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Purified Protein Delivery to Activate an Epigenetically Silenced Allele in Mouse Brain.

Pyles B, Bailus BJ, O'Geen H, Segal DJ.

Methods Mol Biol. 2018;1767:227-239. doi: 10.1007/978-1-4939-7774-1_12.


Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain.

Gallego-Bartolomé J, Gardiner J, Liu W, Papikian A, Ghoshal B, Kuo HY, Zhao JM, Segal DJ, Jacobsen SE.

Proc Natl Acad Sci U S A. 2018 Feb 27;115(9):E2125-E2134. doi: 10.1073/pnas.1716945115. Epub 2018 Feb 14.


Methods for Scarless, Selection-Free Generation of Human Cells and Allele-Specific Functional Analysis of Disease-Associated SNPs and Variants of Uncertain Significance.

Coggins NB, Stultz J, O'Geen H, Carvajal-Carmona LG, Segal DJ.

Sci Rep. 2017 Nov 8;7(1):15044. doi: 10.1038/s41598-017-15407-4.


dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression.

O'Geen H, Ren C, Nicolet CM, Perez AA, Halmai J, Le VM, Mackay JP, Farnham PJ, Segal DJ.

Nucleic Acids Res. 2017 Sep 29;45(17):9901-9916. doi: 10.1093/nar/gkx578.


UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons.

Lopez SJ, Dunaway K, Islam MS, Mordaunt C, Vogel Ciernia A, Meguro-Horike M, Horike SI, Segal DJ, LaSalle JM.

Epigenetics. 2017;12(11):982-990. doi: 10.1080/15592294.2017.1376151. Epub 2017 Nov 6.


Corrigendum: SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation.

Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, Zhong X, Marson G, Pellegrini M, Segal DJ, Patel DJ, Jacobsen SE.

Nature. 2017 Mar 2;543(7643):136. doi: 10.1038/nature21398. Epub 2017 Feb 8. No abstract available.


Allele-Specific Reduction of the Mutant Huntingtin Allele Using Transcription Activator-Like Effectors in Human Huntington's Disease Fibroblasts.

Fink KD, Deng P, Gutierrez J, Anderson JS, Torrest A, Komarla A, Kalomoiris S, Cary W, Anderson JD, Gruenloh W, Duffy A, Tempkin T, Annett G, Wheelock V, Segal DJ, Nolta JA.

Cell Transplant. 2016;25(4):677-86. doi: 10.3727/096368916X690863. Epub 2016 Feb 4.


Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells.

Tak YG, Hung Y, Yao L, Grimmer MR, Do A, Bhakta MS, O'Geen H, Segal DJ, Farnham PJ.

Nucleic Acids Res. 2016 May 19;44(9):4123-33. doi: 10.1093/nar/gkv1530. Epub 2016 Jan 6.


Protein Delivery of an Artificial Transcription Factor Restores Widespread Ube3a Expression in an Angelman Syndrome Mouse Brain.

Bailus BJ, Pyles B, McAlister MM, O'Geen H, Lockwood SH, Adams AN, Nguyen JT, Yu A, Berman RF, Segal DJ.

Mol Ther. 2016 Mar;24(3):548-55. doi: 10.1038/mt.2015.236. Epub 2016 Jan 4.


How specific is CRISPR/Cas9 really?

O'Geen H, Yu AS, Segal DJ.

Curr Opin Chem Biol. 2015 Dec;29:72-8. doi: 10.1016/j.cbpa.2015.10.001. Epub 2015 Oct 24. Review.


The Shelterin TIN2 Subunit Mediates Recruitment of Telomerase to Telomeres.

Frank AK, Tran DC, Qu RW, Stohr BA, Segal DJ, Xu L.

PLoS Genet. 2015 Jul 31;11(7):e1005410. doi: 10.1371/journal.pgen.1005410. eCollection 2015 Jul.


A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture.

O'Geen H, Henry IM, Bhakta MS, Meckler JF, Segal DJ.

Nucleic Acids Res. 2015 Mar 31;43(6):3389-404. doi: 10.1093/nar/gkv137. Epub 2015 Feb 20.


Carlos F. Barbas III (1964-2014): Visionary at the interface of chemistry and biology.

Rader C, Segal DJ, Shabat D.

ACS Chem Biol. 2014 Aug 15;9(8):1645-6. doi: 10.1021/cb5005993. No abstract available.


Engineering specificity changes on a RanBP2 zinc finger that binds single-stranded RNA.

Vandevenne M, O'Connell MR, Helder S, Shepherd NE, Matthews JM, Kwan AH, Segal DJ, Mackay JP.

Angew Chem Int Ed Engl. 2014 Jul 21;53(30):7848-52. doi: 10.1002/anie.201402980. Epub 2014 Jul 9.


Miz-1 activates gene expression via a novel consensus DNA binding motif.

Barrilleaux BL, Burow D, Lockwood SH, Yu A, Segal DJ, Knoepfler PS.

PLoS One. 2014 Jul 1;9(7):e101151. doi: 10.1371/journal.pone.0101151. eCollection 2014. Erratum in: PLoS One. 2014;9(9):e108565.


The functional significance of common polymorphisms in zinc finger transcription factors.

Lockwood SH, Guan A, Yu AS, Zhang C, Zykovich A, Korf I, Rannala B, Segal DJ.

G3 (Bethesda). 2014 Jun 26;4(9):1647-55. doi: 10.1534/g3.114.012195.


The prospect of molecular therapy for Angelman syndrome and other monogenic neurologic disorders.

Bailus BJ, Segal DJ.

BMC Neurosci. 2014 Jun 19;15:76. doi: 10.1186/1471-2202-15-76. Review.


Conformational elasticity can facilitate TALE-DNA recognition.

Lei H, Sun J, Baldwin EP, Segal DJ, Duan Y.

Adv Protein Chem Struct Biol. 2014;94:347-64. doi: 10.1016/B978-0-12-800168-4.00009-3. Review.


SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation.

Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, Zhong X, Marson G, Pellegrini M, Segal DJ, Patel DJ, Jacobsen SE.

Nature. 2014 Mar 6;507(7490):124-128. doi: 10.1038/nature12931. Epub 2014 Jan 22. Erratum in: Nature. 2017 Mar 2;543(7643):136.


Is there a telltale RH fingerprint in zinc fingers that recognizes methylated CpG dinucleotides?

Mackay JP, Segal DJ, Crossley M.

Trends Biochem Sci. 2013 Sep;38(9):421-2. doi: 10.1016/j.tibs.2013.06.005. No abstract available.


Transcription activator like effector (TALE)-directed piggyBac transposition in human cells.

Owens JB, Mauro D, Stoytchev I, Bhakta MS, Kim MS, Segal DJ, Moisyadi S.

Nucleic Acids Res. 2013 Oct;41(19):9197-207. doi: 10.1093/nar/gkt677. Epub 2013 Aug 5.


Genome engineering at the dawn of the golden age.

Segal DJ, Meckler JF.

Annu Rev Genomics Hum Genet. 2013;14:135-58. doi: 10.1146/annurev-genom-091212-153435. Epub 2013 May 20. Review.


New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217.

Vandevenne M, Jacques DA, Artuz C, Nguyen CD, Kwan AH, Segal DJ, Matthews JM, Crossley M, Guss JM, Mackay JP.

J Biol Chem. 2013 Apr 12;288(15):10616-27. doi: 10.1074/jbc.M112.441451. Epub 2013 Feb 22.


Quantitative analysis of TALE-DNA interactions suggests polarity effects.

Meckler JF, Bhakta MS, Kim MS, Ovadia R, Habrian CH, Zykovich A, Yu A, Lockwood SH, Morbitzer R, Elsäesser J, Lahaye T, Segal DJ, Baldwin EP.

Nucleic Acids Res. 2013 Apr;41(7):4118-28. doi: 10.1093/nar/gkt085. Epub 2013 Feb 13.


Bacteria herald a new era of gene editing.

Segal DJ.

Elife. 2013 Jan 29;2:e00563. doi: 10.7554/eLife.00563.


Highly active zinc-finger nucleases by extended modular assembly.

Bhakta MS, Henry IM, Ousterout DG, Das KT, Lockwood SH, Meckler JF, Wallen MC, Zykovich A, Yu Y, Leo H, Xu L, Gersbach CA, Segal DJ.

Genome Res. 2013 Mar;23(3):530-8. doi: 10.1101/gr.143693.112. Epub 2012 Dec 5.


Beyond the genome and into the clinic.

Segal DJ.

Genome Med. 2012 Oct 30;4(10):78. doi: 10.1186/gm379. eCollection 2012.


Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing.

Meier JL, Yu AS, Korf I, Segal DJ, Dervan PB.

J Am Chem Soc. 2012 Oct 24;134(42):17814-22. doi: 10.1021/ja308888c. Epub 2012 Oct 10.


Modular assembly of RanBP2-type zinc finger domains to target single-stranded RNA.

O'Connell MR, Vandevenne M, Nguyen CD, Matthews JM, Gamsjaeger R, Segal DJ, Mackay JP.

Angew Chem Int Ed Engl. 2012 May 29;51(22):5371-5. doi: 10.1002/anie.201200866. Epub 2012 Apr 19. No abstract available.


Chimeric piggyBac transposases for genomic targeting in human cells.

Owens JB, Urschitz J, Stoytchev I, Dang NC, Stoytcheva Z, Belcaid M, Maragathavally KJ, Coates CJ, Segal DJ, Moisyadi S.

Nucleic Acids Res. 2012 Aug;40(14):6978-91. doi: 10.1093/nar/gks309. Epub 2012 Apr 9.


Adding fingers to an engineered zinc finger nuclease can reduce activity.

Shimizu Y, Şöllü C, Meckler JF, Adriaenssens A, Zykovich A, Cathomen T, Segal DJ.

Biochemistry. 2011 Jun 7;50(22):5033-41. doi: 10.1021/bi200393g. Epub 2011 May 11.


The prospects for designer single-stranded RNA-binding proteins.

Mackay JP, Font J, Segal DJ.

Nat Struct Mol Biol. 2011 Mar;18(3):256-61. doi: 10.1038/nsmb.2005. Epub 2011 Feb 27. Erratum in: Nat Struct Mol Biol. 2011 Apr;18(4):516.


Zinc-finger nucleases transition to the CoDA.

Segal DJ.

Nat Methods. 2011 Jan;8(1):53-5. doi: 10.1038/nmeth0111-53. No abstract available.


A zinc finger protein array for the visual detection of specific DNA sequences for diagnostic applications.

Kim MS, Stybayeva G, Lee JY, Revzin A, Segal DJ.

Nucleic Acids Res. 2011 Mar;39(5):e29. doi: 10.1093/nar/gkq1214. Epub 2010 Dec 5.


Toward a general approach for RNA-templated hierarchical assembly of split-proteins.

Furman JL, Badran AH, Ajulo O, Porter JR, Stains CI, Segal DJ, Ghosh I.

J Am Chem Soc. 2010 Aug 25;132(33):11692-701. doi: 10.1021/ja104395b.


Seeing genetic and epigenetic information without DNA denaturation using sequence-enabled reassembly (SEER).

Porter JR, Lockwood SH, Segal DJ, Ghosh I.

Methods Mol Biol. 2010;649:365-82. doi: 10.1007/978-1-60761-753-2_23.


The generation of zinc finger proteins by modular assembly.

Bhakta MS, Segal DJ.

Methods Mol Biol. 2010;649:3-30. doi: 10.1007/978-1-60761-753-2_1.


Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.

Zykovich A, Korf I, Segal DJ.

Nucleic Acids Res. 2009 Dec;37(22):e151. doi: 10.1093/nar/gkp802.


Systematic evaluation of split-fluorescent proteins for the direct detection of native and methylated DNA.

Furman JL, Badran AH, Shen S, Stains CI, Hannallah J, Segal DJ, Ghosh I.

Bioorg Med Chem Lett. 2009 Jul 15;19(14):3748-51. doi: 10.1016/j.bmcl.2009.04.141. Epub 2009 May 5.


Restricted spacer tolerance of a zinc finger nuclease with a six amino acid linker.

Shimizu Y, Bhakta MS, Segal DJ.

Bioorg Med Chem Lett. 2009 Jul 15;19(14):3970-2. doi: 10.1016/j.bmcl.2009.02.109. Epub 2009 Mar 3.


Critical parameters for genome editing using zinc finger nucleases.

Camenisch TD, Brilliant MH, Segal DJ.

Mini Rev Med Chem. 2008 Jun;8(7):669-76. Review.


Generation and functional analysis of zinc finger nucleases.

Cathomen T, Segal DJ, Brondani V, Müller-Lerch F.

Methods Mol Biol. 2008;434:277-90. doi: 10.1007/978-1-60327-248-3_17.


The protein-binding potential of C2H2 zinc finger domains.

Brayer KJ, Kulshreshtha S, Segal DJ.

Cell Biochem Biophys. 2008;51(1):9-19. doi: 10.1007/s12013-008-9007-6. Epub 2008 Feb 20.


Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.

Brayer KJ, Segal DJ.

Cell Biochem Biophys. 2008;50(3):111-31. doi: 10.1007/s12013-008-9008-5. Epub 2008 Feb 6. Review.


Split beta-lactamase sensor for the sequence-specific detection of DNA methylation.

Porter JR, Stains CI, Segal DJ, Ghosh I.

Anal Chem. 2007 Sep 1;79(17):6702-8. Epub 2007 Aug 8.


Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases.

Szczepek M, Brondani V, Büchel J, Serrano L, Segal DJ, Cathomen T.

Nat Biotechnol. 2007 Jul;25(7):786-93. Epub 2007 Jul 1.


Uranyl acetate as a direct inhibitor of DNA-binding proteins.

Hartsock WJ, Cohen JD, Segal DJ.

Chem Res Toxicol. 2007 May;20(5):784-9. Epub 2007 Apr 14.


Design, construction and in vitro testing of zinc finger nucleases.

Carroll D, Morton JJ, Beumer KJ, Segal DJ.

Nat Protoc. 2006;1(3):1329-41.


Active integration: new strategies for transgenesis.

Shinohara ET, Kaminski JM, Segal DJ, Pelczar P, Kolhe R, Ryan T, Coates CJ, Fraser MJ, Handler AM, Yanagimachi R, Moisyadi S.

Transgenic Res. 2007 Jun;16(3):333-9. Epub 2007 Mar 6.


Direct detection of double-stranded DNA: Molecular methods and applications for DNA diagnostics.

Ghosh I, Stains CI, Ooi AT, Segal DJ.

Mol Biosyst. 2006 Nov;2(11):551-60. Epub 2006 Sep 28. Review.


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