Show simple item record

dc.contributor.author Xu, Minli
dc.contributor.author Lawrence, Jeffrey
dc.contributor.author Durand, Dannie
dc.date.accessioned 2018-02-10T20:03:40Z
dc.date.available 2018-02-10T20:03:40Z
dc.date.issued 2018-01-26
dc.identifier doi:10.5061/dryad.b301d
dc.identifier.citation Xu M, Lawrence JG, Durand D (2018) Selection, periodicity and potential function for Highly Iterative Palindrome-1 (HIP1) in cyanobacterial genomes. Nucleic Acids Research, online in advance of print.
dc.identifier.uri http://hdl.handle.net/10255/dryad.169754
dc.description Highly Iterated Palindrome 1 (HIP1, GCGATCGC) is hyper-abundant in most cyanobacterial genomes. In some cyanobacteria, average HIP1 abundance exceeds one motif per gene. Such high abundance suggests a significant role in cyanobacterial biology. However, 20 years of study have not revealed whether HIP1 has a function, much less what that function might be. We show that HIP1 is 15-300 fold over-represented in genomes analysed. More importantly, HIP1 sites are conserved both within and between open reading frames, suggesting that their overabundance is maintained by selection rather than by continual replenishment by neutral processes, such as biased DNA repair. This evidence for selection suggests a functional role for HIP1. No evidence was found to support a functional role as a peptide or RNA motif or a role in the regulation of gene expression. Rather, we demonstrate that the distribution of HIP1 along cyanobacterial chromosomes is significantly periodic, with periods ranging from 10 to 90 kb, consistent in scale with periodicities reported for co-regulated, co-expressed, and evolutionarily correlated genes. The periodicity we observe is also comparable in scale to chromosomal interaction domains previously described in other bacteria. In this context, our findings imply HIP1 functions associated with chromosome and nucleoid structure.
dc.relation.haspart doi:10.5061/dryad.b301d/3
dc.relation.haspart doi:10.5061/dryad.b301d/5
dc.relation.haspart doi:10.5061/dryad.b301d/1
dc.relation.haspart doi:10.5061/dryad.b301d/2
dc.relation.haspart doi:10.5061/dryad.b301d/4
dc.relation.isreferencedby doi:10.1093/nar/gky075
dc.subject repetitive element
dc.subject periodicity
dc.subject selection
dc.subject supercoiling
dc.subject chromosome architecture
dc.title Data from: Selection, periodicity and potential function for highly iterative Palindrome-1 (HIP1) in cyanobacterial genomes
dc.type Article
dwc.ScientificName Cyanobacteria
dc.contributor.correspondingAuthor Durand, Dannie
prism.publicationName Nucleic Acids Research

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Synechococcus elongatus PCC 7942 transcript data derived from Vijayan et al. (2011)
Downloaded 26 times
Download README.txt (3.074 Kb)
Download syf-transcript-info.zip (59.08 Kb)
Details View File Details
Title Parameters estimated from sine wave fitting for HIP1 and control hexamers
Downloaded 18 times
Download README.txt (3.508 Kb)
Download HIP1_periodicity_parameters.zip (128.7 Mb)
Details View File Details
Title The genuine and randomized genomic coordinates for HIP1-like motifs
Downloaded 12 times
Description The genuine and randomized genomic coordinates for HIP1-like motifs, for all the 50 genomes in our study
Download HIP1_from_50_HIP1_rich_genomes.zip (259.9 Mb)
Download README.txt (1.167 Kb)
Details View File Details
Title The genuine and randomized genomic coordinates for control motifs - Part 1
Downloaded 10 times
Description The genuine and randomized genomic coordinates for control motifs, for genomes with names that begin with A to N.
Download Ctrl_from_50_HIP1_rich_genomes_Part1.zip (633.2 Mb)
Download README.txt (1.513 Kb)
Details View File Details
Title The genuine and randomized genomic coordinates for control motifs - Part 2
Downloaded 8 times
Description The genuine and randomized genomic coordinates for control motifs, for genomes with names that begin with O to Z.
Download Ctrl_from_50_HIP1_rich_genomes_Part2.zip (535.0 Mb)
Download README.txt (1.819 Kb)
Details View File Details

Search for data

Be part of Dryad

We encourage organizations to: