Data from: Selection, periodicity and potential function for highly iterative Palindrome-1 (HIP1) in cyanobacterial genomes

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.

高度迭代回文序列1（Highly Iterated Palindrome 1，简称HIP1，其核心基序为GCGATCGC）在多数蓝细菌基因组中呈超高丰度分布。在部分蓝细菌中，HIP1的平均丰度超过每基因一个基序的水平。如此高的丰度暗示其在蓝细菌生物学过程中发挥着重要作用。然而，历经20余年的研究，学界仍未明确HIP1是否具备生物学功能，更无从知晓其功能具体为何。本研究证实，在所分析的蓝细菌基因组中，HIP1的富集程度可达15至300倍。更为关键的是，HIP1位点在开放阅读框内部以及开放阅读框之间均呈现保守性，这表明其高丰度并非由偏向性DNA修复等中性过程的持续补充所维持，而是源于选择压力的作用。这一针对选择压力的证据，提示HIP1确实存在对应的生物学功能。本研究未发现任何证据支持HIP1作为肽基序或RNA基序发挥功能，亦未发现其参与基因表达调控的相关迹象。与之相反，本研究发现HIP1在蓝细菌染色体上的分布呈现显著的周期性特征，周期跨度为10至90 kb，其尺度与已报道的共调控、共表达及进化相关基因的周期性尺度相符。本研究观察到的周期性，其尺度也与此前在其他细菌中报道的染色体相互作用结构域（chromosomal interaction domains）相当。在此背景下，本研究结果提示，HIP1的功能与染色体及类核结构密切相关。