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Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination.
Austenaa LM, Barozzi I, Simonatto M, Masella S, Della Chiara G, Ghisletti S, Curina A, de Wit E, Bouwman BA, de Pretis S, Piccolo V, Termanini A, Prosperini E, Pelizzola M, de Laat W, Natoli G. Austenaa LM, et al. Among authors: bouwman ba. Mol Cell. 2015 Nov 5;60(3):460-74. doi: 10.1016/j.molcel.2015.09.018. Epub 2015 Oct 22. Mol Cell. 2015. PMID: 26593720 Free article.
Robust 4C-seq data analysis to screen for regulatory DNA interactions.
van de Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, Splinter E, Valdes-Quezada C, Oz Y, Bouwman BA, Verstegen MJ, de Wit E, Tanay A, de Laat W. van de Werken HJ, et al. Among authors: bouwman ba. Nat Methods. 2012 Oct;9(10):969-72. doi: 10.1038/nmeth.2173. Epub 2012 Sep 9. Nat Methods. 2012. PMID: 22961246
The pluripotent genome in three dimensions is shaped around pluripotency factors.
de Wit E, Bouwman BA, Zhu Y, Klous P, Splinter E, Verstegen MJ, Krijger PH, Festuccia N, Nora EP, Welling M, Heard E, Geijsen N, Poot RA, Chambers I, de Laat W. de Wit E, et al. Among authors: bouwman ba. Nature. 2013 Sep 12;501(7466):227-31. doi: 10.1038/nature12420. Epub 2013 Jul 24. Nature. 2013. PMID: 23883933
A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia.
Gröschel S, Sanders MA, Hoogenboezem R, de Wit E, Bouwman BAM, Erpelinck C, van der Velden VHJ, Havermans M, Avellino R, van Lom K, Rombouts EJ, van Duin M, Döhner K, Beverloo HB, Bradner JE, Döhner H, Löwenberg B, Valk PJM, Bindels EMJ, de Laat W, Delwel R. Gröschel S, et al. Cell. 2014 Apr 10;157(2):369-381. doi: 10.1016/j.cell.2014.02.019. Epub 2014 Apr 3. Cell. 2014. PMID: 24703711 Free article.
Architectural hallmarks of the pluripotent genome.
Bouwman BA, de Laat W. Bouwman BA, et al. FEBS Lett. 2015 Oct 7;589(20 Pt A):2905-13. doi: 10.1016/j.febslet.2015.04.055. Epub 2015 May 7. FEBS Lett. 2015. PMID: 25957773 Free article. Review.
Enhancer hubs and loop collisions identified from single-allele topologies.
Allahyar A, Vermeulen C, Bouwman BAM, Krijger PHL, Verstegen MJAM, Geeven G, van Kranenburg M, Pieterse M, Straver R, Haarhuis JHI, Jalink K, Teunissen H, Renkens IJ, Kloosterman WP, Rowland BD, de Wit E, de Ridder J, de Laat W. Allahyar A, et al. Nat Genet. 2018 Aug;50(8):1151-1160. doi: 10.1038/s41588-018-0161-5. Epub 2018 Jul 9. Nat Genet. 2018. PMID: 29988121
Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations.
Dellino GI, Palluzzi F, Chiariello AM, Piccioni R, Bianco S, Furia L, De Conti G, Bouwman BAM, Melloni G, Guido D, Giacò L, Luzi L, Cittaro D, Faretta M, Nicodemi M, Crosetto N, Pelicci PG. Dellino GI, et al. Nat Genet. 2019 Jun;51(6):1011-1023. doi: 10.1038/s41588-019-0421-z. Epub 2019 May 20. Nat Genet. 2019. PMID: 31110352
25 results