA Synthetases 57 Until the year 1973, there was no firm information that was available in the three - dimensional structure of the molecule. In early 1973, the polynucleotide chain of yeast tRNA phe has been traced in a 4--X ray diffraction analysis. Structural work is noticed to progress rapidly, from then to the point where the atomic coordinates is now available. As these coordinates are derived from 2.5.-X ray diffraction analyses from the two different crystal forms of the same molecule. Knowledge about the detailed three-dimensional structure of the molecule that makes a change that occur separately in the type of research that can be also carried out. The main aim behind describing some of the details in the manner to obtain knowledge about the three -dimensional structure of tRNA species. they also want to discuss the extent to which it can be explained and can make various aspects understandable that are involved in chemistry and solution behavior of the same and tRNA species. The major biological function of the tRNA is related to the role of the tRNA in protein synthesis. The existence of a molecule like tRNA is a sense that is made necessary by the fact that nature encodes the information about the genetics in the nucleotide sequence in the nucleic acid. This helps in expressing the biological information in the ordered sequence in the polypeptide structure of amino acids. Transfer RNA is said to have a fundamental biological role which is being used in acting as an interface between the polypeptide and polynucleotides. tRNA works by interacting with the messenger RNA in the ribosome at one end. While at the other end it is containing the growing peptide chain. tRNA is often seen to be involved in a large number of biological processes. Aminoacyl-tRNAs are the substrates that are used for the translation process and they are considered as an essential for determining how the genetic code is being interpreted as an amino acid.

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  The Human Genome

  • Julia E. Richards, R. Scott Hawley(Authors)
  • 2010(Publication Date)
  • Academic Press

    (Publisher)

  60–300 bases. Help with chemical modification of rRNAs, tRNAs, and snRNAsMicro RNAmiRNA~21–22 bases. Single-stranded RNA binds to the 3′ untranslated region of a specific mRNA to block translationSmall interfering RNA20–25 bases. Double-stranded RNA becomes part of the silencing complex that degrades targeted RNAs that are homologous to the siRNA

  In some cases RNA is a structural molecule that carries out functions that the cell needs. Some of the most important examples of structural RNAs are the ribosomal RNAs. These RNAs combine with ribosomal proteins to make up the ribosomes. When the cell is metabolically active it needs a lot of ribosomes to be able to make the many kinds of proteins being used by the cell. Thus an actively dividing cell transcribes ribosomal RNA very actively (Figure 3.6 ), at such a high rate that it causes the region called the nucleolus to be visibly distinct within the nucleus.

  Figure 3.6 Transcription of RNA is carried out very actively in a cell that is getting ready to divide. The genes are organized in a cluster, and a new transcript from a gene begins before the previous transcript has been completed. The result is a cluster of RNA molecules that appear to stream from the chromosome like branches on an evergreen tree. The chromosome is the vertical line from which the branches radiate. (Image by Professor Oscar Miller/Science Photo Library. © All rights reserved.)

  In other cases, RNA serves as an enzyme, a type of molecule that catalyzes a chemical reaction. An example of an important class of enzymatic RNA would be those RNAs that play a role in splicing of other RNA molecules.

  Some RNAs are part of a composite molecule that combines some RNA with some other types of molecules such as proteins or a given amino acid. A good example would be the transfer RNA, or tRNA (Figure 3.5 ), that forms a composite molecule consisting of an RNA mole­cule with an amino acid fastened to it. As we will discuss in Chapter 4

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  Snyder and Champness Molecular Genetics of Bacteria

  • Tina M. Henkin, Joseph E. Peters(Authors)
  • 2020(Publication Date)
  • ASM Press

    (Publisher)

  anticodon that is complementary to the codon in the mRNA. The base-pairing rules for codons and anticodons are basically the same as the base-pairing rules for DNA replication, and the pairing is antiparallel. The only major differences are that RNA has uracil (U) rather than thymine (T) and that the pairing between the last of the 3 bases in the codon and the first base in the anticodon is less stringent.

  This basic outline of gene expression leaves many important questions unanswered. How does mRNA synthesis begin and end at the correct places and on the correct strand in the DNA? Similarly, how does translation start and stop at the correct places on the mRNA? What actually happens to the tRNA and ribosomes during translation? What happens to the mRNA and proteins after they are made? The answers to these questions and many others are important for the interpretation of genetic experiments, so we will discuss the structure of RNA and proteins and the processes by which they are synthesized in more detail.

  The Structure and Function of RNA

  In this section, we review the basic components of RNA and how it is synthesized. We also review how structure varies among different types of cellular RNAs and the role each type plays in cellular processes.

  Types of RNA

  There are several different classes of RNA in cells. Some of these, including mRNA, rRNA, and tRNA, are involved in protein synthesis. Each of these types of RNA has special properties, which are discussed below. Others are involved in regulation, replication, and protein secretion.

  RNA Precursors

  RNA is similar to DNA in that it is composed of a chain of nucleotides. However, RNA nucleotides contain the sugar ribose instead of deoxyribose. These five-carbon sugars differ in the second carbon, which is attached to a hydroxyl group in ribose rather than the hydrogen found in deoxyribose (see Figure 1.2 ). Figure 2.1A shows the structure of a ribonucleoside triphosphate (rNTP), which is the form that is used as a precursor during RNA synthesis.

  RNA and DNA chains also vary in the bases that are present. Three of the bases—adenine, guanine, and cytosine—are the same, but RNA has uracil instead of the thymine found in DNA (Figure 2.1B

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  Karp's Cell and Molecular Biology

  • Gerald Karp, Janet Iwasa, Wallace Marshall(Authors)
  • 2021(Publication Date)
  • Wiley

    (Publisher)

  Decoding the information in an mRNA is accomplished by transfer RNAs, which act as adaptors. On the one hand, each tRNA is linked to a specific amino acid (as an aa-tRNA), but on the other hand, that same tRNA is able to recognize a particular codon in the mRNA. The inter- action between successive codons in the mRNA and specific aa-tRNAs leads to the synthesis of a polypeptide with an ordered sequence of amino acids. To understand how this occurs, you must first understand the structure of tRNAs. The Structure of tRNAs In 1965, after seven years of work, Robert Holley of Cornell Uni- versity reported the first base sequence of an RNA molecule, that of a yeast transfer RNA that carries the amino acid alanine (Figure 11.40a). This tRNA is composed of 77 nucleotides, 10 of which are modified from the standard 4 nucleotides of RNA (A, G, C, U), as indicated by the shading in the figure. Over the following years, other tRNA species were puri- fied and sequenced, and a number of distinct similarities pres- ent in all the different tRNAs became evident (Figure 11.40b). All tRNAs were roughly the same length—between 73 and 93 nucleotides—and all had a significant percentage of unusual bases that were found to result from enzymatic modifications of one of the four standard bases after it had been incorpo- rated into the RNA chain, that is, posttranscriptionally. In addi- tion, all tRNAs had sequences of nucleotides in one part of the molecule that were complementary to sequences located in other parts of the molecule. Because of these complementary sequences, the various tRNAs become folded in a similar way to form a structure that can be drawn in two dimensions as a cloverleaf. The base-paired stems and unpaired loops of the tRNA cloverleaf are shown in Figures 11.42 and 11.43. The unusual bases, which are concentrated in the loops, disrupt hydrogen bond formation in these regions and serve as poten- tial recognition sites for various proteins.

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  Chemistry and Biology of Non-canonical Nucleic Acids

  • Naoki Sugimoto(Author)
  • 2021(Publication Date)
  • Wiley-VCH

    (Publisher)

  7 Translation

  The main points of the learning

  1. Study basic molecular mechanisms of translation reaction.
  2. Understand presence of various reaction steps for translation modulation and maintenance.
  3. Study contributions of RNA structures to the translation modulation.

  7.1 Introduction

  Protein is biopolymer consisting of amino acids polymerized in one dimension. In living system, the amino acid sequence of each protein is encoded in the sequence of messenger RNA (mRNA) that is originally encoded in DNA sequence. The sequence code on mRNA is decoded by a ribosome though a reaction termed translation. Since the protein is the main functional molecule in extant living system, translation is one of the most important biological reactions. Intracellular protein expression is modulated at not only transcription level but also at translation level. The formation of unique RNA structures and their dynamic behaviors are the key factors to modulate and maintain the translation system. This chapter describes contribution of RNA structures on translation reaction as well as its basic knowledge. The contributions of structure dynamics of RNAs on gene expressions including replication, transcription, and translation are described in Chapter 10 .

  7.2 RNAs Involved in Translation Machinery

  There are three categories of RNAs such as mRNA, tRNA, and rRNA, which are directly involved in translation machinery. mRNA is a template for the translation. A region of nucleotide sequence in mature mRNA that is translated to a given protein is known as an open reading frame (ORF) (Figure 7.1 ). Correlation between nucleotide sequence and amino acid sequence was first proposed by Francis Crick as a sequence hypothesis. George Gamow, who is a theoretical physicist and cosmologist famous for his big bang theory, proposed that specific trinucleotide encodes one specific amino acid. The trinucleotide, which encodes a specific amino acid, is now known as a codon. Correlations between each codon and amino acid, which are conserved in all extant living system with few exceptions, have resolved by contributions from Marshall Nirenberg and Har Khorana (Figure 7.2 ). Outside of coding sequence, mRNA contains noncoding sequences. Untranslated regions (UTRs) at 5′ and 3′ ends of mRNA are called 5′ UTR and 3′ UTR, respectively. Prokaryotic mRNAs are polycistronic, which contains multiple ORFs in one mRNA. There are noncoding sequences between adjacent ORFs. In the case of eukaryotic mRNAs, primary transcript is a precursor messenger RNA (pre-mRNA) consisting of alternating exon and intron regions. Noncoding introns are excluded by posttranscriptional splicing that result in connected exons as a mature mRNA (Figure 7.1

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  Karp's Cell and Molecular Biology

  Concepts and Experiments

  • Gerald Karp, Janet Iwasa, Wallace Marshall(Authors)
  • 2016(Publication Date)
  • Wiley

    (Publisher)

  The particles associated with the nascent RNAs are ribosomes in the act of translation; in bacteria, transcription and translation occur simultaneously. The RNA molecules increase in length as the distance from the initiation site increases. SOURCE: From Oscar L. Miller, Jr., Barbara A. Hamkalo, and C. A. Thomas, Science 169:392, 1970; © 1970, reprinted with permission from AAAS. REVIEW 1. What is a polyribosome? How does its formation differ in prokaryotes and eukaryotes? 11.20 EXPERIMENTAL PATHWAYS The Role of RNA as a Catalyst Research in biochemistry and molecular biology through the 1970s had solidified our understanding of the roles of proteins and nucleic acids. Proteins were the agents that made things happen in the cell, and the enzymes that accelerated the rates of chemical reactions within organisms. Nucleic acids, on the other hand, were the informational molecules in the cell, storing genetic instructions in their nucleotide sequence. The division of labor between protein and nucleic acids seemed as well defined as any distinction that had been drawn in the biological sciences. Then, in 1981, a paper was published that began to blur this distinction. 1 Thomas Cech and his co‐workers at the University of Colorado had been studying the process by which the ribosomal RNA precursor synthesized by the ciliated protozoan Tetrahymena thermophila was converted to mature rRNA molecules. The T. thermophila pre‐rRNA contained an intron of about 400 nucleo- tides that had to be excised from the primary transcript before the adjoining segments could be linked together (ligated). Cech had previously found that nuclei isolated from the cells were able to synthesize the pre‐rRNA precursor and carry out the entire splicing reaction. Splicing enzymes had yet to be 451 11.20 The Human Perspective isolated from any type of cell, and it seemed that Tetrahymena might be a good system in which to study these enzymes.

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  Cell Biology E-Book

  Cell Biology E-Book

  • Thomas D. Pollard, William C. Earnshaw, Jennifer Lippincott-Schwartz, Graham Johnson(Authors)
  • 2022(Publication Date)
  • Elsevier

    (Publisher)

  Fig. 12.7 ). It is likely that the modifications help the tRNAs fold into precisely the correct shape. They also aid accurate recognition of different tRNAs by the aminoacyl-tRNA synthases, which are responsible for charging each species of tRNA with the correct amino acid.

  Ribosome Synthesis

  The synthesis of ribosomes is a major activity of any actively growing cell. Three of the four rRNAs—the 18S, 5.8S, and 25S/28S rRNAs—are cotranscribed by RNA polymerase I as a polycistronic transcript. This pre-rRNA is the only RNA synthesized by RNA polymerase I and is transcribed from tandemly repeated arrays of the ribosomal DNA (rDNA). In humans, approximately 300 to 400 rDNA repeats are present in five clusters (on chromosomes 13, 14, 15, 21, and 22). These sites often are referred to as nucleolar organizer regions, reflecting the fact that nucleoli assemble at these locations in newly formed interphase nuclei. The pre-rRNAs are very actively transcribed and can be visualized as “Christmas trees” in electron micrographs taken following spreading of the chromatin using low-salt conditions and detergent (Fig. 11.12A ). The 5S rRNA is independently transcribed by RNA polymerase III. In most eukaryotes, the 5S rRNA genes are present in separate repeat arrays.

  Figure 11.12 RIBOSOME SYNTHESIS. A, “Christmas trees” of nascent prerRNA transcripts. This electron micrograph shows ribosomal DNA (rDNA) genes in the process of transcription. Note the numerous molecules of RNA polymerase I (Pol I) along the rDNA, each associated with a pre–ribosomal RNA (rRNA) transcript. In the enlarged inset, the terminal balls can be seen on the transcripts. These large pre-rRNA–processing complexes (small subunit processomes) assemble around the binding site for the U3 small nucleolar RNA (snoRNA) and are required for the early pre-rRNA processing steps. B–C, Roles of the modification guide snoRNAs. The pre-rRNAs undergo extensive covalent modification. Most modification involves methylation of the sugar 2′ hydroxyl group (2′-O -methylation) or pseudouridine (ψ) formation, at sites that are selected by base pairing with a host of small nucleolar ribonucleoprotein (snoRNP) particles. Human cells contain well over 100 different species of snoRNPs, and each pre-rRNA molecule must transiently associate with every snoRNP in order to mature properly. Sites of 2′-O -methylation are selected by base pairing with the box C/D class of snoRNAs, which carry the methyltransferase Nop1/fibrillarin. Sites of pseudouridine formation are selected by base pairing with the box H/ACA class of snoRNAs, which carry the pseudouridine synthase Cbf5/dyskerin. D, Key steps in eukaryotic ribosome synthesis. Following transcription of the pre-rRNAs, most steps take place within the nucleolus. The preribosomes are then released from association with nucleolar structures and are believed to diffuse to the nuclear pore complex (NPC). Passage through the NPC is preceded by structural rearrangements and the release of processing and assembly factors. Further ribosome synthesis factors are released during late structural rearrangements in the cytoplasm that convert the pre–ribosomal particles to the mature ribosomal subunits. During pre-rRNA transcription and processing, many of the approximately 80 ribosomal proteins assemble onto the mature rRNA regions of the pre-RNA. E, The pre-rRNA processing pathway. The pathway is presented for the budding yeast Saccharomyces cerevisiae,

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  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.

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  Bidirectional Gene Promoters

  Transcription system and chromosomal structure

  • Fumiaki Uchiumi(Author)
  • 2022(Publication Date)
  • Elsevier

    (Publisher)

  + molecules could be polymerized to generate fatty acids, polysaccharides, polypeptides, and poly(ADP-ribose)s. These biological polymers failed to become genetic materials but contributed towards other biological purposes. We could easily understand that RNAs have been the most advantageous within these molecules, carrying the genetic information and biological functions or primitive enzymatic activities. They might have replicated from the ribonucleotide sequences to complimentary ribonucleotide sequences with the help of a biological catalyst, which might have been RNA polymers. If life emerged from the RNA world, all the RNA molecules were non-coding, because functional proteins were probably not present. At that time, even if RNAs were not coding amino acids, that was alright. Presently, in both prokaryotic and eukaryotic cells, protein coding RNAs or mRNAs are the minority, consisting of only several percent among the total RNAs. Most of the RNAs are rRNAs and tRNAs. In this regard, is it not just a little bit strange if we call the non-mRNAs the “non-coding RNAs”? Because during the chemical evolution, RNAs originally have not been necessary to code amino acid sequences. RNAs are essentially non-coding from the beginning.

  The term “non-coding” seems to have come from non-coding DNAs, which represent specific genomic regions to be transcribed, but not encoding functional amino acid sequences. In this chapter, following convention, non mRNAs/hnRNAs are referred to as non-coding RNAs. They include rRNAs, tRNAs, small nuclear RNAs (snRNAs), micro RNAs (miRNAs) [1] , circular RNAs (circRNAs) [2 , 3] , and long non-coding RNAs (lncRNAs) [4 , 5] .

  In accordance with the innovational progress in molecular biology or nucleotide-sequence analyzing technology, genomic databases of human and other organisms have been continuously updated. Thanks to ENCODE [6] , GENCODE [7] and FANTOM [8] projects, non-coding RNAs and small/short RNAs, which have been previously taken as junk RNAs to be discarded, were identified one after another and re-evaluated to be registered on human genome DNA databases. In this chapter, I will briefly review biological functions of miRNAs, and lncRNAs, before surveillance of their promoter regions that are head-head bound with other genes. The other ncRNAs to be noticed are enhancer RNAs (eRNAs), which can enhance transcription of specific genes [9] . The eRNA region can frequently be found near or around promoter regions of various genes. As you may speculate, the dysregulation of their expression could lead to human diseases, especially aging-associated diseases, including cancer and neurodegenerative diseases. The essential characteristics and functions of the intergenic enhancers in the mammalian genomes are to be discussed in Chapter 8 .

  Classification of ncRNAs and relationships with DNA repair, mitochondrial function, and the immune system

  Presently, classification of the ncRNAs has been almost completely settled and summarized [10] . However, biological roles or functions of the ncRNAs have been increasingly discussed and it has been revealed that they are quite divergent [4 , 11-13 ]. Among lncRNAs, for example, NEAT1 (nuclear-enriched abundant transcript 1) and MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) are well known to localize at active chromatin [14] , implying that they are playing a role in the regulation of various nuclear events, including transcription. Specific miRNAs are known to regulate stability of mRNAs and translation [15 , 16] . For example, BACE1-AS, which is transcribed to the opposite direction of the BACE1 gene, can stabilize BACE1 transcripts, preventing their degradation [17] . They not only regulate transcription/translation, but also splicing of immature RNAs [18] and chromosomal rearrangement/maintenance/segregation [19 , 20] . Telomerase, which plays an essential role in the elongation of telomeres and thereby maintains the integrity of chromosomes, are known to contain an ncRNA, TERC (TER) [21] . Interestingly, recent studies showed that the TERC is involved in the regulation of immune responses [22] and mitochondrial functions [23 , 24]

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