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2021

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. Apr 16:e1657. doi: 10.1002/wrna.1657. PMID: 33861025

Weidmann, C.A., Mustoe, A.M., Jariwala, P.B., Calabrese, J.M., Weeks, K.M. Analysis of RNA–protein 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.

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

2020

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.

Sigmon, J. Blanchard, M., … Calabrese, J.M., … 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.

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′ end of Xist harbor SPEN-independent transcriptional antiterminator activity. 2020. Nucleic Acids Res., gkaa789, https://doi.org/10.1093/nar/gkaa789. PMID: 32986830.  PMCID: PMC7544216.

Trotman J.B. and Calabrese J.M. 2020. How to silence an X chromosome. Nature News & Views. Feb 5. DOI: 10.1038/d41586-020-00207-0.

2019

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. Dec;213(4):1093-1110. PMID: 31796550. DOI: 10.1534/genetics.119.302661.

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. Molecular Cell. Aug 8;75(3):523-537.e10. doi: 10.1016/j.molcel.2019.05.028.

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. RNA. Aug;25(8):1047-1058. doi: 10.1261/rna.068932.118.

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. RNA. Aug;25(8):1004-1019. doi: 10.1261/rna.069815.118.

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. Nature Genetics 51(1):26-29.

2018

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. Nature Genetics 50, 1474–1482.

UNC press release: http://news.unchealthcare.org/news/2018/september/scientist-reveal-way-to-map-vast-unknown-territory-of-long-non-coding-rna

2016

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. PNAS 113(37):10322-7.

2015

Smola, M.J., Calabrese J.M., Weeks, K.M. 2015. Detection of RNA-Protein Interactions in Living Cells with SHAPE. Biochemistry 54(46):6867-6875.

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. Cell 161:404-416.

Calabrese J.M.ca, Starmer J., Schertzer M.D., Yee D., Magnuson T. 2015. A survey of imprinted gene expression in mouse trophoblast stem cells. G3 Feb 23.

2014

Pohlers M., Calabrese J.M., Magnuson T. 2014. Small RNA expression from the human macrosatellite DXZ4. G3 4(10):1981-9.

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. Genetics 197(2):715-723.

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. Nucleic Acids Research 42(8): e68.

2013

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. Nature 501(7465):58-62. PMC3767287

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

2012

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. Cell 151(5): 951-63. PMC3511858. Press release.

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

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. Genome Biology 13(8): R70. PMC3491370

2011

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. PLoS Genet. 2011 May;7(5):e1002054. PMC3088722

2008

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. Science 322:1849-1851. PMC2692996

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. Cell 134(3): 521-533. PMC2586071

2007

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. Proc Natl Acad Sci USA 104(46): 18097-18102. PMC2084302

2006

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. Rna 12(12): 2092-2102. PMC1664724

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

 

*denotes co-first author

ca denotes corresponding author