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This type of work will be quite helpful in the near future to develop a hotspots monitoring system using these operational satellites data.
Taking these findings together with the findings of a) hotspots at multiple spatial scales and b) the findings from the semi-variogram and log-log plot used to calculate a fractal dimension (see response below), we conclude that our findings are indeed the result of spatial clustering of transmission varying consistently at every scale examined.
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In the genome-wide map of all CENP-A hotspots identified in this study, we noted a qualitative clustering of CENP-A hotspots in subtelomeric and pericentromeric regions.
Although 36% of the 942 HeLa CENP-A hotspots correlate with HeLa HJURP sites, only 5% of SW480 CENP-A hotspots co-localize with SW480 HJURP sites.
Lastly, large clusters of CENP-A hotspots exist in regions spanning pericentric and subtelomeric regions specifically in colorectal cancer cells.
A distinct class of CENP-A hotspots also accumulates at subtelomeric chromosomal locations, including at the 8q24/ Myc region long-associated with genomic instability.
Globally, about approximately 380 CENP-A sites overlap with DHS sites in HeLa, whereas twice that number, approximately 740 SW480 CENP-A hotspots align perfectly with SW480 DHS.
To investigate the nature of ectopic CENP-A hotspots, we next classified them with respect to known genomic and epigenetic features.
Approximately half of normal colon or SW480 CENP-A hotspots (61% and 45%, respectively) overlap with ENCODE DNase I clusters; and a majority of normal colon and SW480 CENP-A hotspots (63% and 48%, respectively) overlap with transcription factor binding clusters found in a variety of cells (Table 5).
Using the DNA consensus detection algorithm TOMTOM to detect motifs common amongst CENP-A hotspots, we discovered that CENP-A enriched sequences are not AT-rich, nor do they contain centromere-like repetitive DNA.
Whether from normal colon, HeLa, or SW480, ectopic CENP-A hotspots contain CpG motifs, and motifs associated with transcription factors, especially those of the zinc-finger and helix-turn-helix classes.
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