ERIC/IRU Repeats

Description:

The Intergenic Repeat Unit (IRU) repeats are also called Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences.

Details:

When this 124-127 bp long intergenic repeat family was initially reported they were named IRU (Sharples, 1990). Shortly thereafter another group also reported their discovery amd named them ERIC sequences (Hulton, 1991). The IRU/ERIC repeats are imperfect palindromes, and thus have orientations, with 20 near full length copies (124-128 bp) on the E. coli K-12 MG1655 genome. All are in intergenic transcribed regions and make RNA hairpins that can affect mRNA stabilty, much like the REP family of intergenic repeats. After REP, ERIC are the most prevelant IGRs in MG1655. IRU/ERIC repeats are found in E. coli, Salmonella and other closely related enterobacterial species.

Some instances of IRU/ERICS have accumulated deletions or insertions; MG1655 has 10 shortened IRU (19-99 bp) but has no instances of IRU with insertions; the 19 bp IRU fragment was only detected because an intact copy was present at the same position in another genome (Sharp, 1996; Cromie, 1997; Sharp, 1997; Wilson, 2006). The partial IRU in the yjbE-yjbF interval stabilizes the upstream gene mRNA in the yjbEFGH operon (Wilson, 2006; Ferrières, 2007).

The IRU/ERIC intervals in EcoGene were added in 1998 based on in-house alignments and were assigned EcoGene instance/allele numbers IRU1-IRU19 in their order on the chromosome. As was done with the REP instance/allele number specific to EcoGene, instances of IRUs discovered after the original numbering are assigned the next number in the series to preserve the original numbering. Thus the full length IRU/ERIC copy in the gntR-yhhW intergenic region has been assigned IRU20 and is out of order, lying between IRU13 and IRU14. IRU20 is the least conserved full length IRU and is the only full length IRU reported to be less than 60% identical to the original IRU (Wilson, 2006).



Dr. Sophie Bachellier has a webpage for the IRUs (Intergenic Repeat Units).