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| Status |
Public on Jan 01, 2020 |
| Title |
Mutating Zta(N182) to S, Q, T, I, and V changes sequence specific DNA binding to four types of DNA (32k data set) |
| Platform organism |
synthetic construct |
| Sample organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
The Epstein-Barr virus (EBV) bZIP transcription factor (TF) Zta is a sequence-specific DNA binding protein that recognizes both unmethylated and methylated double stranded DNA (dsDNA). To study the contribution to sequence specific dsDNA binding of the conserved asparagine in the DNA binding region (Zta(N182)), we replaced it with five other amino acids: serine (S), glutamine (Q), threonine (T), isoleucine (I), or valine (V). We used protein binding microarrays (PBMs) to evaluate sequence-specific DNA binding to four types of dsDNA: 1) DNA with cytosine in both strands (DNA(C|C), 2) DNA with 5-methylcytosine (5mC, M) in one strand and cytosine in the second strand (DNA(5mC|C)), 3) DNA with 5-hydroxymethylcytosine (5hmC, H) in one strand and cytosine in the second strand (DNA(5hmC|C)), and 4) DNA with methylated cytosine in both strands in all CG dinucleotides (DNA(5mCG)). With unmethylated DNA, Zta binds the consensus TRE motif, also known as the AP1 motif (T-4G-3A-2G/C0T2C3A4). Zta(N182S) binds the variants andwhere C3 is replaced with G3 in one (T-4G-3A-2G/CT2G3A4) or both T-4C-3A-2G/CT2G3A4 half sites. Zta(N182S) also binds stronger to DNA containing modified cytosines compared to wildtype. Zta(N182Q) binds new sequences containing G0T2A3A4 with DNA(C|C), DNA(5mC|C) and DNA(5hmC|C) where C3 is replaced with A3 only on one half site. Zta(N182I) and Zta(N182V) bind sequence specifically to DNA(5mC|C), and weakly with all other types of DNA examined. Zta(N182T) DNA binding is weaker to all types of DNA examined. Our data highlights that mutation of Zta(N182) with the hydrophilic amino acids serine and glutamine alters Zta sequence specific DNA binding, while mutation with hydrophobic amino acids (I and V) increases binding to DNA(5mC|C).
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| Overall design |
Protein binding microarray (PBM) experiments were performed for the DNA binding domain of Zta, Zta(N182S), Zta(N182Q), Zta(N182I), Zta(N182V), and Zta(N182T). Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded 44K Agilent microarrays (Berger et al., Nature Biotechnology 2006) in order to determine their binding preferences to sequences containing modified cytosines. We modified the double stranding step of the PBM protocol in which the nucleotide mixture contained 5-methylcytosine or 5-hydroxymethylcytosine. Details of the modified cytosine PBM protocol are described in Khund-Sayeed S et al., Integrative Biology, 2016.
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| Contributor(s) |
Nima A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Feb 14, 2019 |
| Last update date |
Jan 03, 2020 |
| Contact name |
Charles Vinson |
| E-mail(s) |
vinsonc@dc37a.nci.nih.gov
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| Organization name |
National Institutes of Health
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| Department |
National Cancer Institute
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| Lab |
Laboratory of Metabolism
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| Street address |
37 Convent Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
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| Platforms (1) |
| GPL11260 |
Agilent custom ME and HK design array [8mer] |
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| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE126590 |
Mutating Zta(N182) to S, Q, T, I, and V changes sequence specific DNA binding to four types of DNA |
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| Relations |
| BioProject |
PRJNA522465 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE126589_N182_32k_8mer_Z-score.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSE126589_RAW.tar |
122.0 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data are available on Series record |
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