Shuang-Yong Xu
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Explore the profile of Shuang-Yong Xu including associated specialties, affiliations and a list of published articles.
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71
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1408
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Recent Articles
11.
Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu S, et al.
Nucleic Acids Res
. 2021 Jan;
49(3):1708-1723.
PMID: 33450012
Many modification-dependent restriction endonucleases (MDREs) are fusions of a PUA superfamily modification sensor domain and a nuclease catalytic domain. EVE domains belong to the PUA superfamily, and are present in...
12.
Flodman K, Correa Jr I, Dai N, Weigele P, Xu S
Front Microbiol
. 2020 Nov;
11:604618.
PMID: 33193286
To counteract host-encoded restriction systems, bacteriophages (phages) incorporate modified bases in their genomes. For example, phages carry in their genomes modified pyrimidines such as 5-hydroxymethyl-cytosine (5hmC) in T4 deficient in...
13.
Lutz T, Czapinska H, Fomenkov A, Potapov V, Heiter D, Cao B, et al.
Front Microbiol
. 2020 Oct;
11:1960.
PMID: 33013736
Modification dependent restriction endonucleases (MDREs) restrict modified DNA, typically with limited sequence specificity (∼2-4 bp). Here, we focus on MDREs that have an SRA and/or SBD (sulfur binding domain) fused...
14.
Chin H, Sun Z, Vishnu U, Hao P, Cejas P, Spracklin G, et al.
Clin Epigenetics
. 2020 Sep;
12(1):143.
PMID: 32962734
Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional...
15.
Lutz T, Flodman K, Copelas A, Czapinska H, Mabuchi M, Fomenkov A, et al.
Nucleic Acids Res
. 2019 Sep;
47(18):9761-9776.
PMID: 31504772
Modification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or...
16.
Flodman K, Tsai R, Xu M, Correa Jr I, Copelas A, Lee Y, et al.
Front Microbiol
. 2019 Apr;
10:584.
PMID: 30984133
To counteract bacterial defense systems, bacteriophages (phages) make extensive base modifications (substitutions) to block endonuclease restriction. Here we evaluated Type II restriction of three thymidine (T or 5-methyldeoxyuridine, 5mdU) modified...
17.
Kisiala M, Copelas A, Czapinska H, Xu S, Bochtler M
Nucleic Acids Res
. 2018 Sep;
46(19):10489-10503.
PMID: 30202937
TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1). Here, we present a crystal structure of dimeric TagI,...
18.
Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu S, et al.
Nucleic Acids Res
. 2018 Aug;
46(18):9829-9841.
PMID: 30107581
Escherichia coli McrA (EcoKMcrA) acts as a methylcytosine and hydroxymethylcytosine dependent restriction endonuclease. We present a biochemical characterization of EcoKMcrA that includes the first demonstration of its endonuclease activity, small...
19.
Lyu M, Wang Y, Fan G, Wang X, Xu S, Zhu Y
Front Microbiol
. 2017 Nov;
8:2146.
PMID: 29167659
It has become apparent that gut microbiota is closely associated with cardiometabolic diseases (CMDs), and alteration in microbiome compositions is also linked to the host environment. Next generation sequencing (NGS)...
20.
Kweon S, Zhu B, Chen Y, Aravind L, Xu S, Feldman D
Cell Rep
. 2017 Oct;
21(2):482-494.
PMID: 29020633
Enzymatic oxidation of 5-methylcytosine (5mC) in DNA by the Tet dioxygenases reprograms genome function in embryogenesis and postnatal development. Tet-oxidized derivatives of 5mC such as 5-hydroxymethylcytosine (5hmC) act as transient...