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Active and Repressed Chromatin Domains Exhibit Distinct Nucleosome Segregation during DNA Replication.

Escobar TM, Oksuz O, Saldaña-Meyer R, Descostes N, Bonasio R, Reinberg D.

Cell. 2019 Oct 31;179(4):953-963.e11. doi: 10.1016/j.cell.2019.10.009.


Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach.

Yan Q, Shields EJ, Bonasio R, Sarma K.

Cell Rep. 2019 Oct 29;29(5):1369-1380.e5. doi: 10.1016/j.celrep.2019.09.052.


lncRedibly versatile: biochemical and biological functions of long noncoding RNAs.

Shields EJ, Petracovici AF, Bonasio R.

Biochem J. 2019 Apr 10;476(7):1083-1104. doi: 10.1042/BCJ20180440. Review.


RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2.

Zhang Q, McKenzie NJ, Warneford-Thomson R, Gail EH, Flanigan SF, Owen BM, Lauman R, Levina V, Garcia BA, Schittenhelm RB, Bonasio R, Davidovich C.

Nat Struct Mol Biol. 2019 Mar;26(3):237-247. doi: 10.1038/s41594-019-0197-y. Epub 2019 Mar 4.


H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification.

Nicetto D, Donahue G, Jain T, Peng T, Sidoli S, Sheng L, Montavon T, Becker JS, Grindheim JM, Blahnik K, Garcia BA, Tan K, Bonasio R, Jenuwein T, Zaret KS.

Science. 2019 Jan 18;363(6424):294-297. doi: 10.1126/science.aau0583. Epub 2019 Jan 3.


SAVER: gene expression recovery for single-cell RNA sequencing.

Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR.

Nat Methods. 2018 Jul;15(7):539-542. doi: 10.1038/s41592-018-0033-z. Epub 2018 Jun 25.


High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains.

Shields EJ, Sheng L, Weiner AK, Garcia BA, Bonasio R.

Cell Rep. 2018 Jun 5;23(10):3078-3090. doi: 10.1016/j.celrep.2018.05.014.


Loss of KLHL6 promotes diffuse large B-cell lymphoma growth and survival by stabilizing the mRNA decay factor roquin2.

Choi J, Lee K, Ingvarsdottir K, Bonasio R, Saraf A, Florens L, Washburn MP, Tadros S, Green MR, Busino L.

Nat Cell Biol. 2018 May;20(5):586-596. doi: 10.1038/s41556-018-0084-5. Epub 2018 Apr 25.


Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH.

Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A.

Cell Syst. 2018 Feb 28;6(2):171-179.e5. doi: 10.1016/j.cels.2018.01.014. Epub 2018 Feb 14.


Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions.

Warneford-Thomson R, He C, Sidoli S, Garcia BA, Bonasio R.

J Vis Exp. 2017 Sep 28;(127). doi: 10.3791/56004.


Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis.

Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS, Bonasio R, Wagner D.

Nat Genet. 2017 Oct;49(10):1546-1552. doi: 10.1038/ng.3937. Epub 2017 Aug 21.


Specialized odorant receptors in social insects that detect cuticular hydrocarbon cues and candidate pheromones.

Pask GM, Slone JD, Millar JG, Das P, Moreira JA, Zhou X, Bello J, Berger SL, Bonasio R, Desplan C, Reinberg D, Liebig J, Zwiebel LJ, Ray A.

Nat Commun. 2017 Aug 17;8(1):297. doi: 10.1038/s41467-017-00099-1.


The Neuropeptide Corazonin Controls Social Behavior and Caste Identity in Ants.

Gospocic J, Shields EJ, Glastad KM, Lin Y, Penick CA, Yan H, Mikheyev AS, Linksvayer TA, Garcia BA, Berger SL, Liebig J, Reinberg D, Bonasio R.

Cell. 2017 Aug 10;170(4):748-759.e12. doi: 10.1016/j.cell.2017.07.014.


An Engineered orco Mutation Produces Aberrant Social Behavior and Defective Neural Development in Ants.

Yan H, Opachaloemphan C, Mancini G, Yang H, Gallitto M, Mlejnek J, Leibholz A, Haight K, Ghaninia M, Huo L, Perry M, Slone J, Zhou X, Traficante M, Penick CA, Dolezal K, Gokhale K, Stevens K, Fetter-Pruneda I, Bonasio R, Zwiebel LJ, Berger SL, Liebig J, Reinberg D, Desplan C.

Cell. 2017 Aug 10;170(4):736-747.e9. doi: 10.1016/j.cell.2017.06.051.


Photoactivated In Vivo Proximity Labeling.

Beck DB, Bonasio R.

Curr Protoc Chem Biol. 2017 Jun 19;9(2):128-146. doi: 10.1002/cpch.18.


A cut above.

He C, Bonasio R.

Elife. 2017 Feb 15;6. pii: e25000. doi: 10.7554/eLife.25000.


RNA Binding to CBP Stimulates Histone Acetylation and Transcription.

Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger SL.

Cell. 2017 Jan 12;168(1-2):135-149.e22. doi: 10.1016/j.cell.2016.12.020. Epub 2017 Jan 12.


High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells.

He C, Sidoli S, Warneford-Thomson R, Tatomer DC, Wilusz JE, Garcia BA, Bonasio R.

Mol Cell. 2016 Oct 20;64(2):416-430. doi: 10.1016/j.molcel.2016.09.034.


Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus.

Simola DF, Graham RJ, Brady CM, Enzmann BL, Desplan C, Ray A, Zwiebel LJ, Bonasio R, Reinberg D, Liebig J, Berger SL.

Science. 2016 Jan 1;351(6268):aac6633. doi: 10.1126/science.aac6633.


The expanding epigenetic landscape of non-model organisms.

Bonasio R.

J Exp Biol. 2015 Jan 1;218(Pt 1):114-22. doi: 10.1242/jeb.110809. Review.


DNA methylation in social insects: how epigenetics can control behavior and longevity.

Yan H, Bonasio R, Simola DF, Liebig J, Berger SL, Reinberg D.

Annu Rev Entomol. 2015 Jan 7;60:435-52. doi: 10.1146/annurev-ento-010814-020803. Epub 2014 Oct 17. Review.


In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions.

Beck DB, Narendra V, Drury WJ 3rd, Casey R, Jansen PW, Yuan ZF, Garcia BA, Vermeulen M, Bonasio R.

J Proteome Res. 2014 Dec 5;13(12):6135-43. doi: 10.1021/pr500196b. Epub 2014 Oct 29.


Regulation of transcription by long noncoding RNAs.

Bonasio R, Shiekhattar R.

Annu Rev Genet. 2014;48:433-55. doi: 10.1146/annurev-genet-120213-092323. Epub 2014 Sep 18. Review.


Eusocial insects as emerging models for behavioural epigenetics.

Yan H, Simola DF, Bonasio R, Liebig J, Berger SL, Reinberg D.

Nat Rev Genet. 2014 Oct;15(10):677-88. doi: 10.1038/nrg3787. Epub 2014 Sep 9. Review.


Nascent RNA interaction keeps PRC2 activity poised and in check.

Kaneko S, Son J, Bonasio R, Shen SS, Reinberg D.

Genes Dev. 2014 Sep 15;28(18):1983-8. doi: 10.1101/gad.247940.114. Epub 2014 Aug 28.


Interactions with RNA direct the Polycomb group protein SCML2 to chromatin where it represses target genes.

Bonasio R, Lecona E, Narendra V, Voigt P, Parisi F, Kluger Y, Reinberg D.

Elife. 2014 Jul 1;3:e02637. doi: 10.7554/eLife.02637.


CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53.

Saldaña-Meyer R, González-Buendía E, Guerrero G, Narendra V, Bonasio R, Recillas-Targa F, Reinberg D.

Genes Dev. 2014 Apr 1;28(7):723-34. doi: 10.1101/gad.236869.113.


The role of chromatin and epigenetics in the polyphenisms of ant castes.

Bonasio R.

Brief Funct Genomics. 2014 May;13(3):235-45. doi: 10.1093/bfgp/elt056. Epub 2014 Jan 24. Review.


Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin.

Kaneko S, Bonasio R, Saldaña-Meyer R, Yoshida T, Son J, Nishino K, Umezawa A, Reinberg D.

Mol Cell. 2014 Jan 23;53(2):290-300. doi: 10.1016/j.molcel.2013.11.012. Epub 2013 Dec 26.


Polycomb protein SCML2 regulates the cell cycle by binding and modulating CDK/CYCLIN/p21 complexes.

Lecona E, Rojas LA, Bonasio R, Johnston A, Fernández-Capetillo O, Reinberg D.

PLoS Biol. 2013 Dec;11(12):e1001737. doi: 10.1371/journal.pbio.1001737. Epub 2013 Dec 17.


PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells.

Kaneko S, Son J, Shen SS, Reinberg D, Bonasio R.

Nat Struct Mol Biol. 2013 Nov;20(11):1258-64. doi: 10.1038/nsmb.2700. Epub 2013 Oct 20.


SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors.

Zhang J, Bonasio R, Strino F, Kluger Y, Holloway JK, Modzelewski AJ, Cohen PE, Reinberg D.

Genes Dev. 2013 Apr 1;27(7):749-66. doi: 10.1101/gad.210963.112.


A chromatin link to caste identity in the carpenter ant Camponotus floridanus.

Simola DF, Ye C, Mutti NS, Dolezal K, Bonasio R, Liebig J, Reinberg D, Berger SL.

Genome Res. 2013 Mar;23(3):486-96. doi: 10.1101/gr.148361.112. Epub 2012 Dec 3.


SIRT3 functions in the nucleus in the control of stress-related gene expression.

Iwahara T, Bonasio R, Narendra V, Reinberg D.

Mol Cell Biol. 2012 Dec;32(24):5022-34. doi: 10.1128/MCB.00822-12. Epub 2012 Oct 8.


Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator.

Bonasio R, Li Q, Lian J, Mutti NS, Jin L, Zhao H, Zhang P, Wen P, Xiang H, Ding Y, Jin Z, Shen SS, Wang Z, Wang W, Wang J, Berger SL, Liebig J, Zhang G, Reinberg D.

Curr Biol. 2012 Oct 9;22(19):1755-64. doi: 10.1016/j.cub.2012.07.042. Epub 2012 Aug 9.


PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes.

Gao Z, Zhang J, Bonasio R, Strino F, Sawai A, Parisi F, Kluger Y, Reinberg D.

Mol Cell. 2012 Feb 10;45(3):344-56. doi: 10.1016/j.molcel.2012.01.002.


Emerging topics in epigenetics: ants, brains, and noncoding RNAs.

Bonasio R.

Ann N Y Acad Sci. 2012 Jul;1260:14-23. doi: 10.1111/j.1749-6632.2011.06363.x. Epub 2012 Jan 12.


Chromatin in the nuclear landscape.

Beck DB, Bonasio R, Kaneko S, Li G, Li G, Margueron R, Oda H, Sarma K, Sims RJ 3rd, Son J, Trojer P, Reinberg D.

Cold Spring Harb Symp Quant Biol. 2010;75:11-22. doi: 10.1101/sqb.2010.75.052. Epub 2011 Apr 18. Review.


The C-terminal domain of RNA polymerase II is modified by site-specific methylation.

Sims RJ 3rd, Rojas LA, Beck DB, Bonasio R, Schüller R, Drury WJ 3rd, Eick D, Reinberg D.

Science. 2011 Apr 1;332(6025):99-103. doi: 10.1126/science.1202663.


Molecular signals of epigenetic states.

Bonasio R, Tu S, Reinberg D.

Science. 2010 Oct 29;330(6004):612-6. doi: 10.1126/science.1191078. Review.


Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator.

Bonasio R, Zhang G, Ye C, Mutti NS, Fang X, Qin N, Donahue G, Yang P, Li Q, Li C, Zhang P, Huang Z, Berger SL, Reinberg D, Wang J, Liebig J.

Science. 2010 Aug 27;329(5995):1068-71. doi: 10.1126/science.1192428.


MBT domain proteins in development and disease.

Bonasio R, Lecona E, Reinberg D.

Semin Cell Dev Biol. 2010 Apr;21(2):221-30. doi: 10.1016/j.semcdb.2009.09.010. Epub 2009 Sep 22. Review.


Specific and covalent labeling of a membrane protein with organic fluorochromes and quantum dots.

Bonasio R, Carman CV, Kim E, Sage PT, Love KR, Mempel TR, Springer TA, von Andrian UH.

Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14753-8. Epub 2007 Sep 4.


Clonal deletion of thymocytes by circulating dendritic cells homing to the thymus.

Bonasio R, Scimone ML, Schaerli P, Grabie N, Lichtman AH, von Andrian UH.

Nat Immunol. 2006 Oct;7(10):1092-100. Epub 2006 Sep 3. Erratum in: Nat Immunol. 2006 Nov;7(11):1234.


Generation, migration and function of circulating dendritic cells.

Bonasio R, von Andrian UH.

Curr Opin Immunol. 2006 Aug;18(4):503-11. Epub 2006 Jun 13. Review.


Activation of bone marrow-resident memory T cells by circulating, antigen-bearing dendritic cells.

Cavanagh LL, Bonasio R, Mazo IB, Halin C, Cheng G, van der Velden AW, Cariappa A, Chase C, Russell P, Starnbach MN, Koni PA, Pillai S, Weninger W, von Andrian UH.

Nat Immunol. 2005 Oct;6(10):1029-37. Epub 2005 Sep 11.


The S1P-analog FTY720 differentially modulates T-cell homing via HEV: T-cell-expressed S1P1 amplifies integrin activation in peripheral lymph nodes but not in Peyer patches.

Halin C, Scimone ML, Bonasio R, Gauguet JM, Mempel TR, Quackenbush E, Proia RL, Mandala S, von Andrian UH.

Blood. 2005 Aug 15;106(4):1314-22. Epub 2005 May 3.


Bone marrow is a major reservoir and site of recruitment for central memory CD8+ T cells.

Mazo IB, Honczarenko M, Leung H, Cavanagh LL, Bonasio R, Weninger W, Engelke K, Xia L, McEver RP, Koni PA, Silberstein LE, von Andrian UH.

Immunity. 2005 Feb;22(2):259-70.


Elimination in vivo of developing T cells by natural killer cells.

Schott E, Bonasio R, Ploegh HL.

J Exp Med. 2003 Oct 20;198(8):1213-24.


Dendritic cells, loaded with recombinant bacteria expressing tumor antigens, induce a protective tumor-specific response.

Rescigno M, Valzasina B, Bonasio R, Urbano M, Ricciardi-Castagnoli P.

Clin Cancer Res. 2001 Mar;7(3 Suppl):865s-870s.


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