Chapter category: RNA
Introns and Noncoding RNAs: The Hidden Layer of Eukaryotic Complexity
Noncoding RNAs: Molecular Biology and Molecular Medicine
Edited by: Jan Barciszewski and Volker A. ErdmannISBN: 0-306-47835-8
» Get more information about this book at landesbioscience.com «
Chapter authors:
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 are developmentally regulated and which may also be spliced. Intronic RNAs comprise around 95% of the average protein-coding transcript in humans, and have high sequence complexity with interesting patterns of conservation, suggesting that these RNAs contain information that is expressed in parallel with protein-coding sequences. In addition there are thousands of noncoding RNA genes, which appear to account for at least half of all transcripts in humans, but most have not been studied, largely because there has been no expectation that such RNAs may be common or important, although evidence is rapidly emerging that they are both. Moreover, it is now evident that there are a number of complex genetic phenomena in the higher organisms, such as RNA interference, cosuppression, transgene silencing, methylation, imprinting, and transvection, which are related through intersecting pathways, and which are mediated by or connected to RNA signaling. It has also recently been shown that intronic and other noncoding RNAs are processed into multiple smaller species (snoRNAs and microRNAs), at least some of which are capable of carrying out trans-acting regulatory functions. It also appears that chromatin architecture is influenced by RNA signals. Taken together the available evidence suggests that, far from being evolutionary hangovers or curiosities, noncoding RNAs are central to the genetic control architecture of the higher organisms, and form a higher order system for gene regulation and gene-gene communication, which enables integration of complex networks of gene activity during eukaryotic differentiation and development, via RNA-DNA/chromatin, RNA-RNA and RNA-protein interactions. In addition, this system (the cis- and trans-acting RNA-based regulatory network) would be expected to have entirely different and generally much more subtle genetic signatures compared to protein coding sequences, and probably lies at the heart of quantitative trait variation and genetic susceptibility to disease, as opposed to the more severe phenotypes associated with loss of protein function.
John S. Mattick
ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
Additional chapters 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 a...
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 ha...
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 myot...
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...
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 seq...
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 famil...
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 o...
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 DN...
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 RN...
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...
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 ev...
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...
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 quan...
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...
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 ...
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 unders...
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 tra...
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 su...
