| dataset_desc |
Chronological age, a count of how many orbits of t Chronological age, a count of how many orbits of the sun an individual has made as a passenger of planet earth, is a useful but limited proxy of aging processes. Some individuals die of age related diseases in their sixties, while others live to double that age. As a result, a great deal of effort has been put into identifying biomarkers that reflect the underlying biological changes involved in aging. These markers would provide insights into what processes were involved, provide measures of how much biological aging had occurred and provide an outcome measure for monitoring the effects of interventions to slow ageing processes. Our DNA sequence is the fixed reference template from which all our proteins are produced. With the sequencing of the human genome we now have an accurate reference library of gene sequences. The recent development of a new generation of high throughput array technology makes it relatively inexpensive to simultaneously measure a large number of base sequences in DNA (or RNA, the molecule of gene expression). In the last decade, array technologies have supported great progress in identifying common DNA sequence differences (SNPs) that confer risks for age related diseases, and similar approaches are being used to identify variants associated with exceptional longevity [1]. A striking feature of the findings is that the majority of common disease-associated variants are located not in the protein coding sequences of genes, but in regions of the genome that do not produce proteins. This indicates that they may be involved in the regulation of nearby genes, or in the processing of their messages. While DNA holds the static reference sequences for life, an elaborate regulatory system influences whether and in what abundance gene transcripts and proteins are produced. The relative abundance of each tran
script is a good guide to the demand for each protein product in cells (see section 2 below). Thus, by examining gene expression patterns or signatures associated with aging or age related traits we can peer into the underlying production processes at a fundamental level. This approach has already proved successful in clinical applications, for example using gene signatures to classify cancer subtypes [2]. In aging research, recent work conducted in the InCHIANTI cohort has identified gene-expression signatures in peripheral leucocytes linked to several aging phenotypes, including low muscle strength, cognitive impairment, and chronological age itself. In the sections that follow we provide a brief introduction to the underlying processes involved in gene expression, and summarize key work in laboratory models of aging. We then provide an overview of recent work in humans, thus far mostly from studies of circulating white cells.
2 Introducing gene expression
Since the early 1900s a huge worldwide research effort has lead to the discovery and widespread use of genetic science (see the NIH website [3] for a comprehensive review of the history of the subject, and a more detailed description of the transfer of genetic information). The human genome contains the information needed to create every protein used by cells. The information in the DNA is transcribed into an intermediate molecule known as the messenger RNA (mRNA), which is then translated into the sequence of aminoacids (proteins) which ultimately determine the structural and functional characteristics of cells, tissues and organisms (see figure 1 for a summary of the process). RNA is both an intermediate to proteins and a regulatory molecule; therefore the transcriptome (the RNA ∗Address correspondence to Prof. David Melzer, Epidemiology and Public Health Group, Medical School, University of Exeter, Exeter EX1 2LU, UK. E-mail: D.Melzer@exeter.ac.uk
1
2 INTRODUCING GENE EXPRESSION
Figure 1: Representation of the transcription and translation processes from DNA to RNA to Protein — DNA makes RNA makes Protein. This is the central dogma of molecular biology, and describes the transfer of information from DNA (made of four bases; Adenine, Guanine, Cytosine and Thymine) to RNA to Protein (made of up to 20 different amino acids). Machinery known as RNA polymerase carries out transcription, where a single strand of RNA is created that is complementary to the DNA (i.e. the sequence is the same, but inverted although in RNA thymine (T) is replaced by uracil (U)). Not all RNA molecules are messenger RNA (mRNA) molecules: RNA can have regulatory functions (e.g. micro RNAs), and or can be functional themselves, for example in translation transfer RNA (tRNA) molecules have an amino acid bound to one end (the individual components of proteins) and at the other bind to a specific sequence of RNA (a codon again, this is complementary to this original sequence) for instance in the figure a tRNA carrying methionine (Met) can bind to the sequence of RNA, and the ribosome (also in part made of RNA) attaches the amino acids together to form a protein.
production of a particular cell, or sample of cells, at a given time) is of particular interest in determining the underlying molecular mechanisms behind specific traits and phenotypes. Genes are also regulated at the posttranscriptional level, by non-coding RNAs or by posttranslational modifications to the encoded proteins. Transcription is a responsive process (many factors regulate transcription and translation in response to specific intra and extra-cellular signals), and thus the amount of RNA produced varies over time and between cell types and tissues. In addition to the gene and RNA transcript sequences that will determine the final protein sequence (so called exons) there are also intervening sections (the introns) that are removed by a process known as mRNA splicing. While it was once assumed that each gene produced only one protein, it is now
clear that up to 90% of our genes can produce different versions of their protein through varying the number of exons included in the protein, a process called alternative splicing. Alteration in the functional properties of the protein can be introduced by varying which exons are included in the transcript, giving rise to different isoforms of the same gene. Many RNA regulatory factors govern this process, and variations to the DNA sequence can affect the binding of these factors (which can be thousands of base pairs from the gene itself) and alter when, where and for how long a particular transcript is produced. The amount of mRNA produced for a protein is not necessarily directly related to the amount of protein produced or present, as other regulatory processes are involved. The amount of mRNA is broadly indicative of... |