scholarly journals Enhanced JBrowse plugins for epigenomics data visualization

2017 ◽  
Author(s):  
Brigitte T. Hofmeister ◽  
Robert J. Schmitz
Keyword(s):  
Data Visualization ◽  
Histone Modifications ◽  
Scientific Communication ◽  
Sequence Motif ◽  
Read Coverage ◽  
High Quality ◽  
Dna Base ◽  
Non Coding Rnas ◽  
Base Modifications ◽  
Motif Density

ABSTRACTNew sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifically, we have focused on visualizing DNA base modifications, small non-coding RNAs, stranded read coverage, and sequence motif density. Additionally, we present several plugins for improved user experience such as configurable, high-quality screenshots. In visualizing epigenomics with traditional genomics data, we see these plugins improving scientific communication and leading to discoveries within the field of epigenomics.

scholarly journals Oxidative DNA base modifications as factors in carcinogenesis.

1998 ◽  
Vol 45 (2) ◽  
pp. 561-572 ◽  
Author(s):  
R Olinski ◽  
P Jaruga ◽  
T H Zastawny
Keyword(s):  
Metastatic Potential ◽  
Base Damage ◽  
Normal Tissues ◽  
Dna Base ◽  
Dna Modifications ◽  
Cancer Initiation ◽  
Base Modifications ◽  
Therapeutic Doses ◽  
Oxidative Base Damage

Reactive oxygen species can cause extensive DNA modifications including modified bases. Some of the DNA base damage has been found to possess premutagenic properties. Therefore, if not repaired, it can contribute to carcinogenesis. We have found elevated amounts of modified bases in cancerous and precancerous tissues as compared with normal tissues. Most of the agents used in anticancer therapy are paradoxically responsible for induction of secondary malignancies and some of them may generate free radicals. The results of our experiments provide evidence that exposure of cancer patients to therapeutic doses of ionizing radiation and anticancer drugs causes base modifications in genomic DNA of lymphocytes. Some of these base damages could lead to mutagenesis in critical genes and ultimately to secondary cancers such as leukemias. This may point to an important role of oxidative base damage in cancer initiation. Alternatively, the increased level of the modified base products may contribute to genetic instability and metastatic potential of tumor cells.

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