Noncoding RNAs: Molecular Biology and Molecular Medicine
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Edited By:Jan BarciszewskiInstitute of Bioorganic Chemistry of the Polish Academy of Sciences Volker A. Erdmann Freie Universitat-Berlin ISBN: 978-0-306-47835-2 Published: 2003-08-15 This book may be purchased as an eBook (pdf) for $99, or individual chapters (pdf) may be purchased from the list below for $19. |
General inspection of a role performed in the cell by RNAs allows us to distinguish three major groups of transcripts: i) protein-coding mRNAs and ii) non-coding housekeeping and iii) regulatory RNAs.
The housekeeping RNAs include RNA classes that are generally, constitutively expressed and whose presence is required for normal function and viability of the cells. On the other hand, a group of regulatory RNAs includes RNA species that are expressed at certain stages of organism development or cell differentiation or as a response to external stimuli and can affect expression of other genes on the levels of transcription or translation.
Noncoding RNA transcripts form a heterogeneous class of RNAs that can not be characterized by a single specific function. Initially, the term noncoding RNA (ncRNA) was used primarily to describe polyadenylated and a capped eukaryotic RNAs transcribed by RNA polymerase II, but lacking long open reading frames. Now, this definition can be extended to cover all RNA transcripts that do not show protein-coding capacity and is sometimes used to describe any RNA that does not encode protein, including introns.
This book is an in-depth look at the function of NonCoding RNAs and their relationship to molecular biology and molecular biology. This is the first book on the subject to be published.
Chapters available from this book
We Are Legion: Noncoding Regulatory RNAs and Hfq
Cristin C. Brescia and Darren Sledjeski
Regulation by small, noncoding RNAs (ncRNA) has a long history in bacteria. Plasmid copy number control via the antisense interaction of two RNAs (RNAI and RNAII) was first described over 30 years ago in Escherichia coli. One of the first trans-acting ncRNAs discovered was the E. coli MicF RNA. I...
Noncoding RNAs Encoded by Bacterial Chromosomes
E. Gerhart H. Wagner and Joerg Vogel
Small noncoding RNAs are common to bacterial plasmids, phages and transposons, in which they regulate biological processes by acting as antisense RNAs. By contrast, only few small, noncoding RNAs had been shown to be encoded by bacterial chromosomes until very recently. Some of these provided hou...
RNA Pathogenesis in Dominant Noncoding Microsatellite Expansion Disorders
Laura P.W. Ranum and John W. Day
Microsatellite expansions cause 18 inherited human neurodegenerative diseases, including Huntington’s disease (HD), Friedreich’s ataxia (FA), nine forms of spinocerebellar ataxia (SCA), and myotonic dystrophy (DM). Most of these disorders are caused by trinucleotide expansions, although recently ...
The Noncoding Developmentally Active and Stress Inducible hsr• Gene of Drosophila melanogaster Integrates Post-Transcriptional Processing of Other Nuclear Transcripts
S.C. Lakhotia
The 93D or the hsr-omega (hsr •) gene of Drosophila melanogaster became an in teresting gene more than 3 decades ago in view of its unique inducibility with a brief benzamide treatment. Subsequent studies revealed many unusual features of this gene, a homologue of which is present in all Drosophi...
New Perspectives on Noncoding or Short ORF-Encoding RNAs in Plants
Martin Crespi, Anna Campalans, Claude Thermes and Adam Kondorosi
mRNAs that do not contain a long open reading frame (longer than 100 amino acids; sORF-RNAs) have received considerable attention in recent years. These genes are generally not detected by usual sequence analysis and a large number of them likely remain to be discovered. Their functions may invol...
New Frontiers for the snoRNA World
Jean-Pierre Bachellerie and Jérôme Cavaillé
Eukaryal rRNAs contain two prevalent types of modified nucleotides, 2'-O-methylated nucleotides and pseudouridines. The site of each of these modifications is accurately specified by two large families of snoRNAs (small nucleolar RNAs) termed box C/D and H/ACA snoRNAs, respectively, through forma...
Brain-Specific Nonmessenger RNAs
Jürgen Brosius, Alexander Hüttenhofer and Henri Tiege
RNAs that do not encode proteins, as do messenger RNAs, play much more prominent roles in the functioning of cells than we first anticipated–qualitatively and quantitatively. At least in Eukarya one has the impression that we have hardly left the RNA world. This RNA life is not only a remnant fro...
RNA-Directed DNA Methylation and Chromatin Modifications
Marjori A. Matzke, M. Florian Mette, Tatsuo Kanno, István Papp, Werner Aufsatz and Antonius J. M. Matzke
Discovered nearly ten years ago in viroid-infected transgenic plants, RNA-directed DNA methylation (RdDM) provided the first example of an RNA-mediated epigenetic alteration of homologous nuclear DNA. Until recently, research on RdDM was conducted exclusively by plant biologists, who viewed it as...
Post-Transcriptional Gene Silencing in Plants
Matthew Escobar and Abhaya M. Dandekar
Accumulating genetic and biochemical evidence suggests that antisense-mediated gene silencing, cosuppression, RNA interference and virus-induced gene silencing are all unique inputs into a common RNA silencing pathway triggered by double stranded RNA. This pathway, termed post-transcriptional gen...
Short Interfering and MicroRNAs: Tiny but Mighty
Martin Tabler, Alexandra Boutla, Kriton Kalantidis and Tsagris Mina
Two functionally distinct classes of short noncoding RNAs consisting of ca. 20-25 nucleotides have been discovered recently. Both classes of RNAs are generated from longer single- or double-stranded RNA precursors by the same ribonuclease. Either of the two categories of short RNAs is involved in...
MicroRNAs
Eric Moss
MicroRNAs are the smallest functional noncoding RNAs of plants and animals. They are about 22 nucleotides in length with no common structural or sequence features. Some are conserved across great evolutionary distances, indicating that their sequence is not arbitrary. A single organism may have h...
The Structure, Regulation and Function of the Imprinted H19 RNA
Raluca I. Verona and Marisa S. Bartolomei
H19 is a member of a small subset of genes that are subject to the parent-of-origin dependent expression known as genomic imprinting. The H19 gene is transcribed exclusively from the maternal allele, and this paternal imprinting is evolutionarily conserved in mammals. In addition to its imprintin...
Dosage Compensation in Drosophila: A Ribonucleoprotein Complex Mediates Transcriptional Up-Regulation
Dianne Kindel and Hubert Amrein
Sex-specific chromosomes (commonly referred to as X and Y) provide the basis for sex determination in many animal species. However, this difference in karyotype has drastic consequences for the quantitative set-up of the genome of the two sexes, as sex chromosomes harbor thousands of genes with n...
Xist RNA Associates with Chromatin and Causes Gene Silencing
Anton Wutz
The mammalian Xist gene produces a long, spliced and poly-adenylated noncoding RNA that is uniquely distributed in the nucleus. Xist RNA spreads in cis from its site of transcription over the entire X-chromosome and mediates X-inactivation, the transitional silencing of one of the two X-chromosom...
Introns and Noncoding RNAs: The Hidden Layer of Eukaryotic Complexity
John S. Mattick
Although it is not yet widely appreciated by the molecular biological community, the vast majority of the transcriptional output of the genomes of the higher organisms is noncoding RNA, composed of introns spliced out from protein-coding transcripts, and separate noncoding RNA transcripts that ar...
Riboregulators: An Overview
Maciej Szymanski, Volker A. Erdmann and Jan Barciszewski
One of the most important aspects of functioning of living organisms is the regulation of gene expression. Resolving the mechanisms regulating transcription of particular genes is crucial for understanding biological phenomena connected to changes in environmental conditions, development and dise...
Adapt Gene RNA Transcripts as Riboregulators
Dana Crawford and Kelvin J. A. Davies
There is growing interest in the study of so-called riboregulator or non-coding RNAs. These spliced and polyadenylated RNAs contain either a very short or no apparent open reading frame or translational product. However, they are associated with a wide range of biological activities that...
Computational Gene-Finding for Noncoding RNAs
Peter Schattner
Computer gene-finding programs have been quite successful at locating protein-coding genes in both prokaryotic and eukaryotic genomes. However these programs—which use genomic features such as long open-reading-frames and codon signatures—are not designed to identify non-coding RNA (n...


