in increased response to subsequent inputs. Additionally, microglia resident in the spinal cord respond to damage or inflammation by releasing growth factors and cytokines that alter the excitability of spinal neurons. In certain cases, this can lead to the ongoing activation of pain pathways. Brain Derived Neurotrophic Factor (BDNF), fractalkine, and chemokines have been invoked as important mediators. Descending input from the brain to the spinal cord can both inhibit and facilitate the transmission of information in nociceptive circuits. From the spinal cord, information is transmitted to the brain stem via nociceptor-specific and wide dynamic range projection neurons. It is then processed by a pain matrix of multiple brain regions, resulting in both sensory-discriminative and affective pain perception ([3], reviewed in [20]). Pain pathways in the CNS are modulated by endogenous opioid peptides and arachidonic acid metabolites, acting through G-protein coupled receptors (opioid receptors and cannabinoid receptors) to limit neuronal excitability. GABAergic pathways also act to regulate the excitability of neuronal circuits involved in pain perception. doi:10.1371/journal.pgen.1000086.g001 function SCN9A human mutants that have a defective NaV1.7 channel appear to be completely pain free but are otherwise normal. This observation [7] is an important breakthrough in terms of novel target validation for new classes of sodium channel selective analgesic drugs. As an interesting corollary of this observation, human gain of function mutations of SCN9A, resulting in lowered thresholds of activation, result in erythermal- gia, a chronic inflammatory condition. Rarer mutations that impede the inactivation of the channel seem to cause acute paroxysmal pain [8,9]. Finally SCN10A (NaV1.8), a specific marker for nociceptive neurons, is a major contributor to electrogenesis in primary pain pathways, and is an important target for inflamma- tory mediators. It is also essential for cold pain [10,11]. Regulation of sodium channel expression, both transcriptionally and posttranscriptionally, is an important element in determining neuronal excitability. A short sequence found upstream of neuronal sodium channel genes (as well as other neuronal genes) was identified and named NRSE (Neuron restricted silencing element) or RE-1 (repressor element 1) [12,13]. Transcription factors that bound to the motif were found to act as inhibitors of gene expression in non-neuronal cells. These proteins were named REST (RE-1 silencing transcription factor), or NRSF (Neuron- restrictive silencer factor). The inhibitory activity of the complex can be further modulated by double-stranded RNA molecules that have the same sequence as NRSE/RE-1, and are found in developing neuronal precursors. These regulatory RNA molecules are able to switch the repressor function of the complex to an activator role [14]. Splicing and editing are also important regulatory elements in controlling sodium channel function. Editing events in cockroach sodium channels and Drosophila Para have been correlated with functional changes. Liu et al. [15] have shown that a U to C editing event resulting in a phenylalanine to serine modification can produce a sodium channel with persistent tetrodotoxin (TTX)–sensitive properties, raising the possibility that similar events could occur in mammals. Tan et al. [16] have also found that alternatively spliced transcripts can have distinct pharmacological profiles as well as altered gating characteristics. In mammals, mutually exclusive exon usage also occurs. The SCN3A (NaV1.3) channel exists as an embryonic or adult spliced form, with different exons that code for the S3 and S4 segments in domain one of the rat channel. A similar pattern is present with SCN9A, where some differences in biophysical properties and the effects of cAMP on splice variants have been described [17]. A unique repertoire of sodium channel splice variants has been catalogued in DRG [18]. The presence of a transcript with a three exon repeat encoding NaV1.8 is enhanced by treatment with NGF, suggesting that this neurotrophin may regulate trans- splicing events in these cells [19]. All of these regulatory events are the subject of studies to assess their functional significance. CNS Pain Pathways and Pain Perception Neural correlates of consciousness have been the focus of much attention, especially with the advent of functional imaging. Pain perception seems to involve a variety of discrete CNS structures [20]. Attempts to map ascending pain pathways using genetic approaches have been made [21], and there is now an appreciation of the complexity of central pain processing that involves a number of anatomically defined regulatory pathways [3]. The relationship between the level of pain perceived and the amount of input into the CNS generated by damage sensing neurons is extremely complex. The sensory–discriminatory and affective–evaluative elements that determine the nature of pain perception have been associated with distinct brain areas, but few genetic studies have attempted to address these complex issues (a study of genetic variants of COMT that influence the activities of endogenous opioids is discussed in Box 2). The difficulty of using genetic approaches to study central pain perception is underlined by studies from the Mogil group demonstrating empathic changes in pain thresholds in transgenic mice observing other mice in pain [22]. Altered Pain States Altered pain states, such as inflammatory hyperalgesia and neuropathic allodynia, are discussed in Box 3. Genetic approaches have proved valuable in revealing the mechanisms by which these states arise and are maintained. Mammalian Genetics A wide variety of pain assays have been developed for the mouse, examining different pain modalities. Models of inflamma- tory and neuropathic pain are also well-described, and may have more relevance to human clinical conditions than assays of acute pain. These models have been discussed in detail by the Mogil group [23–25]. The variety of strains of Mus musculus means that the extent of genetic contributions to disease can be evaluated. For example, work on behaviour in response to various pain modalities [26,27] identified three distinct clusters of nociception, each controlled by distinct genetic factors. Strain differences can also be used to map quantitative trait loci affecting pain thresholds. For the investigation of the function of specific DNA sequences, transgenic and gene targeting techniques have proved useful. Examples of transgenics that have generated insights into pain pathways are numerous, and include reports of modulation of pain behaviour by the overexpression of the neuropeptide galanin [28], and the enhancement of inflammatory pain by overexpression of the NMDA receptor subunit N2RB in the forebrain [29]. Gene targeting, particularly exploiting the site-specific Cre-loxP recom- bination system to effect conditional gene deletion, has been productive [30]. Temporal control of gene expression is also possible, using inducible Cre constructs to delete loxP-flanked sequences upon chemical induction of Cre expression [31,32]. Gene deletion in the mouse has proved particularly valuable to the study of pain pathways. For example, a mouse lacking SCN10A, the gene encoding the voltage-gated sodium channel NaV1.8, was recently reported to have almost complete insensitivity to cold pain [10]. The Mogil group have created a database of existing animals PLoS Genetics | www.plosgenetics.org 3 July 2008 | Volume 4 | Issue 7 | e1000086