Science

Our expertise is exemplified by a series of scientific publications and patents. Examples include:

1: Pais JE, Dai N, Tamanaha E, Vaisvila R, Fomenkov AI, Bitinaite J, Sun Z, Guan
S, Corrêa IR Jr, Noren CJ, Cheng X, Roberts RJ, Zheng Y, Saleh L. Biochemical
characterization of a Naegleria TET-like oxygenase and its application in single
molecule sequencing of 5-methylcytosine. Proc Natl Acad Sci U S A. 2015 Apr
7;112(14):4316-21. doi: 10.1073/pnas.1417939112. Epub 2015 Mar 23. PubMed PMID:
25831492; PubMed Central PMCID: PMC4394277.

2: Sun Z, Dai N, Borgaro JG, Quimby A, Sun D, Corrêa IR Jr, Zheng Y, Zhu Z, Guan
S. A sensitive approach to map genome-wide 5-hydroxymethylcytosine and
5-formylcytosine at single-base resolution. Mol Cell. 2015 Feb 19;57(4):750-61.
doi: 10.1016/j.molcel.2014.12.035. Epub 2015 Jan 29. PubMed PMID: 25639471.

3: Han T, Yamada-Mabuchi M, Zhao G, Li L, Liu G, Ou HY, Deng Z, Zheng Y, He X.
Recognition and cleavage of 5-methylcytosine DNA by bacterial SRA-HNH proteins.
Nucleic Acids Res. 2015 Jan;43(2):1147-59. doi: 10.1093/nar/gku1376. Epub 2015
Jan 6. PubMed PMID: 25564526; PubMed Central PMCID: PMC4333417.

4: Horton JR, Wang H, Mabuchi MY, Zhang X, Roberts RJ, Zheng Y, Wilson GG, Cheng
X. Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine
out of the DNA helix. Nucleic Acids Res. 2014 Oct 29;42(19):12092-101. doi:
10.1093/nar/gku871. Epub 2014 Sep 27. PubMed PMID: 25262349; PubMed Central
PMCID: PMC4231741.

5: Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X. Wilms tumor
protein recognizes 5-carboxylcytosine within a specific DNA sequence. Genes Dev.
2014 Oct 15;28(20):2304-13. doi: 10.1101/gad.250746.114. Epub 2014 Sep 25. PubMed
PMID: 25258363; PubMed Central PMCID: PMC4201290.

6: Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S, Zhang X, Wilson GG, Zheng
Y, Zhu Z, Cheng X. Structure of 5-hydroxymethylcytosine-specific restriction
enzyme, AbaSI, in complex with DNA. Nucleic Acids Res. 2014 Jul;42(12):7947-59.
doi: 10.1093/nar/gku497. Epub 2014 Jun 3. PubMed PMID: 24895434; PubMed Central
PMCID: PMC4081097.

7: Horton JR, Nugent RL, Li A, Mabuchi MY, Fomenkov A, Cohen-Karni D, Griggs RM,
Zhang X, Wilson GG, Zheng Y, Xu SY, Cheng X. Structure and mutagenesis of the DNA
modification-dependent restriction endonuclease AspBHI. Sci Rep. 2014 Mar
7;4:4246. doi: 10.1038/srep04246. PubMed PMID: 24604015; PubMed Central PMCID:
PMC3946040.

8: Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X.
Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res. 2014
Apr;42(8):4859-67. doi: 10.1093/nar/gku134. Epub 2014 Feb 11. PubMed PMID:
24520114; PubMed Central PMCID: PMC4005678.

9: Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Corrêa IR Jr, Zheng Y,
Cheng X. Structure of a Naegleria Tet-like dioxygenase in complex with
5-methylcytosine DNA. Nature. 2014 Feb 20;506(7488):391-5. doi:
10.1038/nature12905. Epub 2013 Dec 25. PubMed PMID: 24390346; PubMed Central
PMCID: PMC4364404.

10: Sun Z, Terragni J, Borgaro JG, Liu Y, Yu L, Guan S, Wang H, Sun D, Cheng X,
Zhu Z, Pradhan S, Zheng Y. High-resolution enzymatic mapping of genomic
5-hydroxymethylcytosine in mouse embryonic stem cells. Cell Rep. 2013 Feb
21;3(2):567-76. doi: 10.1016/j.celrep.2013.01.001. Epub 2013 Jan 24. Erratum in:
Cell Rep. 2013 Mar 28;3(3):968. Jolyon, Terragni [corrected to Terragni, Jolyon].
PubMed PMID: 23352666; PubMed Central PMCID: PMC3743234.

11: Zhuang F, Fuchs RT, Sun Z, Zheng Y, Robb GB. Structural bias in T4 RNA
ligase-mediated 3′-adapter ligation. Nucleic Acids Res. 2012 Apr;40(7):e54. doi:
10.1093/nar/gkr1263. Epub 2012 Jan 12. PubMed PMID: 22241775; PubMed Central
PMCID: PMC3326334.

12: Terragni J, Bitinaite J, Zheng Y, Pradhan S. Biochemical characterization of
recombinant β-glucosyltransferase and analysis of global 5-hydroxymethylcytosine
in unique genomes. Biochemistry. 2012 Feb 7;51(5):1009-19. doi:
10.1021/bi2014739. Epub 2012 Jan 27. Erratum in: Biochemistry. 2012 Aug
7;51(31):6261. PubMed PMID: 22229759; PubMed Central PMCID: PMC3273966.

13: Xu SY, Nugent RL, Kasamkattil J, Fomenkov A, Gupta Y, Aggarwal A, Wang X, Li
Z, Zheng Y, Morgan R. Characterization of type II and III
restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC
14579. J Bacteriol. 2012 Jan;194(1):49-60. doi: 10.1128/JB.06248-11. Epub 2011
Oct 28. PubMed PMID: 22037402; PubMed Central PMCID: PMC3256598.

14: Wang H, Guan S, Quimby A, Cohen-Karni D, Pradhan S, Wilson G, Roberts RJ, Zhu
Z, Zheng Y. Comparative characterization of the PvuRts1I family of restriction
enzymes and their application in mapping genomic 5-hydroxymethylcytosine. Nucleic
Acids Res. 2011 Nov;39(21):9294-305. doi: 10.1093/nar/gkr607. Epub 2011 Aug 3.
PubMed PMID: 21813453; PubMed Central PMCID: PMC3241641.

15: Kinney SM, Chin HG, Vaisvila R, Bitinaite J, Zheng Y, Estève PO, Feng S,
Stroud H, Jacobsen SE, Pradhan S. Tissue-specific distribution and dynamic
changes of 5-hydroxymethylcytosine in mammalian genomes. J Biol Chem. 2011 Jul
15;286(28):24685-93. doi: 10.1074/jbc.M110.217083. Epub 2011 May 24. PubMed PMID:
21610077; PubMed Central PMCID: PMC3137044.

16: Xu SY, Corvaglia AR, Chan SH, Zheng Y, Linder P. A type IV
modification-dependent restriction enzyme SauUSI from Staphylococcus aureus
subsp. aureus USA300. Nucleic Acids Res. 2011 Jul;39(13):5597-610. doi:
10.1093/nar/gkr098. Epub 2011 Mar 17. PubMed PMID: 21421560; PubMed Central
PMCID: PMC3141236.

17: Zheng Y, Cohen-Karni D, Xu D, Chin HG, Wilson G, Pradhan S, Roberts RJ. A
unique family of Mrr-like modification-dependent restriction endonucleases.
Nucleic Acids Res. 2010 Sep;38(16):5527-34. doi: 10.1093/nar/gkq327. Epub 2010
May 5. PubMed PMID: 20444879; PubMed Central PMCID: PMC2938202.

18: Zheng Y, Posfai J, Morgan RD, Vincze T, Roberts RJ. Using shotgun sequence
data to find active restriction enzyme genes. Nucleic Acids Res. 2009
Jan;37(1):e1. doi: 10.1093/nar/gkn883. Epub 2008 Nov 6. PubMed PMID: 18988632;
PubMed Central PMCID: PMC2615612.

19: Zheng Y, Roberts RJ. Selection of restriction endonucleases using artificial
cells. Nucleic Acids Res. 2007;35(11):e83. Epub 2007 Jun 12. PubMed PMID:
17567609; PubMed Central PMCID: PMC1920265.