Abstract
Yeast artificial chromosomes (YACs) are important tools for sequencing, gene cloning, and transferring large quantities of genetic information. However, the structure and activity of YAC chromatin, as well as the unintended impacts of introducing foreign DNA sequences on DNA-associated biochemical events, have not been widely explored. Here, we showed that abundant genetic elements like TATA box and transcription factor-binding motifs occurred unintentionally in a previously reported data-carrying chromosome (dChr). In addition, we used state-of-the-art sequencing technologies to comprehensively profile the genetic, epigenetic, transcriptional, and proteomic characteristics of the exogenous dChr. We found that the data-carrying DNA formed active chromatin with high chromatin accessibility and H3K4 tri-methylation levels. The dChr also displayed highly pervasive transcriptional ability and transcribed hundreds of noncoding RNAs. The results demonstrated that exogenous artificial chromosomes formed chromatin structures and did not remain as naked or loose plasmids. A better understanding of the YAC chromatin nature will improve our ability to design better data-storage chromosomes.
Highlights
Yeast artificial chromosomes (YACs) play an important role in genome sequencing (Sasaki et al, 2005), gene cloning (Kouprina and Larionov, 2008), and transgenesis (Lamb and Gearhart, 1995)
We found that the datacarrying chromosome (dChr) forms active chromatin with high accessibility and high histone H3K4 trimethylation (H3K4me3) levels, factors that may facilitate the widespread transcription of the artificial chromosome
These results suggest a high abundance of genetic elements were generated by chance in the artificial chromosome
Summary
Yeast artificial chromosomes (YACs) play an important role in genome sequencing (Sasaki et al, 2005), gene cloning (Kouprina and Larionov, 2008), and transgenesis (Lamb and Gearhart, 1995). Yeast cells can carry an additional YAC up to several megabase pairs in length (Marschall et al, 1999). YACs persist in the host cell, with approximately one copy per haploid genome (Tschumper and Carbon, 1983). YACs have been considered to be yeast centromeric plasmids (YCps) (Gnügge and Rudolf, 2017). Asymmetric segregation of YACs during mitosis occurs at a frequency of about 10% per plasmid pair (Gnügge and Rudolf, 2017). Studying the epigenetic features of exogenous DNA in yeast can provide a better understanding of YACs
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