The Proceedings of the Eighth International Conference on Creationism (2018)

behooves both creationist and secular researchers to investigate alternative functions for the types of sequence motifs involved, particularly the alleged fusion site sequence, which is the chief hallmark of the whole fusion-based evolutionary story. The characterization of interstitial telomeric-like repeats across the human genome has been documented in previous reports using both cytogenetic and bioinformatic techniques (Azzalin et al. 2001; Nergadze et al. 2007; Lin and Yan 2008; Ruiz-Herrera et al. 2008; Bolzan 2017). Based on the evolutionary assumption that the genome is littered with the non-functional remnants of stochastic evolutionary processes, very little research has been done to investigate whether interstitial telomeric-like sites, like those at the alleged fusion site, might actually serve some useful purpose. Most research has focused on the evolutionary origins of interstitial telomeric repeats being accidentally and randomly transferred from chromosome ends along with the possibility that the sites of these alleged events might be associated with chromosome instability and disease (Nergadze et al. 2007; Lin and Yan 2008; Ruiz-Herrera et al. 2008; Bolzan 2017). However, such research has been inconclusive as to the definitive association of these types of sites with human disease (Bolzan 2017). In light of over a decade of inconclusive research related to attempts at associating interstitial telomeric-like repeats with chromosome instability and disease, one evolutionary researcher stated, “future research should focus on the possible biological significance of ITSs by investigating the role of these telomeric-like sequences in the regulation of gene expression” (Bolzan 2017).  In light of the research I have uncovered regarding the role of the alleged fusion site in the regulation of gene expression, this statement could not be more timely or profound. Towards identifying the possibility of interstitial telomeric-like repeats having purpose and function within a creation model, like those found at the alleged fusion site, I have completed a research project which involves identifying both intact and degenerate telomeric-like repeats within the internal regions of human chromosomes and then intersecting their genomic coordinates with a wide variety of ENCODE project data sets. These results will help build a creationist model of designed and engineered functionality for interstitial telomeric repeats. METHODS TheGRCh38 version of the human genomewas downloaded at ftp:// ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/dna/. Each of the chromosome FASTA files were manually end-trimmed in a text editor to remove telomeric sequence from both chromosome ends. Perfect interstitial telomeric motifs (TTAGGG and CCCTAA) of two tandem repeats or more were identified and binned by chromosome. The common degenerate telomeric forms of the motif (TTNGGG and CCCNAA) were also identified in tandem repeats of two or more and binned by chromosome. Data was outputted in bed file format containing data columns of chromosome ID, genome coordinates, feature ID (eg. forward telomere, reverse telomere). Based on genomic coordinates, each identified telomeric repeat was then intersected with a variety of ENCODE data sets: gencode v. 22 gene annotation (www.gencodegenes.org) , human lincRNAs (long intergenic noncoding RNA) genes from hg38 (https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38 ), lincRNAs from a publication (Hangauer et al. 2013), robust enhancers, permissive enhancers, ubiquitous enhancers, transcription start site association enhancers (http://enhancer.binf.ku.dk/presets/ ), remap transcription factor binding ( http://tagc.univ-mrs.fr/remap/ index.php?page=download), and the trusight inherited disease loci ( https://support.illumina.com/downloads/trusight_inherited_ disease_product_files.html). ENCODE-related BED files based on previous versions of the human genome (e.g. hg16 and hg18) were converted to GRCh38 coordinates using the Python program CrossMap and the appropriate liftover chain conversion files (http:// crossmap.sourceforge.net ). Multiple hits to the same ENCODE- related target bed file were reduced to a single unique output hit to remove redundancy produced by multiple overlapping telomeric repeats at a single locus. Python scripts and modules written by author Tomkins for locating and intersecting interstitial telomeric sequence can be viewed and/or downloaded at https://github.com/ jt-icr/interstitial_telomeric_repeats. RESULTS In this current study, I have queried the entire interstitial space of the latest version of the human genome (hg38) using a Python module I wrote for the identification of perfect and degenerate interstitial telomeric sequence (ITS) sites comprising signatures of 2 repeats or larger. These ITS sites were then intersected using their genome coordinates with a wide variety of ENCODE-related data Tomkins ◀ Interstitial telomeres and chromosome 2 fusion ▶ 2018 ICC 225 Figure 5. The 41,608 base cryptic centromere region on chromosome 2 that is positioned within the ANKRD30BL protein coding gene.