We identified a long-distance interaction between the genomic regions of the gene encoding linc-MAF-4 and MAF, where linc-MAF-4 associated with the chromatin modifiers LSD1 and EZH2; this suggested that linc-MAF-4 regulated MAF transcription through the recruitment of chromatin modifiers.
The experiments reported here were able to identify a long-distance interaction using 3C, based on a hypothesis generated using eQTL data.
Four deep intronic mutations were predicted to destabilize a long-distance interaction structure in the secondary PLP1 RNA fragment involved in regulating PLP1/ DM20 alternative splicing.
In accordance with the preferential insertion of SDs into the gene-rich euchromatic portion of the genome, SD regions have a higher probability to be located within long distance interaction bundles (for chr7: adjusted p-value = 1.3332 × 10−4, for all chromosomes: adjusted p-value = 1.3332 × 10−4, 10000 simulations; Additional file 3).
The concept of equivalent distance is introduced to macroscopically account for the further attenuation effects produced by the inhomogeneity upon the long distance interaction forces.
Known for its spectacular tombs and adobe talud tablero architecture, the highland Guatemalan city of Kaminaljuyu is key to models of long distance interaction in Mesoamerica.
Enrichment of the above-mentioned SD categories within long distance interaction bundles was tested.
Long distance interaction bundles were visualised by means of Circos plots [ 40].
This prompted us to search for particularities of long distance interaction patterns with respect to evolutionary breakpoints.
Second, the base pair overlap of SD data sets with long distance interaction bundles was calculated (observed base pair overlap) (BEDTools "coverageBed").
In two out of 1474 instances start and target site of long distance interaction bins directly coincide with the location of two SD paralogs (Additional file 2).
