Abstract
BackgroundThe adaptive immune system of vertebrates has an extraordinary potential to sense and neutralize foreign antigens entering the body. De novo evolution of genes implies that the genome itself expresses novel antigens from intergenic sequences which could cause a problem with this immune system. Peptides from these novel proteins could be presented by the major histocompatibility complex (MHC) receptors to the cell surface and would be recognized as foreign. The respective cells would then be attacked and destroyed, or would cause inflammatory responses. Hence, de novo expressed peptides have to be introduced to the immune system as being self-peptides to avoid such autoimmune reactions. The regulation of the distinction between self and non-self starts during embryonic development, but continues late into adulthood. It is mostly mediated by specialized cells in the thymus, but can also be conveyed in peripheral tissues, such as the lymph nodes and the spleen. The self-antigens need to be exposed to the reactive T-cells, which requires the expression of the genes in the respective tissues. Since the initial activation of a promotor for new intergenic transcription of a de novo gene could occur in any tissue, we should expect that the evolutionary establishment of a de novo gene in animals with an adaptive immune system should also involve expression in at least one of the tissues that confer self-recognition.ResultsWe have studied this question by analyzing the transcriptomes of multiple tissues from young mice in three closely related natural populations of the house mouse (M. m. domesticus). We find that new intergenic transcription occurs indeed mostly in only a single tissue. When a second tissue becomes involved, thymus and spleen are significantly overrepresented.ConclusionsWe conclude that the inclusion of de novo transcripts in the processes for the induction of self-tolerance is indeed an important step in the evolution of functional de novo genes in vertebrates.
Highlights
The adaptive immune system of vertebrates has an extraordinary potential to sense and neutralize foreign antigens entering the body
Mutations in the Aire gene in humans cause the Autoimmune-Polyendokrinopathie-Candidiasis-Ektodermaldystrophie-Syndrome Type I (APECED) disease which is a syndrome characterized by the presence of autoantibodies that are specific for multiple self-antigens [13, 14] and Aire deficient mice develop multiple features of the APECED phenotype [15]
Many of these new RNAs include an open reading frame and are translated [23,24,25], producing a completely new protein sequence. Such proteins can assume a functional role and could become true genes. When such a new protein is presented by the major histocompatibility complex (MHC) system to the cell surface, it would be recognized by the immune system as a foreign antigen leading to a destruction of the respective cells or cause inflammations
Summary
Transcriptome data for the focal populations (IRA, GER, FRA) were previously generated for ten tissues (brain, gut, heart, kidney, liver, lung, muscle, spleen, testis and thyroid) [28]. While most CDS are shared between all tissues (at the minimum cutoff level of eight reads), INT is mostly specific to a single tissue only, while NC transcripts have both, many transcripts in single tissues, as well as many across all tissues (Fig. 4 and Additional file 3) This pattern suggests that intergenic transcription is at least initially mostly biased towards single tissues and is expected to reach higher expression levels across more tissues when the transcripts turn into functional genes. We find that transcripts initially expressed only in thymus, spleen, lung and brain in IRA have the highest percentage of gained transcripts in any other tissue in GER or FRA. We can reject the null hypothesis and conclude that the frequencies of different tissues to gain transcription are significantly different
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