| Title |
High resolution mapping of modified DNA nucleobases using excision repair enzymes
|
|---|---|
| Published in |
Genome Research, July 2014
|
| DOI | 10.1101/gr.174052.114 |
| Pubmed ID | |
| Authors |
D. Suzi Bryan, Monica Ransom, Biniam Adane, Kerri York, Jay R. Hesselberth |
| Abstract |
The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the locations of modified nucleobases in genomic DNA. We applied the Excision-seq method to map uracil in E. coli and budding yeast and discovered significant variation in uracil content, wherein uracil is excluded from the earliest and latest replicating regions of the genome, possibly driven by changes in nucleotide pool composition. We also used Excision-seq to identify sites of pyrimidine dimer formation induced by UV light exposure, where the method could distinguish between sites of cyclobutane and 6-4 photoproduct formation. These UV mapping data enabled analysis of local sequence bias around pyrimidine dimers and suggested a preference for an adenosine downstream from 6-4 photoproducts. The Excision-seq method is broadly applicable for high precision, genome-wide mapping of modified nucleobases with cognate repair enzymes. |
X Demographics
The data shown below were collected from the profiles of 10 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 4 | 40% |
| Canada | 1 | 10% |
| Netherlands | 1 | 10% |
| France | 1 | 10% |
| Unknown | 3 | 30% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 7 | 70% |
| Members of the public | 3 | 30% |
Mendeley readers
The data shown below were compiled from readership statistics for 79 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 1 | 1% |
| Germany | 1 | 1% |
| Unknown | 77 | 97% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 23 | 29% |
| Student > Ph. D. Student | 21 | 27% |
| Student > Master | 6 | 8% |
| Student > Bachelor | 4 | 5% |
| Student > Doctoral Student | 4 | 5% |
| Other | 9 | 11% |
| Unknown | 12 | 15% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 29 | 37% |
| Biochemistry, Genetics and Molecular Biology | 22 | 28% |
| Medicine and Dentistry | 7 | 9% |
| Chemistry | 6 | 8% |
| Psychology | 1 | 1% |
| Other | 2 | 3% |
| Unknown | 12 | 15% |
Attention Score in Context
This research output has an Altmetric Attention Score of 7. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 19 August 2014.
All research outputs
#5,399,342
of 25,446,666 outputs
Outputs from Genome Research
#2,304
of 4,429 outputs
Outputs of similar age
#49,943
of 241,427 outputs
Outputs of similar age from Genome Research
#37
of 46 outputs
Altmetric has tracked 25,446,666 research outputs across all sources so far. Compared to these this one has done well and is in the 78th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
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