Long Non-coding RNA

The Dark Side of the Genome

Antonin Morillon

• Publisher: ISTE Press - Elsevier
• Year: 2018
• Print ISBN: 9781785482656
• eBook ISBN: 9780081023556
• Topic: Scienze biologiche
• Subtopic: Genetica e genomica

The dark side of the genome represents vast domains of the genome that are not encoding for proteins – the basic bricks of cellular structure and metabolism. Up to 98% of the human genome is non-coding and produces so-called long non-coding RNA. Some of these non-coding RNA play fundamental roles in cellular identity, cell development and cancer progression. They are now widely studied in many organisms to understand their function.This book reviews this expanding field of research and present the broad functional diversities of those molecules and their putative fundamental and therapeutic roles and develops the recent history of non-coding RNA, their very much debated classification and how they raise a formidable interest for developmental and tumorigenesis biology.Using classical examples and an extensive bibliography, the book illustrates the most studied and attractive examples of these long non-coding RNA, how they interface with epigenetics, genome integrity and expression and what are the current models of their regulatory mechanisms.- This book offers a large review about the long non-coding RNA- It presents the broad functional diversities of those molecules- It presents pioneer works from the field- Provides a comprehensive review of the field- Presents fundamental and therapeutic interests

1

Non-coding RNA, Its History and Discovery Timeline

Abstract

The complexity of eukaryotic transcriptomes and the rapid development of high throughput sequencing technology have led to an explosion in the number of long non-coding RNA (or lncRNA) recently identified and as yet undescribed. Current challenges include not only their precise labeling but also their functional characterization and the clinical pertinence of these biological objects. To begin with, it is important to return to the characteristics of RNA, a molecule essential to cellular functionality.

Keywords

Deoxyribonucleic Acid; Double helix; Micro-RNA; Non-coding genome; Non-coding transcriptome; Permissive transcription; X-inactive-specific-transcript

The complexity of eukaryotic transcriptomes and the rapid development of high throughput sequencing technology have led to an explosion in the number of long non-coding RNA (or lncRNA) recently identified and as yet undescribed. Current challenges include not only their precise labeling but also their functional characterization and the clinical pertinence of these biological objects. To begin with, it is important to return to the characteristics of RNA, a molecule essential to cellular functionality.

The timeline of discoveries linked to non-coding RNA is shown in Figure 1.1 and its history will be detailed in the first half of this chapter, from DNA to the first non-coding transcripts. Next, the role of global genomic and transcriptomic studies in changing our vision of RNA’s capacity in gene expression regulation circuits and cellular complexity will be discussed. This functional diversity has given rise to various extensive classifications of lncRNA.

Figure 1.1 Timeline of the main discoveries of RNA biology and in particular of eukaryotic non-coding RNA. For a color version of this figure, see www.iste.co.uk/morillon/RNA.zip

Notes on Figure 1.1

In light pink are the discoveries of large non-coding RNA families. In red are typical examples of specific non-coding RNA. In yellow are a selection of the big discoveries in molecular biology. Beneath the timeline are the novel technologies that enabled the characterization of non-coding RNA families. In violet are the discoveries of mechanisms regulated by non-coding RNA.

1.1 The biology of RNA, a century of history

The defining and conceptualization of RNA molecules in cell biology date back to 1869 and the discovery of nucleic acids. It took more than a century for researchers to finally identify non-coding transcription and to begin to suggest regulatory possibilities.

1.1.1 From nuclein to the double helix

At the end of the 19th Century, several essential discoveries foreshadowed the era of molecular biology. Although Friedrich Miescher isolated the contents of the cell nucleus, which he named “nuclein” (containing nucleic acid) (Dahm, 2005) in 1869, the interests of scientists at the time focused on the proteins thought to carry genetic information. It was only in 1944 that the link between nucleic acid (of the nucleus) and genetic information was made when Oswald Avery suggested that DNA was the carrier of genetic information (Avery et al., 1944). As such, the association between the Mendellian genetic model and Miescher’s “nuclein” was missing for more than half a century.

Following the visualization of the double helical structure of DNA by James Watson and Francis Crick in 1953, it was suggested, in 1961, that RNA might provide the intermediary molecule in the flow of information between DNA and proteins (Cobb, 2015). Outlined in 1958 by Francis Crick and then by François Jacob and Jacques Monod, the central dogma of molecular biology included gene transcription of DNA to RNA in the nucleus followed by protein synthesis. It was also confirmed that the flow of information was only from DNA to RNA, then from RNA to the protein and never the reverse (Cobb, 2015). The mediator role of RNA has become a central focus for research, essential to the development of modern molecular biology.

1.1.2 The “RNA world” concept

It was only in 1955 that Georges Palade identified the very first non-coding RNA (ncRNA) that made up part of the most abundant RiboNucleoProtein (RNP) complex of a cell: the ribosome. Soon after, in 1958, a second class of ncRNAs were discovered by Mahlon Hoagland and Paul Zamecnik for their role as intermediaries between amino acids and RNA: transfer RNA (tRNA).

In 1960, François Jacob and Jacques Monod defined “messenger RNA” (mRNA) as the intermediate molecule carrying genetic information for protein synthesis. Following this, Crick and his team established that the genetic code is a universal non-overlapping triplet code in which three nucleotides code for one amino acid (Crick, 1968).

The discovery of heterogenous nuclear RNA (hnRNA) in the late 1960s led to the study of rRNA maturation and the discovery of splicing (Berk, 2016; Lewis et al., 1975; Weinberg and Penman, 1968; Zieve and Penman, 1976).

The regulators in red in Figure 1.2 were not known in 1958 during the formulation of the initial dogma of information flow, nor were the permissive transcription and translation processes.

Figure 1.2 Flow of genetic information and its regulators. For a color version of this figure, see www.iste.co.uk/morillon/RNA.zip

Although Jacob, Monod and Crick had all stated that RNA was not just a messenger, for a long time many scientists treated it as a simple unstable intermediate molecule, neglecting the potential active roles of other classes of ncRNA. However, this concept was partially changed in 1980 when Thomas Cech and Sidney Altman discovered that RNA molecules could also act as catalysts for chemical reactions such as self-splicing (Kruger et al., 1982) or RNA degradation through ribonucleotide nuclease P, or RnaseP (Guerrier-Takada et al., 1983). These RNA enzymes, or ribozymes, have since been acknowledged as key actors in the flow of genetic information (Figure 1.2), as part of both the ribosome and the spliceosome (Butcher, 2009; Cech, 2000).

The discovery of ribozymes led to the hypothesis of the “RNA world” which proposed that pre-biotic life revolved around RNA. Further studies of its roles in cell biology have revealed that RNA is necessary for DNA replication and that ribonucleotides are precursors of DNA’s deoxyribonucleotides.

Furthermore, as previously mentioned, RNA plays an important role in all stages of protein synthesis whether as a template (mRNA) or as an actor (ncRNA: rRNA, tRNA, etc.) (Bernhardt, 2012). The latter are constitutively expressed in the cell and are necessary for vital cell functions. These maintenance ncRNAs are the subject of many specialized publications and will not be explored in this book. Other classes of regulatory ncRNA were discovered in the 1990s and will be broadly discussed here. The origin of those noncoding RNA and the fact they constitute an additional layer of genetic expression started to be discussed at this date. Several hypotheses were raised, especially the interconnections with introns (Mattick, 1994; Morris and Mattick 2014). The origin and extension of the “RNA world” concept was increasingly acknowledged. These ncRNAs are expressed very specifically throughout the stages of embryonic development, in certain tissues or pathological states and also play multiple roles in the regulation of gene expression and genomic stability.

1.1.3 Small bacterial RNA: pioneers of non-coding RNA

The very first ncRNA regulator defined was micF, from the Escherichia coli bacteria. It was described in 1987 by Masayuki Inouye and his team (Inouye and Delihas, 1988) as the first RNA that regulates the expression of a gene through sequence complementarity, and represents the main class of bacterial small ncRNA regulators (sRNA). It was shown that the ncRNA of micF suppresses the translation of a target mRNA coding for a porine (outer membrane protein F, OmpF) that is involved in passive tra...

Table of contents

• Cover
• Title page
• Table of Contents
• Copyright
• Foreword: The Modern RNA World
• Preface
• 1: Non-coding RNA, Its History and Discovery Timeline
• 2: Definition and Families of Long Non-coding RNA
• 3: Biological Functions of Long Non-coding RNA
• 4: Non-coding RNA in Development
• 5: Long Non-coding RNA and Cancer
• Concluding Perspectives
• Bibliography
• Glossary
• List of Acronyms
• Index