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High resolution mapping of modified DNA nucleobases using excision repair enzymes
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| Zeitschriftentitel: | Genome Research |
|---|---|
| Personen und Körperschaften: | , , , , |
| In: | Genome Research, 24, 2014, 9, S. 1534-1542 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Cold Spring Harbor Laboratory
|
| Schlagwörter: |
| author_facet |
Bryan, D. Suzi Ransom, Monica Adane, Biniam York, Kerri Hesselberth, Jay R. Bryan, D. Suzi Ransom, Monica Adane, Biniam York, Kerri Hesselberth, Jay R. |
|---|---|
| author |
Bryan, D. Suzi Ransom, Monica Adane, Biniam York, Kerri Hesselberth, Jay R. |
| spellingShingle |
Bryan, D. Suzi Ransom, Monica Adane, Biniam York, Kerri Hesselberth, Jay R. Genome Research High resolution mapping of modified DNA nucleobases using excision repair enzymes Genetics (clinical) Genetics |
| author_sort |
bryan, d. suzi |
| spelling |
Bryan, D. Suzi Ransom, Monica Adane, Biniam York, Kerri Hesselberth, Jay R. 1088-9051 1549-5469 Cold Spring Harbor Laboratory Genetics (clinical) Genetics http://dx.doi.org/10.1101/gr.174052.114 <jats:p>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 <jats:italic>E. coli</jats:italic> 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.</jats:p> High resolution mapping of modified DNA nucleobases using excision repair enzymes Genome Research |
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10.1101/gr.174052.114 |
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Cold Spring Harbor Laboratory, 2014 |
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Cold Spring Harbor Laboratory, 2014 |
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Cold Spring Harbor Laboratory |
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| title |
High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_unstemmed |
High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_full |
High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_fullStr |
High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_full_unstemmed |
High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_short |
High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_sort |
high resolution mapping of modified dna nucleobases using excision repair enzymes |
| topic |
Genetics (clinical) Genetics |
| url |
http://dx.doi.org/10.1101/gr.174052.114 |
| publishDate |
2014 |
| physical |
1534-1542 |
| description |
<jats:p>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 <jats:italic>E. coli</jats:italic> 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.</jats:p> |
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| author | Bryan, D. Suzi, Ransom, Monica, Adane, Biniam, York, Kerri, Hesselberth, Jay R. |
| author_facet | Bryan, D. Suzi, Ransom, Monica, Adane, Biniam, York, Kerri, Hesselberth, Jay R., Bryan, D. Suzi, Ransom, Monica, Adane, Biniam, York, Kerri, Hesselberth, Jay R. |
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| description | <jats:p>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 <jats:italic>E. coli</jats:italic> 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.</jats:p> |
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| spelling | Bryan, D. Suzi Ransom, Monica Adane, Biniam York, Kerri Hesselberth, Jay R. 1088-9051 1549-5469 Cold Spring Harbor Laboratory Genetics (clinical) Genetics http://dx.doi.org/10.1101/gr.174052.114 <jats:p>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 <jats:italic>E. coli</jats:italic> 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.</jats:p> High resolution mapping of modified DNA nucleobases using excision repair enzymes Genome Research |
| spellingShingle | Bryan, D. Suzi, Ransom, Monica, Adane, Biniam, York, Kerri, Hesselberth, Jay R., Genome Research, High resolution mapping of modified DNA nucleobases using excision repair enzymes, Genetics (clinical), Genetics |
| title | High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_full | High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_fullStr | High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_full_unstemmed | High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_short | High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| title_sort | high resolution mapping of modified dna nucleobases using excision repair enzymes |
| title_unstemmed | High resolution mapping of modified DNA nucleobases using excision repair enzymes |
| topic | Genetics (clinical), Genetics |
| url | http://dx.doi.org/10.1101/gr.174052.114 |