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Selection, periodicity and potential function for Highly Iterative Palindrome-1 (HIP1) in cyanobacterial genomes
Minli Xu1, Jeffrey G Lawrence2, Dannie Durand1,3
1Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
Nucleic Acids Research
|February 13, 2018
Summary
Highly Iterated Palindrome 1 (HIP1) DNA sequences are highly abundant in cyanobacteria. Their conserved, periodic distribution suggests HIP1 plays a role in chromosome and nucleoid structure.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Highly Iterated Palindrome 1 (HIP1) is a DNA motif found in high abundance in cyanobacterial genomes.
- Despite its prevalence, HIP1's function has remained elusive for two decades.
Purpose of the Study:
- To investigate the functional role of HIP1 in cyanobacteria.
- To determine the evolutionary and structural significance of HIP1's overabundance.
Main Methods:
- Genome-wide analysis of HIP1 distribution and conservation.
- Statistical analysis of HIP1 site periodicity.
- Comparative genomics across cyanobacterial species.
Main Results:
- HIP1 is 15- to 300-fold over-represented in analyzed genomes.
- HIP1 sites are conserved within and between genes, indicating selection.
- HIP1 distribution exhibits significant periodicity (10-90 kb) along chromosomes.
Conclusions:
- HIP1's overabundance and conserved, periodic distribution suggest a functional role beyond neutral processes.
- Evidence does not support roles as RNA/peptide motifs or in gene expression regulation.
- HIP1 likely functions in association with cyanobacterial chromosome and nucleoid structure.
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