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An interesting question on the evolution of overlapping genes is, "how many overlap gains and losses have occurred in the human and mouse lineages since their divergence"?
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This was found to be the case even between closely related mammal species, with nearly a third of all location-specific consensus motifs exhibiting significant modifications within the human or mouse lineage since their divergence.
Our expectation was that human lineage breaks were kept closer in 3D than mouse lineage breaks since, for the former, the time of conservation of spatial proximity would be shorter (see discussion).
Since a number of transgenic mouse lineages exist where NS3/4A should be present, 16 17 45 we studied the effects of NS3/4A in murine cells.
We detected breakpoint regions resulting from evolutionary rearrangements which occurred since the split of the human and mouse lineages using a method we previously developed [ 5].
Genes that have not recently duplicated in the human lineage (since the human-mouse split) were examined for mouse lineage-specific duplication using data from the Ensembl Compara release 50 [ 25] from human (Homo sapiens) and mouse (Mus musculus).
Since this trend is not observed in breakpoints of mouse lineage origin, correcting for segmental duplication mapping problems proved crucial in our analysis.
Lineage depletion was performed using a Mouse Lineage Depletion Kit (Miltenyi Biotech) according to the manufacturer's instructions.
Mouse lineage negative cells (Lin−) were cultured on the Jagged1-Fc-immobilized substrates.
Mouse lineage tracing experiments in the IPMN GEMM showed that DCLK1+ cells originated from a cell lineage distinct from PDX1+ progenitors.
Comparative analysis of mammalian genomes suggests that nucleotide divergence down the rat lineage since the common ancestor with the house mouse is about 10 20% greater than down the mouse lineage (Rat Genome Sequencing Project Consortium 2004; Lindblad-Toh et al. 2011).
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