Chess Lab


Unperturbed expression bias of imprinted genes in schizophrenia. Gulyás-Kovács A*, Keydar I*, Xia E, Fromer M, Hoffman G, Ruderfer D, Sachidanandam R, Chess A.  Nat Commun. 2018 Jul 25;9(1):2914  *contributed equally


Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing.  Zhu S, Beaulaurier J, Deikus G, Wu TP, Strahl M, Hao Z, Luo G, Gregory JA, Chess A, He C, Xiao A, Sebra R, Schadt EE, Fang G.  Genome Res. 2018 Jul;28(7):1067-1078.

Cocaine-Induced Chromatin Modifications Associate With Increased Expression and Three-Dimensional Looping of Auts2. Engmann O, Labonté B, Mitchell A, Bashtrykov P, Calipari ES, Rosenbluh C, Loh YE, Walker DM, Burek D, Hamilton PJ, Issler O, Neve RL, Turecki G, Hurd Y, Chess A, Shen L, Mansuy I, Jeltsch A, Akbarian S, Nestler EJ. Biol Psychiatry. 2017 Dec 1;82(11):794-805.

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.  McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM; Brain Somatic Mosaicism Network. Science. 2017 Apr 28;356(6336). pii: eaal1641. doi: 10.1126/science.aal1641. Epub 2017 Apr 27.

Monoallelic Gene Expression in Mammals.  Chess A.  Annu Rev Genet. 2016 Nov 23;50:317-327. Review.

Gene expression elucidates functional impact of polygenic risk for schizophrenia.

Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, Ruderfer DM, Oh EC, Topol A, Shah HR, Klei LL, Kramer R, Pinto D, Gümüş ZH, Cicek AE, Dang KK, Browne A, Lu C, Xie L, Readhead B, Stahl EA, Xiao J, Parvizi M, Hamamsy T, Fullard JF, Wang YC, Mahajan MC, Derry JM, Dudley JT, Hemby SE, Logsdon BA, Talbot K, Raj T, Bennett DA, De Jager PL, Zhu J, Zhang B, Sullivan PF, Chess A, Purcell SM, Shinobu LA, Mangravite LM, Toyoshiba H, Gur RE, Hahn CG, Lewis DA, Haroutunian V, Peters MA, Lipska BK, Buxbaum JD, Schadt EE, Hirai K, Roeder K, Brennand KJ, Katsanis N, Domenici E, Devlin B, Sklar P.  Nat Neurosci. 2016 Nov;19(11):1442-1453.

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes.  Beaulaurier J, Zhang XS, Zhu S, Sebra R, Rosenbluh C, Deikus G, Shen N, Munera D, Waldor MK, Chess A, Blaser MJ, Schadt EE, Fang G.  Nat Commun. 2015 Jun 15;6:7438.

Adegbola A, Musante L, Callewaert B, Maciel P, Hu H, Isidor B, Picker-Minh S, Le Caignec C, Delle Chiaie B, Vanakker O, Menten B, Dheedene A, Bockaert N, Roelens F, Decaestecker K, Silva J, Soares G, Lopes F, Najmabadi H, Kahrizi K, Cox GF, Angus SP, Staropoli JF, Fischer U, Suckow V, Bartsch O, Chess A, Ropers HH, Wienker TF, Hubner C, Kaindl AM, Kalscheuer VM. Redefining the MED13L syndrome. Eur J Hum Genet 2015 Oct;23(10):1308-17.

Adegbola AA, Cox GF, Bradshaw EM, Hafler DA, Gimelbrant A, Chess A. Monoallelic expression of the human FOXP2 speech gene. Proc Natl Acad Sci U S A 2015 Jun 2;112(22):6848-54.

Beaulaurier J, Zhang XS, Zhu S, Sebra R, Rosenbluh C, Deikus G, Shen N, Munera D, Waldor MK, Chess A, Blaser MJ, Schadt EE, Fang G. Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nat Commun 2015;6:7438.

Hutchinson JN, Fagerness J, Kirby A, Reynolds R, Zak A, Gimelbrant A, Plenge R, Daly M, Chess A, Seddon JM. (Epi)Genetic analyses of age-related macular degeneration: case-control and discordant twin studies. Hum Hered 2014;78(2):59-72.

Hutchinson JN, Raj T, Fagerness J, Stahl E, Viloria FT, Gimelbrant A, Seddon J, Daly M, Chess A, Plenge R. Allele-specific methylation occurs at genetic variants associated with complex disease. PLoS One 2014;9(6):e98464.

Schadt EE, Banerjee O, Fang G, Feng Z, Wong WH, Zhang X, Kislyuk A, Clark TA, Luong K, Keren-Paz A, Chess A, Kumar V, Chen-Plotkin A, Sondheimer N, Korlach J, Kasarskis A. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res 2013 Jan;23(1):129-41.

Chess A. Random and non-random monoallelic expression. Neuropsychopharmacology 2013 Jan;38(1):55-61.

Reinsborough C, Chess A. An epigenetic trap involved in olfactory receptor gene choice. Dev Cell 2013 Jul 29;26(2):120-1.

Chess A. Mechanisms and consequences of widespread random monoallelic expression. Nat Rev Genet 2012 Jun;13(6):421-8.

Zwemer LM, Zak A, Thompson BR, Kirby A, Daly MJ, Chess A, Gimelbrant AA. Autosomal monoallelic expression in the mouse. Genome Biol 2012;13(2):R10.

Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, Deikus G, Clark TA, Luong K, Murray IA, Davis BM, Keren-Paz A, Chess A, Roberts RJ, Korlach J, Turner SW, Kumar V, Waldor MK, Schadt EE. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol 2012 Dec;30(12):1232-9.

Shen WL, Kwon Y, Adegbola AA, Luo J, Chess A, Montell C. Function of rhodopsin in temperature discrimination in Drosophila. Science 2011 Mar 11;331(6022):1333-6.

Hellman A., and Chess A. (2010) Extensive sequence-influenced DNA methylation polymorphism in the human genome. Epigenetics Chromatin. 3(1):11

Dutta D., Ensminger AW., Zucker JP., Chess A. (2009) Asynchronous replication and autosome-pair non-equivalence in human embryonic stem cells. PLoS One. 4(3):e4970.

Clemson CM., Hutchinson JN., Sara SA., Ensminger AW., Fox AH., Chess A., Lawrence JB. (2009) An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles. Moll Cell. 33(6):717-726.

Adegbola AA., Gonzales ML., Chess A., LaSalle JM., Cox GF. (2009) A novel hypomorphic MECP2 point mutation is associated with a neuropsychiatric phenotype. Hum Genet. 124(6):615-23.

Merriam LC., and Chess A. (2007) cis-Regulatory elements within the odorant receptor coding region. Cell. 131(5):844-846.

Gimelbrant AA., Hutchinson JN., Thompson BR., Chess A. (2007) Widespread Monallelic Expression on Human Autosomes. Science. 318(5853):1136-40

Hellman A., and Chess A. (2007) Gene body-specific methylation on the active X chromosome. Science. 315(5815):1141-3.

Hutchinson JN.*, Ensminger AW.*, Clemson CM., Lynch CR., Lawrence JB., Chess A. (2007) A screen for nulcear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics. 1;8:39  *contributed equally

Diaz-Perez SV., Ferguson DO., Wang C., Csankovszki G., Wang C., Tsai SC., Dutta D., Perez V., Kim S., Eller CD., Salstrom J., Ouyang Y., Teitell MA., Kaltenboeck B., Chess A., Huang S., Marahrens Y. (2006) A deletion at the mouse Xist gene exposes trans-effects that alter the heterochromatin of the inactive X chromosome and the replication time and DNA stability of both X chromosomes. Genetics 174(3):1115-33.

Yonekura S., Ting CY., Neves G., Hung K., Hsu SN., Chiba A,. Chess A., Lee CH. (2006) The variable transmembrane domain of Drosophila N-cadherin regulates adhesive activity. Mol Cell Biol. 26(17):6598-608.

Gimelbrant AA., and Chess A. (2006) An epigenetic state associated with areas of gene duplication.Genome Res.16(6):723-9.

Chess, A. (2005) Monoallelic expression of protocadherin genes. Nature Genetics. 37(2):120-1.

Gimelbrant A., Ensminger, AW., Qi P., Zucker J., Chess A. (2005) Monoallelic expression and asynchronous replication of p120 catenin in mouse and human cells. J Biol Chem. 280(2):1354-9.

Neves G., and Chess A. (2004) Dscam-mediated self-versus non-self-recognition by individual neurons. Cold Spring Harb Symp Quant Biol. 69:485-8.

Ensminger AW., and Chess A. (2004) Bidirectional promoters regulate the monalleclically expressed Ly49 NK receptors. Immunity. 21(1):2-3.

Zhan XL., Clemens J.C., Neves G., Hattori D., Flanagan JJ., Hummel T., Vasconecelos ML., Chess A. and Zipursky SL. (2004) Analysis of Dscam diversity in regulating axon guidance in Drosophila mushroom bodies. Neuron. 43(5):673-86

Gimelbrant AA., Skaletsky H., Chess A. (2004) Selective pressures on the olfactory receptor repertoire since the human-chimpanzee divergence. Proc Natl Acad Sci U S A. 101(24):9019-22.

Eggan K., Baldwin K., Tackett M., Osborne J., Gogos J., Chess A., Axel R., Jaenisch R. (2004) Mice cloned from olfactory sensory neurons. Nature. 428 (6978):44-9.

Neves G., Zucker J., Daly M., Chess A. (2004) Stochastic yet biased expression of multiple Dscam splice variants by individual cells. Nature Genetics. 36(3):240-6.

Ensminger AW., and Chess A. (2004) Coordinated replication timing of monoallelically expressed genes along human autosomes. Hum. Mol. Genetics. 13(6):651-8.

Singh N., Bergman Y., Cedar H., Chess A. (2003) Biallelic germline transcription at the kappa immunoglobulin locus. J Exp Med. 197(6):743-50.

Singh N.*, Ebrahimi FA.*, Gimelbrant AA., Ensminger AW., Tackett MR., Qi P., Gribnau J., Chess A. (2003) Coordination of the random asynchronous replication of autosomal loci. Nature Genetics. 33(3):339-41.  *contributed equally

Hellman A. and Chess A. (2002) OlfactoryAxons: a remarkable convergence. Curr Biol. 12(24):R849-51.

Mostoslavsky R., Singh N., Tenzen T., Goldmit M., Gabay C., Elizur S., Qi P., Chess A., Reubinoff BE., Chess A., Cedar H., Bergman Y. (2001) Asynchronous replication and Allelic exclusion in the immune system. Nature, 414(6860): 221-5.

Gao Q., Yuan B., Chess A. (2000) Convergent projections of Drosophila olfactory neurons to specific glomeruli in the antennal lobe. Nature Neuroscience. 3(8): 780-5.

Rhoades K., Singh N., Simon I., Glidden B., Cedar H., Chess A. (2000) Allele-specific expression patterns of interleukin-2 and Pax-5 revealed by a sensitive single-cell RT-PCR analysis. Curr. Biol. 10(13):789-92.

Ebrahimi FA., Edmondson J., Rothstein R., Chess A. (2000) YAC transgene-mediated olfactory receptor gene choice. Dev Dyn. 217(2):225-31.

Ebrahimi FA. and Chess A. (2000) Olfactory neurons are interdependent in maintaining axonal projections. Curr Biol. 10(4):219-22.

Chess A. (2000) Odorant receptors: axon contact-mediated diversity. Curr Biology 10(4):R152-4.

Gao Q., and Chess A. (1999) Identification of candidate Drosphila olfactory receptors from genomic DNA sequence. Genomics. 60(1):31-39.

Ebrahimi FA. and Chess A. (1998) The Specification of olfactory neurons. Curr Opin Neurobiol. 8(4):453-7.

Chess, A. (1998) Olfactory receptor gene regulation. Adv Immunol. 69:437-47.

Ebrahimi FA. and Chess A. (1998) Olfactory G proteins: simple and complex signal transduction. Curr Biol. 8(12):R431-3.

Mostoslavsky R., Singh N., Kirillov A., Pelanda R., Cedar H., Chess A., Bergman Y. (1998) Kappa chain monoallelic demethylation and the establishment of allelic exclusion. Genes Dev. 12(12):1801-1811.

Chess A. (1998) Expansion of the allelic exclusion principle? Science. 279(5359):2067-8

Chess A., Simon I., Cedar H., Axel R. (1994) Allelic inactivation regulates olfactory receptor gene expression. Cell 78(5):823-34.

Ngai J., Chess A., Dowling MM., Necles N., Macagno ER., Axel R. (1993) Coding of olfactory information: topography of odorant receptor expression in the catfish olfactory epithelium. Cell 72(5):667-80.

Ngai J., Dowling MM., Buck L., Axel R., Chess A. (1993) The family of genes encoding odorant receptors in the channel catfish. Cell. 72(5):657-66.

Goulding EH., Ngai J., Kramer RH., Colicos S., Axel R., Siegelbaum SA., Chess A. (1992) Molecular cloning and single-channel properties of the cyclic nucleotide-gated channel from catfish olfactory neurons. Neuron. 8(1):45-58.

Chess A., Buck L., Dowling MM., Axel R., Ngai J. (1992) Molecular biology of smell: expression of the multigene family encoding putative odorant receptors. Cold Spring Harb Symp Quant Biol. 57:505-16.

Thomas Y., Rogozinski L., Rabbani L., Chess A., Goldstein G., Chess L. (1984) Functional analysis of human T cell subsets defined by monoclonal antibodies. VI. Distinct and opposing immnoregulatory functions within the OKT8+ population. J Mol Cell Immunol 1(2):103-13.