Abstract
To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. We validated ArchAlign using well characterized functional elements, and used it to explore the chromatin structural architecture at CTCF binding sites in the human genome. ArchAlign is freely available at http://www.acsu.buffalo.edu/~mjbuck/ArchAlign.html.
Highlights
To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign)
For all the analysis presented in this manuscript, the Pearson correlation was used as the scoring function
The region with the highest similarity is added to the profile by a weighted average and the process is repeated until all regions have been added to the alignment (Figure 1b)
Summary
To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). Identification of shared chromatin architecture at functional sites has recently become an active area of research [20,21,22,23,24,25], but most studies focus on well-defined transcriptional promoters While these approaches have provided extensive insight into the chromatin architecture at welldefined genomic features, there has been very limited work to identify shared chromatin architectures for unmapped, poorly mapped, or unknown genomic features. We used ArchAlign to align the nucleosome positions at CTCF binding sites, and uncovered a novel directional chromatin architecture containing positioned H2A.Z nucleosomes with the histone tail modifications H3K4me, H3K4me, H3K4me, H3K9me, and H3K20me1 These results define a shared structure at many CTCF sites and provide a framework for further exploration of the chromatin structure at insulator elements
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
