RNA Expression and Gene Networks – From Gene to Function

sequence of DNA is first transcribed into an intermediate product, messenger RNA (mRNA) that is then used as a template for transfer RNA (tRNA), which adds a correct amino acid in the growing protein polypeptide chain thus translating the information into a protein (Figure 3). Proteins are then further modified with

posttranslational modifications and signal sequences that mark the destination for the proteins. DNA is similar in almost all cells in the body, except for white blood cells, where the DNA sequence in the regions encoding pathogen recognizing proteins is actively modified by adding or deleting nucleotides in order to create larger variability of receptors that can detect pathogens. Another exception is germline, which is haploid. The divergence in cellular phenotypes is mediated mainly through changes in the amount of enzymatically functional RNAs and proteins. Similarly, individual SNPs and differences in the genetic code mediate their effect on the phenotype largely due to differential gene expression and thus different amounts of produced proteins (Nica et al., 2010, Nicolae et al., 2010). The normal variation only rarely produces dysfunctional proteins but affects the magnitude of cellular and genetic responses to changes in the environment.

Figure 3. Regulation from DNA to protein level (© Hanna Ollila). The DNA in the nucleus of a cell is first transcribed into mRNA, which is transported to the cytoplasm. The mRNA molecule is then used as a template for tRNA that adds new amino acids into the growing amino acid chain. Once the amino acid chain has been completed the new protein is synthesized. All these events are regulated and can have an effect on the phenotype.

There are a number of elements in the DNA sequence that affect the magnitude and precision of the transcription. Promoter sequences, located typically upstream of the gene, contain binding sites for transcription factors and RNA polymerase that mediate the transcription of DNA to RNA. Transcription factors can modulate the

magnitude of expression either by enhancing the binding and transcription of RNA polymerase or repressing the transcription and binding of the polymerase. Several transcription factors have been identified for sleep regulation. These include the CLOCK and BMAL transcription factors that dimerize into molecular complex.

This binds a basic helix-loop-helix (bHLH) transcription factor binding site on the promoter of their target genes and thereby helps to activate their transcription (Lee et al., 2001).

In addition, the modifications of a DNA molecule can affect the magnitude of RNA expression. These covalent modifications are made onto the histone molecules supporting the structure or into the DNA itself and are called epigenetic modifications. The most studied forms of epigenetics are methylation and acetylation. The modifications in DNA are called epigenetic modifications since they do not affect the coding nucleotide sequence but the activity of the genes.

Epigenetic modifications can also be inherited from one cell generation to the next (Henikoff and Shilatifard, 2011, Law and Jacobsen, 2010). Similarly, the density of DNA packing and the epigenetic modifications are related to the tissue specific expression of genes and may explain part of the difference of gene expression levels in the central nervous system and in the peripheral tissues. Epigenetic modifications are a way to react to the environment and change the activity of genes by making structural changes in the DNA without affecting the coding sequence (Kota and Feil, 2010, Law and Jacobsen, 2010, Okano et al., 1999, Reik, 2007). In the field of psychiatric genetics for example, it has been shown that working in a stressful environment is related to lower methylation of serotonin transporter SLC6A4 and thus potentially higher expression levels (Alasaari J, 2012). Interestingly, a familial form of narcolepsy has been found to be caused by a mutation in gene encoding for DNA methylation transcription factor 1 (DNMT1). Such a mutation is likely to have a wide-range effect on overall methylation at the genome level (Devlin et al., 2010, Winkelmann et al., 2012).

2.1.2.1 Transcriptional Networks

The individual genes in an organism only rarely carry out their function alone but are linked together into pathways and networks where several genes have a joint effect on a biological function.

Genes can be clustered in pathways based on their function, like metabolic pathways, signal transduction pathways or regulatory pathways. Joint efforts from Gene Ontology (Ashburner et al., 2000) and KEGG Consortiums (Kanehisa et al., 2004) have clustered genes into the pathways based on their biological functions.

Similarly, SNPs can be clustered into pathways based on the annotations that define either the closest gene or target gene of whose expression is affected by a SNP. An example of pathways relevant for human diseases is the signal transduction pathway NF-kB signalling cascade that has been shown to be important in autoimmune diseases, especially in Crohn’s disease. In this disease, aberrant integration of the

pro-inflammatory and anti-inflammatory cytokine pathways is partially responsible for disease progression (Abbott et al., 2004).

Most genes or their protein products are integrated in the cells. Integrative networks can include both inhibitory and activating parts so that the sum of the network, such as the overall changes in the expression levels, is more precisely connected to the biological phenomena than the action of the individual proteins or pathways alone. Cells are fine-tuned to receive information from environmental challenges and responses by taking into account the availability of cellular resources. A single gene can be part of several networks. This makes it possible to integrate information in the network and create interactions between the pathways.

Another benefit from networks is that they affect the biological responses by combining responses from two or more pathways (Ashburner et al., 2000).