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Items: 16

1.

The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1.

Ray S, Ufot A, Assad N, Singh J, Durell SR, Porollo A, Tillo D, Vinson C.

Biochim Biophys Acta Gene Regul Mech. 2019 Apr;1862(4):486-492. doi: 10.1016/j.bbagrm.2019.02.002. Epub 2019 Feb 27.

PMID:
30825655
2.

Replacing C189 in the bZIP domain of Zta with S, T, V, or A changes DNA binding specificity to four types of double-stranded DNA.

Ray S, Tillo D, Assad N, Ufot A, Deppmann C, Durell SR, Porollo A, Vinson C.

Biochem Biophys Res Commun. 2018 Jul 2;501(4):905-912. doi: 10.1016/j.bbrc.2018.05.080. Epub 2018 May 18.

3.

The Epstein-Barr Virus B-ZIP Protein Zta Recognizes Specific DNA Sequences Containing 5-Methylcytosine and 5-Hydroxymethylcytosine.

Tillo D, Ray S, Syed KS, Gaylor MR, He X, Wang J, Assad N, Durell SR, Porollo A, Weirauch MT, Vinson C.

Biochemistry. 2017 Nov 28;56(47):6200-6210. doi: 10.1021/acs.biochem.7b00741. Epub 2017 Nov 10.

4.

5-Methylcytosine (5mC) and 5-Hydroxymethylcytosine (5hmC) Enhance the DNA Binding of CREB1 to the C/EBP Half-Site Tetranucleotide GCAA.

Syed KS, He X, Tillo D, Wang J, Durell SR, Vinson C.

Biochemistry. 2016 Dec 13;55(49):6940-6948. Epub 2016 Nov 29.

PMID:
27951657
5.

Inheritance of Cytosine Methylation.

Tillo D, Mukherjee S, Vinson C.

J Cell Physiol. 2016 Nov;231(11):2346-52. doi: 10.1002/jcp.25350. Epub 2016 Mar 15. Review.

PMID:
26910768
6.

Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution.

He X, Tillo D, Vierstra J, Syed KS, Deng C, Ray GJ, Stamatoyannopoulos J, FitzGerald PC, Vinson C.

Genome Biol Evol. 2015 Oct 27;7(11):3155-69. doi: 10.1093/gbe/evv205.

7.

GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays.

He X, Syed KS, Tillo D, Mann I, Weirauch MT, Vinson C.

G3 (Bethesda). 2015 Jul 16;5(9):1909-18. doi: 10.1534/g3.115.020248.

8.

Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes.

He X, Chatterjee R, Tillo D, Smith A, FitzGerald P, Vinson C.

Epigenetics Chromatin. 2014 Dec 2;7(1):34. doi: 10.1186/1756-8935-7-34. eCollection 2014.

9.

Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein.

Zalckvar E, Paulus C, Tillo D, Asbach-Nitzsche A, Lubling Y, Winterling C, Strieder N, Mücke K, Goodrum F, Segal E, Nevels M.

Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):13126-31. doi: 10.1073/pnas.1305548110. Epub 2013 Jul 22.

10.

Nucleosome sequence preferences influence in vivo nucleosome organization.

Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Hughes TR, Lieb JD, Widom J, Segal E.

Nat Struct Mol Biol. 2010 Aug;17(8):918-20. doi: 10.1038/nsmb0810-918. No abstract available.

11.

High nucleosome occupancy is encoded at human regulatory sequences.

Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TR.

PLoS One. 2010 Feb 9;5(2):e9129. doi: 10.1371/journal.pone.0009129.

12.

G+C content dominates intrinsic nucleosome occupancy.

Tillo D, Hughes TR.

BMC Bioinformatics. 2009 Dec 22;10:442. doi: 10.1186/1471-2105-10-442.

13.

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR.

Mol Cell. 2008 Dec 26;32(6):878-87. doi: 10.1016/j.molcel.2008.11.020.

14.

The DNA-encoded nucleosome organization of a eukaryotic genome.

Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E.

Nature. 2009 Mar 19;458(7236):362-6. doi: 10.1038/nature07667. Epub 2008 Dec 17.

15.

A high-resolution atlas of nucleosome occupancy in yeast.

Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C.

Nat Genet. 2007 Oct;39(10):1235-44. Epub 2007 Sep 16.

PMID:
17873876
16.

Codep: maximizing co-evolutionary interdependencies to discover interacting proteins.

Tillier ER, Biro L, Li G, Tillo D.

Proteins. 2006 Jun 1;63(4):822-31.

PMID:
16634043

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