BNFO 301 
Introduction to Bioinformatics
Research Group - Very Short Dispersed Repeats
Spring 2015
(updated 3/9/15)
This category includes some of the first repeated sequences that were recognized in bacteria, including Chi sites (8-nt sites in E. coli used by the mechanism of DNA recombination), and HIP (Highly Iterated Palindromes) sequences (8-nt sequences that may also be related to recombination), DNA uptake signals (9-nt sites important for certain bacteria to recognize exogenous DNA as self). You may include in this category sites that are unusually common (e.g. HIP sequences) or unusually uncommon.

Identifying these sites is certainly of interest, but greater insights can come from comparing them, either within a single genome or amongst several genomes. For example:

  • Where do they occur in the genome? In genes? Downstream from genes? Upstream?
  • Are their sequences conserved between different related bacteria?
  • How fast do their sequences change in evolutionary time?
  • How fast do their positions change in evolutionary time?
  • Is the spacing of these sites interesting? Or their context?
...and so forth.

Articles of possible interest:

  • Smith HO, Gwinn ML, Salzberg SL (1999).
    DNA uptake signal sequences in naturally transformable bacteria.
    Res Microbiol 150:603-616.
     
  • Stahl F (2005).
    Chi: A little sequence controls a big enzyme.
    Genetics 170:487-493.
     
  • Robinson NJ, Robinson PJ, Gupta A, Bleasby AJ, Whitton BA, Morby, AP (1995).
    Singular over-representation of an octameric palindrome, HIP1, in DNA from many cyanobacteria.
    Nucl Acids Res 23:729-735.
     
  • Elhai J (2015). Highly iterated palindromic sequences (HIPs) and their relationship to DNA methyltransferases.
    Life 5:921-948.
     
  • Kobayashi I (2001). Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.
    Nucl Acids Res 29:3742-3756.

Prior research of possible interest:

  • Garnett C (2014). The Evolution of DNA uptake sequences in Neisseria genus from Chromobacterium violaceum.
     
  • Halpern C (2014). Six nucleotide palindrome occurrence in mycobacteriophages.
     
  • Mudhaffar N (2014). The occurrences of DNA uptake sequence in Haemophilus influenzae and other Pasteurellaceae bacteria.
     
  • Vuong M (2014). Occurrence of highly iterated palindromes (HIP1) in Synechoccocus versus Gloebacter violaceus.

Notes of possible interest: