{"id":2272,"date":"2014-07-30T01:45:00","date_gmt":"2014-07-30T05:45:00","guid":{"rendered":"https:\/\/med.sites.unc.edu\/pharm\/calabreselab\/calabreselab-2\/publications\/"},"modified":"2025-02-05T05:06:03","modified_gmt":"2025-02-05T10:06:03","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/pharm\/calabreselab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

2024<\/h3>\n

Li S., Eberhard Q. E., Ni L., Calabrese J.M. Improved functions for non-linear sequence comparison using SEEKR. RNA. 2024 Oct 16;30(11):1408-1421. PMID: 38496437. PMCID: PMC10942450.<\/p>\n

Saha D., Animireddy S., Lee J., Thommen A., Murvin M.M,. Lu Y., Calabrese J.M., Bartholomew B. Enhancer switching in cell lineage priming is linked to eRNA, Brg1’s AT-hook, and SWI\/SNF recruitment. Mol Cell. 2024 May 16;84(10):1855-1869.e5. PMID: 38593804. PMCID: PMC11104297.<\/p>\n

2023<\/h3>\n

Trotman, J.B., Braceros, A.K., Bischoff, S.R., Murvin, M.M., Boyson, S.P., Cherney, R.E., Eberhard, Q.E., Abrash, E.W., Calabrese, J.M. Ectopically expressed Airn<\/em> lncRNA deposits Polycomb with a potency that rivals Xist<\/em>. 2023. bioRxiv<\/em>. doi: 10.1101\/2023.05.09.539960<\/a><\/p>\n

Cherney, R.E., Eberhard, Q.E., Gir,i G., Mills, C.A., Porrello, A., Zhang, Z., White, D., Trotman, J.B., Herring, L.E., Dominguez, D., Calabrese, J.M. SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells. RNA. 2023 Oct;29(10):1535-1556. PMID: 37468167. PMCID: PMC10578485.<\/p>\n

Braceros, A.K., Schertzer, M.D., Omer, A., Trotman, J.B., Davis, E.S., Dowen, J.M., Phanstiel, D.H., Aiden, E.L., Calabrese, J.M. Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn. Cell Reports. 2023 Jul 25;42(7):112803. doi: 10.1016\/j.celrep.2023.112803. PMID: 37436897. PMCID: PMC10441531.<\/p>\n

Cherney, R.E., Mills, C.A., Herring, L.E., Braceros, A.K., Calabrese, J.M. A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB. Biology Open. 2023. doi: 10.1242\/bio.059955. Epub 2023 Jun 7. PubMed PMID: 37283223. PMCID: PMC10259849.<\/p>\n

2022<\/h3>\n

Abrash E.W., Calabrese J.M. Oncogenic transcription factors and neogenes: New opportunities for cancer immunotherapy?. Mol Cell. 2022 Jul 7;82(13):2353-2355. doi: 10.1016\/j.molcel.2022.06.006.<\/p>\n

Cerase A., Calabrese J.M., Tartaglia G.G. Phase separation drives X-chromosome inactivation. Nat Struct Mol Biol. 2022 Mar;29(3):183-185. doi: 10.1038\/s41594-021-00697-0.<\/p>\n

2021<\/h3>\n

Trotman, J.B., Braceros, K.C.A., Cherney, R.E., Murvin, M.M., Calabrese J.M. The control of Polycomb Repressive Complexes by long noncoding RNAs. 2021. WIREs RNA<\/i>. Apr 16:e1657. doi: 10.1002\/wrna.1657. PMID: 33861025<\/p>\n

Weidmann, C.A., Mustoe, A.M., Jariwala, P.B., Calabrese, J.M., Weeks, K.M. Analysis of RNA\u2013protein networks with RNP-MaP defines functional hubs on RNA. 2021. Nature Biotechnology. 2021 Mar;39(3):347-356. doi: 10.1038\/s41587-020-0709-7 PMID: 33077962. PMCID: PMC7956044.<\/p>\n

Kirk J.M.*, Sprague D.*, Calabrese J.M. Classification of long noncoding RNAs by k<\/i>-mer content. 2021. Methods in Molecular Biology<\/i>. 2254:41-60. PMID: 33326069\u00a0 PMCID: PMC7850294.<\/p>\n

2020<\/h3>\n

Schertzer, M. D., Murvin, M. M. and Calabrese, J. M. Using RNA Sequencing and Spike-in RNAs to Measure Intracellular Abundance of lncRNAs and mRNAs. 2020. Bio-protocol 10(19): e3772. doi: 10.21769\/bioprotoc.3772 PMID: 33204768. PMCID: PMC7668557.<\/p>\n

Sigmon, J. Blanchard, M., \u2026 Calabrese, J.M., \u2026 Ferris, M., McMillan, L., Pardo-Manuel de Villena, F. 2020. Content and performance of the MiniMUGA genotyping array, a new tool to improve rigor and reproducibility in mouse research. 2020. G3. Online ahead of print. DOI: 10.1534\/genetics.120.303596 PMID: 33067325. PMCID: PMC7768238.<\/p>\n

Trotman J.B., Lee D.M., Cherney R.E., Inoue, K. Schertzer M.D., Bischoff S.R., Cowley D.O., Calabrese J.M. Elements at the 5\u2032 end of Xist<\/i> harbor SPEN-independent transcriptional antiterminator activity. 2020. Nucleic Acids Res., gkaa789, https:\/\/doi.org\/10.1093\/nar\/gkaa789. PMID: 32986830.\u00a0 PMCID: PMC7544216.<\/p>\n

Trotman J.B. and Calabrese J.M.\u00a02020.\u00a0How to silence an X chromosome. Nature News & Views<\/em>. Feb 5. DOI: 10.1038\/d41586-020-00207-0.<\/p>\n

2019<\/h3>\n

Smith K.N., Miller S.C., Varani G., Calabrese J.M., Magnuson T. Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification. Genetics<\/em>. Dec;213(4):1093-1110. PMID: 31796550. DOI: 10.1534\/genetics.119.302661.<\/p>\n

Schertzer M.D., Braceros K.C.A., Starmer J., Cherney R.E., Lee D.M., Salazer G., Justice M., Bischoff S.R., Cowley D.O., Ariel P., Zylka M.J., Dowen J.M., Magnuson T., Calabrese J.M. 2019. lncRNA-Induced Spread of Polycomb Controlled by Genome Architecture, RNA Abundance, and CpG Island DNA.\u00a0Molecular Cell. <\/em>Aug 8;75(3):523-537.e10.\u00a0doi:\u00a010.1016\/j.molcel.2019.05.028. *F1000Prime Recommended by Dr. Neil Brockdorff<\/p>\n

Schertzer M.D., Thulson E., Braceros K.C.A., Lee D.M., Hinkle E.R., Murphy R.M., Kim S.O., Vitucci E.M., Calabrese J.M. 2019. A piggyBac-based toolkit for inducible genome editing in mammalian cells.\u00a0RNA<\/em>. Aug;25(8):1047-1058.\u00a0doi:\u00a010.1261\/rna.068932.118.<\/p>\n

Sprague D., Waters S., Kirk J.M., Wang J., Samollow P., Waters P., Calabrese J.M. 2019. Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains.\u00a0RNA<\/em>. Aug;25(8):1004-1019.\u00a0doi:\u00a010.1261\/rna.069815.118.<\/p>\n

Raab J.R., Smith K.N., Spear C.C., Manner C.J., Calabrese J.M., Magnuson T. 2019. SWI\/SNF remains localized to chromatin in the presence of SCHLAP1.\u00a0Nature Genetics<\/em>\u00a051(1):26-29.<\/p>\n

2018<\/h3>\n

Kirk J.M., Kim S.O., Inoue K., Smola M.J., Lee D.M., Schertzer M.D., Wooten J.S., Baker A.R., Sprague D., Collins D.W., Horning C.R., Wang S., Chen Q., Weeks K.M., Mucha P.J., and Calabrese J.M. 2018. Functional classification of long non-coding RNAs by kmer content.<\/a> Nature Genetics<\/em> 50, 1474\u20131482.<\/p>\n

UNC press release:\u00a0http:\/\/news.unchealthcare.org\/news\/2018\/september\/scientist-reveal-way-to-map-vast-unknown-territory-of-long-non-coding-rna<\/a><\/p>\n

2016<\/h3>\n

Smola, M.J., Christy, T.W., Inoue, K., Nicholson, C., Friedersdorf, M., Keene, J., Lee, D.M., Calabrese J.M., Weeks, K.M. 2016. SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells<\/a>. PNAS <\/em>113(37):10322-7.<\/p>\n

2015<\/span><\/h3>\n

Smola, M.J., Calabrese J.M., Weeks, K.M. 2015. Detection of RNA-Protein Interactions in Living Cells with SHAPE<\/a>. Biochemistry <\/em>54(46):6867-6875.<\/p>\n

Chu C., Zhang Q.C., da Rocha S.T., Flynn R.A., Bharadwaj M., Calabrese J.M., Magnuson T., Heard E., Chang H.Y. 2015. Systematic discovery of Xist RNA binding proteins<\/a>. Cell<\/em> 161:404-416.<\/p>\n

Calabrese J.M.ca<\/sup>, Starmer J., Schertzer M.D., Yee D., Magnuson T. 2015. A survey of imprinted gene expression in mouse trophoblast stem cells<\/a>. G3<\/em> Feb 23.<\/p>\n

2014<\/h3>\n

Pohlers M., Calabrese J.M., Magnuson T. 2014. <\/span>Small RNA expression from the human macrosatellite DXZ4<\/a>. <\/span>G3<\/em> 4(10):1981-9.<\/span><\/p>\n

Mugford J.W., Starmer J., Williams R.L., Calabrese J.M., Mieczkowski P., Yee D., Magnuson T. 2014. Evidence for local regulatory control of escape from imprinted X chromosome inactivation<\/a>. Genetics<\/i> 197(2):715-723.<\/p>\n

Williams R.L.*, Starmer J.*, Mugford J.W., Calabrese J.M., Mieczkowski P., Yee D., Magnuson T. 2014. A Method for Determining Chromosomal Interactions in 4C-Seq Data<\/a>. Nucleic Acids Research<\/i> 42(8): e68.<\/p>\n

2013<\/h3>\n

King I.F., Yandava C.N., Mabb A.M., Hsiao J.S., Huang H.S., Pearson B.L., Calabrese J.M., Starmer J., Parker J.S., Magnuson T., Chamberlain S.J., Philpot B.D., Zylka M.J. 2013. Topoisomerases facilitate transcription of long genes linked to autism<\/a>. Nature<\/i> 501(7465):58-62. PMC3767287<\/p>\n

Calabrese, J.M.\u00a0and Magnuson, T. 2013. Roles of long noncoding RNAs in X-chromosome Inactivation<\/a>. In The Molecular Biology of Long Non-coding RNAs<\/i>, Coller J and Khalil A, (Eds). Springer Science. 69-94.<\/p>\n

2012<\/h3>\n

Calabrese, J.M., Sun, W. Song, L., Mugford, J.W., Williams, L., Yee, D., Starmer, J., Mieczkowski, P., Crawford, G.E., Magnuson, T. 2012. Site-specific silencing of regulatory elements as a mechanism of X-inactivation<\/a>. Cell<\/i> 151(5): 951-63. PMC3511858. Press release<\/a>.<\/p>\n

Fedoriw, A.M., Calabrese, J.M., Mu, W., Yee, D., Magnuson, T. 2012. Differentiation-Driven Nucleolar Association of the Mouse Imprinted Kcnq1 locus<\/a>. Genes, Genomes, Genetics<\/i> 2(12): 1521-8. PMC3516474<\/p>\n

Horakova, A.H., Calabrese, J.M., McLaughlin, C.R., Tremblay, D.C., Magnuson, T., Chadwick, B.P. 2012. The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite<\/a>. Genome Biology<\/i> 13(8): R70. PMC3491370<\/p>\n

2011<\/h3>\n

Zheng, G.X.*, Ravi, A.*, Calabrese, J.M., Medeiros, L.A., Kirak, O., Dennis, L.M., Jaenisch, R., Burge, C.B., Sharp P.A.. 2011. A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells<\/a>. PLoS Genet<\/i>. 2011 May;7(5):e1002054. PMC3088722<\/p>\n

2008<\/h3>\n

Seila, A.C.*, Calabrese, J.M.*, Levine, S.S., Yeo, G.W. Rahl, P.B, Young, R.A., and Sharp, P.A. 2008. Divergent transcription from active promoters<\/a>. Science<\/i> 322:1849-1851. PMC2692996<\/p>\n

Marson, A.*, Levine S.S.*, Cole, M.F., Frampton, G.M., Brambrink, T., Johnstone, S., Guenther, M.G., Johnston, W.K., Wernig M., Newman, J., Calabrese, J.M., Dennis, L.M., Volkert, T.L., Gupta, S., Love, J., Hannett, N., Sharp, P.A., Bartel, D.P., Jaenisch, R., and Young, R.A. 2008. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells<\/a>. Cell<\/i> 134(3): 521-533. PMC2586071<\/p>\n

2007<\/h3>\n

Calabrese, J.M.*, Seila, A.C.*, Yeo, G.W., and Sharp, P.A. 2007. RNA sequence analysis defines Dicer’s role in mouse embryonic stem cells<\/a>. Proc Natl Acad Sci USA <\/i>104(46): 18097-18102. PMC2084302<\/p>\n

2006<\/h3>\n

Calabrese, J.M. and Sharp, P.A. 2006. Characterization of the short RNAs bound by the P19 suppressor of RNA silencing in mouse embryonic stem cells<\/a>. Rna<\/i> 12(12): 2092-2102. PMC1664724<\/p>\n

Leung, A.K., Calabrese, J.M., and Sharp, P.A. 2006. Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules<\/a>. Proc Natl Acad Sci U S A<\/i> 103(48): 18125-18130. PMC1838717<\/p>\n

 <\/p>\n

*denotes co-first author<\/p>\n

ca<\/sup> denotes corresponding author<\/p>\n","protected":false},"excerpt":{"rendered":"

2024 Li S., Eberhard Q. E., Ni L., Calabrese J.M. Improved functions for non-linear sequence comparison using SEEKR. RNA. 2024 Oct 16;30(11):1408-1421. PMID: 38496437. PMCID: PMC10942450. Saha D., Animireddy S., Lee J., Thommen A., Murvin M.M,. Lu Y., Calabrese J.M., Bartholomew B. Enhancer switching in cell lineage priming is linked to eRNA, Brg1’s AT-hook, and … Read more<\/a><\/p>\n","protected":false},"author":32335,"featured_media":0,"parent":0,"menu_order":13,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2272","page","type-page","status-publish","hentry","odd"],"acf":[],"yoast_head":"\nPublications - Calabrese Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.med.unc.edu\/pharm\/calabreselab\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications - Calabrese Lab\" \/>\n<meta property=\"og:description\" content=\"2024 Li S., Eberhard Q. E., Ni L., Calabrese J.M. 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