Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution
Although various methods have been developed for sequencing cytosine modifications, it is still challenging for specific and quantitative sequencing of individual modification at base-resolution. For example, to obtain both true 5-methylcytosine (5mC) and true 5-hydroxymethylcytosine (5hmC) informat...
| Main Authors: | , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Springer Nature
2021
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| _version_ | 1826293326975860736 |
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| author | Liu, Y Hu, Z Cheng, J Siejka-Zielinska, P Chen, J Chen, J Inoue, M Ahmed, A Song, C |
| author_facet | Liu, Y Hu, Z Cheng, J Siejka-Zielinska, P Chen, J Chen, J Inoue, M Ahmed, A Song, C |
| author_sort | Liu, Y |
| collection | OXFORD |
| description | Although various methods have been developed for sequencing cytosine modifications, it is still challenging for specific and quantitative sequencing of individual modification at base-resolution. For example, to obtain both true 5-methylcytosine (5mC) and true 5-hydroxymethylcytosine (5hmC) information, the two major epigenetic modifications, it usually requires subtraction of two methods, which increases noise and requires high sequencing depth. Recently, we developed TET-assisted pyridine borane sequencing (TAPS) for bisulfite-free direct sequencing of 5mC and 5hmC. Here we demonstrate that two sister methods, TAPSβ and chemical-assisted pyridine borane sequencing (CAPS), can be effectively used for subtraction-free and specific whole-genome sequencing of 5mC and 5hmC, respectively. We also demonstrate pyridine borane sequencing (PS) for whole-genome profiling of 5-formylcytosine and 5-carboxylcytosine, the further oxidized derivatives of 5mC and 5hmC. This work completes the set of versatile borane reduction chemistry-based methods as a comprehensive toolkit for direct and quantitative sequencing of all four cytosine epigenetic modifications. |
| first_indexed | 2024-03-07T03:28:23Z |
| format | Journal article |
| id | oxford-uuid:b9d4284d-e5fc-4a1d-8a24-bfc7d4b8749b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T03:28:23Z |
| publishDate | 2021 |
| publisher | Springer Nature |
| record_format | dspace |
| spelling | oxford-uuid:b9d4284d-e5fc-4a1d-8a24-bfc7d4b8749b2022-03-27T05:05:54ZSubtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolutionJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:b9d4284d-e5fc-4a1d-8a24-bfc7d4b8749bEnglishSymplectic ElementsSpringer Nature2021Liu, YHu, ZCheng, JSiejka-Zielinska, PChen, JChen, JInoue, MAhmed, ASong, CAlthough various methods have been developed for sequencing cytosine modifications, it is still challenging for specific and quantitative sequencing of individual modification at base-resolution. For example, to obtain both true 5-methylcytosine (5mC) and true 5-hydroxymethylcytosine (5hmC) information, the two major epigenetic modifications, it usually requires subtraction of two methods, which increases noise and requires high sequencing depth. Recently, we developed TET-assisted pyridine borane sequencing (TAPS) for bisulfite-free direct sequencing of 5mC and 5hmC. Here we demonstrate that two sister methods, TAPSβ and chemical-assisted pyridine borane sequencing (CAPS), can be effectively used for subtraction-free and specific whole-genome sequencing of 5mC and 5hmC, respectively. We also demonstrate pyridine borane sequencing (PS) for whole-genome profiling of 5-formylcytosine and 5-carboxylcytosine, the further oxidized derivatives of 5mC and 5hmC. This work completes the set of versatile borane reduction chemistry-based methods as a comprehensive toolkit for direct and quantitative sequencing of all four cytosine epigenetic modifications. |
| spellingShingle | Liu, Y Hu, Z Cheng, J Siejka-Zielinska, P Chen, J Chen, J Inoue, M Ahmed, A Song, C Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution |
| title | Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution |
| title_full | Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution |
| title_fullStr | Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution |
| title_full_unstemmed | Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution |
| title_short | Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution |
| title_sort | subtraction free and bisulfite free specific sequencing of 5 methylcytosine and its oxidized derivatives at base resolution |
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