DOI: 10.5061/dryad.s85s9
title: Data from: Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences

description: Background: The 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.
 Results: We 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. Conclusions: We 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.
description: Data Table 1 CDS
 listData Table 1: List of
 all CDS transcripts with read numbers per sample. Only entries with read
 counts 8 or higher in at least one tissue. Includes three Tabs, one for
 each population. Each population is represented by four individuals.
 Sample designations and underlying ready numbers are listed in the first
 tab of the table.Data Table 2 NC
 listData Table 1: List of
 all CDS transcripts with read numbers per sample. Only entries with read
 counts 8 or higher in at least one tissue. Includes three Tabs, one for
 each population. Each population is represented by four individuals.
 Sample designations and underlying ready numbers are listed in the first
 tab of the table.Data Table 3 INT
 listData Table 3: List of
 all INT transcripts with read numbers per sample. Only entries with read
 counts 8 or higher in at least one tissue. Includes three Tabs, one for
 each population. Each population is represented by four individuals.
 Sample designations and underlying ready numbers are listed in the first
 tab of the file.Data Table 4 -
 Assignments for MCA analysisData Table 4: List of
 all transcripts with expression category assignment per population for MCA
 analysis.