Publications


MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution.

M. V. Neguembor, J. P. Arcon, D. Buitrago, R. Lema, J. Walther, X. Garate, L. Martin, P. Romero, J. A. Abed, M. Gut, J. Blanc, M. Lakadamyali, C. Wu, I. B. Heath, M. Orozco, P. D. Dans, M. P. Cosma, Nat Struct Mol Biol. 29, 1011–1023 (2022). https://doi.org/10.1038/s41594-022-00839-y 

Transcription-mediated supercoiling regulates genome folding and loop formation

M. V. Neguembor, L. Martin, Á. Castells-García, P. A. Gómez-García, C. Vicario, D. Carnevali, J. A. Abed, A. Granados, R. Sebastian-Perez, F. Sottile, J. Solon, C. Wu, M. Lakadamyali, M. P. Cosma,. Mol Cell (2021). DOI: 10.1016/j.molcel.2021.06.009.

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

Huy Q. Nguyen, Shyamtanu Chattoraj, David Castillo, Son C. Nguyen, Guy Nir, Antonios Lioutas, Elliot A. Hershberg, Nuno M. C. Martins, Paul L. Reginato, Mohammed Hannan, Brian J. Beliveau, George M. Church, Evan R. Daugharthy, Marc A. Marti-Renom & C.-ting Wu. Nat Methods 17, 822–832 (2020). https://doi.org/10.1038/s41592-020-0890-0

Opinions piece: Paircounting

X inactivation presents two longstanding puzzles: the counting and choice of X chromosomes. Here, we consider counting and choice in the context of pairing, both of the X and of the autosomes.

Nguyen HQ, Lee SD, Wu CT. Trends Genet. 2019 Sep 11. pii: S0168-9525(19)30159-3.DOI: 10.1016/j.tig.2019.07.010

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos

Homologs are paired in Drosophila somatic cells from embryogenesis to adulthood. Using a computational approach for haplotype-resolved Hi-C, the authors reveal highly structured homolog pairing in Drosophila embryos during zygotic genome activation and demonstrate its application to mammalian embryos.

Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT. Nat Commun. 2019 Oct 3;10(1):4486. DOI:10.1038/s41467-019-12211-8

Highly structured homolog pairing reflects functional organization of the Drosophila genome

Trans-homolog interactions, such as homolog pairing, are highly structured and associated with gene function in Drosophila cells. Here, the authors use haplotype-resolved Hi-C to identify genome-wide trans-homolog interactions in a Drosophila hybrid cell line and investigate complex types of pairing and functional roles.

AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT. Nat Commun. 2019 Oct 3;10(1):4485. DOI:10.1038/s41467-019-12208-

Islands of retroelements are major components of Drosophila centromeres

Chang, C.-H., Chavan, A., Palladino, J., Wei, X., Martins, N.M.C., Santinello, B., Chen, C.-C., Erceg, J., Beliveau, B.J., Wu, C.-T., et al. (2019).. Plos Biol 17, e3000241.DOI:10.1371/journal.pbio.3000241

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

Guy Nir, Irene Farabella, Cynthia Pérez Estrada, Carl G. Ebeling, Brian J. Beliveau, Hiroshi M. Sasaki, S. Dean Lee, Son C. Nguyen, Ruth B. McCole, Shyamtanu Chattoraj, Jelena Erceg, Jumana AlHaj Abed, Nuno M. C. Martins, Huy Q. Nguyen, Mohammed A. Hannan, Sheikh Russell, Neva C. Durand, Suhas S. P. Rao, Jocelyn Y. Kishi, Paula Soler-Vila, Michele Di Pierro, José N. Onuchic, Steven P. Callahan, John M. Schreiner, Jeff A. Stuckey, Peng Yin, Erez Lieberman Aiden, Marc A. Marti-Renom, C.-ting Wu. 

PLoS Genet. 2018 Dec 28; https://doi.org/10.1371/journal.pgen.1007872

In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT

B.J. Beliveau, A.N. Boettiger, G. Nir, B. Bintu, P. Yin, X. Zhuang, C.T. Wu Methods Mol. Biol. 1663 231-252, 2017; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5919218/

Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei

Senaratne TN, Joyce EF, Nguyen SC, Wu CT

PLoS Genet. 2016 Aug 19; http://dx.doi.org/10.1371/journal.pgen.1006169

Spatial organization of chromatin domains and compartments in single chromosomes

Wang S, Su J-H, Beliveau BJ, Bintu1 B, Moffitt1 JR, Wu CT, Zhuang X.

Science 21 Jul 2016. doi: 10.1126/science.aaf8084

Pairing and anti-pairing: a balancing act in the diploid genome

Joyce EF, Erceg J, Wu CT

Curr Opin Genet Dev. 2016 Apr 8;37:119-128. doi: 10.1016/j.gde.2016.03.002 (LINK)

Genes with monoallelic expression contribute disproportionately to genetic diversity in humans.

Savova V, Chun S, Sohail M, McCole RB, Witwicki R, Gai L, Lenz TL, Wu CT, Sunyaev SR, Gimelbrant AA.

Nat Genet. 2016 Jan 25. doi: 10.1038/ng.3493. [Epub ahead of print].  PMID: 26808112

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Xiaowei Zhuang X.

Nature 2016 Jan 13. doi: 10.1038/nature16496. Epub 2016 Jan 13 (Pubmed)

Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries.

Schmidt TL, Beliveau BJ, Uca YO, Theilmann M, Da Cruz F, Wu CT, Shih WM

Nat Commun. 2015 Nov 16;6:8634. doi: 10.1038/ncomms9634. (link)

Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.

Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu CT, Lee JT.

Genetics. 2015 Jun;200(2):537-49. doi: 10.1534/genetics.115.176263. Epub 2015 Apr 9. (pubmed)

Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries.

Murgha Y, Beliveau B, Semrau K, Schwartz D, Wu CT, Gulari E, Rouillard JM.

Biotechniques. 2015 Jun 1;58(6):301-7. doi: 10.2144/000114298. eCollection 2015 Jun. PMID:26054766

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. 

BJ Beliveau, AN Boettiger, MS Avendaño, R Jungmann, RB McCole, EF Joyce, C Kim-Kiselak, F Bantignies, CYFonseka, J Erceg, MA Hannan, HG Hoang, D Colognori, JT Lee, WM Shih, P Yin, X Zhuang, C-t Wu

Nature Communications 2015. May 12; 6:7147. doi: 10.1038/ncomms8147 (pubmed).

Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells.

McCole RB, Fonseka CY, Koren A, Wu CT.

PLoS Genet. 2014 Oct 23;10(10):e1004646. doi: 10.1371/journal.pgen.1004646

Visualizing Genomes with Oligopaint FISH Probes.

Beliveau BJ, Apostolopoulos N, Wu CT.

Current Protocols in Molecular Biology  2014. 105:14.23.1–14.23.20.

Germline Progenitors Escape the Widespread Phenomenon of Homolog Pairing during Drosophila Development.

Joyce EF, Apostolopoulos N, Beliveau BJ, Wu CT.

PLoS Genet. 2013 Dec;9(12):e1004013. doi: 10.1371/journal.pgen.1004013. Epub 2013 Dec 19.

Versatile deign and synthesis platform for visualizing genomes with Oligopaint FISH probes.

Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT.

Proc Natl Acad Sci USA. 2012. 109(52):21301-6

Restoration of Topoisomerase 2 function by complementation of defective monomers in Drosophila.

Hohl AM, Thompson M, Soshnev AA, Wu J, Morris J, Hsieh T-S, Wu C-t, Geyer PK.

Genetics. 2012 Aug 24 (in press)

Identification of genes that promote or antagonize somatic homolog pairing using a high-throughput FISH-based screen.

Joyce EF, Williams BR, Xie T, Wu C-t.

PLoS Genet 2012. 8(5): e1002667. doi:10.1371/journal.pgen.1002667

Effects of chromosomal rearrangements on transvection at the yellow gene of Drosophila melanogaster.

Ou SA, Chang E, Lee S, So K, Wu CT, Morris JR.

Genetics. 2009 Oct;183(2):483-96. Epub 2009 Aug 10.

The twin spot generator for differential Drosophila lineage analysis.

Griffin R, Sustar A, Bonvin M, Binari R, del Valle Rodriguez A, Hohl AM, Bateman JR, Villalta C, Heffern E, Grunwald D, Bakal C, Desplan C, Schubiger G, Wu CT, Perrimon N.

Nat Methods. 2009 Aug;6(8):600-2. Epub 2009 Jul 26.

Molecular genetic analysis of Suppressor 2 of zeste identifies key functional domains

Emmons RB, Genetti H, Filandrinos S, Lokere J, Wu CT. 

Genetics. 2009 Aug;182(4):999-1013. Epub 2009 Jun 15.

Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries

Chiang CW, Derti A, Schwartz D, Chou MF, Hirschhorn JN, Wu CT.

Genetics. 2008 Dec;180(4):2277-93. Epub 2008 Oct 28.

A simple polymerase chain reaction-based method for the construction of recombinase-mediated cassette exchange donor vectors.

Bateman JR, Wu CT.

Genetics. 2008 Nov;180(3):1763-6. Epub 2008 Sep 14.

A genomewide survey argues that every zygotic gene product is dispensable for the initiation of somatic homolog pairing in Drosophila.

Bateman JR, Wu CT.

Genetics. 2008 Nov;180(3):1329-42. Epub 2008 Sep 14.

Disruption of topoisomerase II perturbs pairing in drosophila cell culture.

Williams BR, Bateman JR, Novikov ND, Wu CT.

Genetics. 2007 Sep;177(1):31-46.

DNA replication and models for the origin of piRNAs.

Bateman JR, Wu CT.

Bioessays. 2007 Apr;29(4):382-5.

Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions.

Lee AM, Wu CT.

Genetics. 2006 Dec;174(4):1867-80. Epub 2006 Oct 22.

Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants.

Derti A, Roth FP, Church GM, Wu CT.

Nat Genet. 2006 Oct;38(10):1216-20. Epub 2006 Sep 24.

Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange.

Bateman JR, Lee AM, Wu CT.

Genetics. 2006 Jun;173(2):769-77. Epub 2006 Mar 17.

Analysis of a Polycomb Group protein defines regions that link repressive activity on nucleosomal templates to in vivo function.

King IFG, Emmons RB, Francis NJ, Wild B, Müller J, Kingston RE, Wu C-t.

Mol. Cell. Biol. 2005; 25: 6578-91.

Does random X-inactivation in mammals reflect a random choice between two X chromosomes?

Williams BR, Wu CT.

Genetics. 2004 Jul;167(3):1525-8.

Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter.

Morris JR, Petrov DA, Lee AM, Wu CT.

Genetics. 2004 Aug;167(4):1739-47.

Enhancer action in trans is permitted throughout the Drosophila genome.

Chen J-L, Huisinga KL, Viering MM, Ou SA, Wu C-t, Geyer PK.

Proc Natl Acad Sci USA 2002; 99: 3723-8.

Homology Effects.

Dunlap JC, Wu C-t, editors.

Adv Gen 2002; vol 46.

Homology effects: The difference between 1 and 2.

Wu C-t, Dunlap JC.

Adv Gen 2002; 46: xvii-xxiii.

Genes, genetics, and epigenetics: a correspondence.

Wu Ct, Morris JR.

Science. 2001 Aug 10;293(5532):1103-5.

Spt5 and Spt6 are associated with active transcription and have characteristics of general elongation factors in Drosophila melanogaster.

Kaplan C, Morris JR, Wu C-t, Winston F.

Genes Dev 2000; 14: 2623-34.

Stabilization of chromatin structure by PRC1, a Polycomb complex.

Shao Z, Raible F, Mollaaghababa R, Guyon JR, Wu C-t, Bender W, Kingston RE.

Cell 1999; 98: 37-46.

Transvection and other homology effects.

Wu CT, Morris JR.

Curr Opin Genet Dev. 1999 Apr;9(2):237-46. Review.

Core promoter elements can regulate transcription on a separate chromosome in trans.

Morris JR, Geyer PK, Wu CT.

Genes Dev. 1999 Feb 1;13(3):253-8.

An analysis of transvection at the yellow locus of Drosophila melanogaster.

Morris JR, Chen J-l, Filandrinos ST, Dunn RC, Fisk R, Geyer PK, Wu C-t.

Genetics 1999; 151: 633-51.

Two modes of transvection: enhancer action in trans and bypass of a chromatin insulator in cis.

Morris JR, Chen JL, Geyer PK, Wu CT.

Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10740-5.

A genetic analysis of the Suppressor 2 of zeste complex of Drosophila melanogaster.

Wu CT, Howe M.

Genetics. 1995 May;140(1):139-81.

Transvection, nuclear structure, and chromatin proteins.

Wu CT.

J Cell Biol. 1993 Feb;120(3):587-90. Review.

Isolation and characterization of Drosophila multidrug resistance gene homologues.

Wu C-t, Budding M, Griffin MS, Croop JM.

Mol Cell Biol 1991; 11: 3940-8.

The Drosophila zeste gene and transvection.

Wu C-t, Goldberg ML.

Trends Genet 1989; 5: 189-94.

Homeosis and the interaction of zeste and white in Drosophila.

Wu C-t, Jones RS, Lasko PF, Gelbart WM.

Mol Gen Genet 1989; 218: 559-64.

Interactions of zeste mutations with loci exhibiting transvection effects in Drosophila melanogaster

Gelbart WM, Wu C-t.

Genetics 1982; 102: 179-89.