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Replicating Nucleosomes.
Ramachandran S, Henikoff S. Ramachandran S, et al. Sci Adv. 2015 Aug 7;1(7):e1500587. doi: 10.1126/sciadv.1500587. Sci Adv. 2015. PMID: 26269799 Free PMC article.
Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates.
Ramachandran S, Ahmad K, Henikoff S. Ramachandran S, et al. Mol Cell. 2017 Dec 21;68(6):1038-1053.e4. doi: 10.1016/j.molcel.2017.11.015. Epub 2017 Dec 7. Mol Cell. 2017. PMID: 29225036 Free PMC article.
MINCE-Seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing.
Ramachandran S, Henikoff S. Ramachandran S, et al. Methods Mol Biol. 2018;1832:159-168. doi: 10.1007/978-1-4939-8663-7_8. Methods Mol Biol. 2018. PMID: 30073526
Precise genome-wide mapping of single nucleosomes and linkers in vivo.
Chereji RV, Ramachandran S, Bryson TD, Henikoff S. Chereji RV, et al. Genome Biol. 2018 Feb 9;19(1):19. doi: 10.1186/s13059-018-1398-0. Genome Biol. 2018. PMID: 29426353 Free PMC article.
Capitalizing on disaster: Establishing chromatin specificity behind the replication fork.
Ramachandran S, Ahmad K, Henikoff S. Ramachandran S, et al. Bioessays. 2017 Apr;39(4):10.1002/bies.201600150. doi: 10.1002/bies.201600150. Epub 2017 Jan 30. Bioessays. 2017. PMID: 28133760 Free PMC article. Review.
However, localized chromatin features are transiently obliterated by DNA replication every S phase of the cell cycle. Genomic strategies now observe the rebuilding of locus-specific chromatin features, and reveal surprising delays in transcription factor binding behind rep …
However, localized chromatin features are transiently obliterated by DNA replication every S phase of the cell cycle. Genomic strateg …
Transcriptional Regulators Compete with Nucleosomes Post-replication.
Ramachandran S, Henikoff S. Ramachandran S, et al. Cell. 2016 Apr 21;165(3):580-92. doi: 10.1016/j.cell.2016.02.062. Epub 2016 Apr 7. Cell. 2016. PMID: 27062929 Free PMC article.
Nucleosome dynamics during chromatin remodeling in vivo.
Ramachandran S, Henikoff S. Ramachandran S, et al. Nucleus. 2016;7(1):20-6. doi: 10.1080/19491034.2016.1149666. Epub 2016 Mar 2. Nucleus. 2016. PMID: 26933790 Free PMC article.
Asymmetric nucleosomes flank promoters in the budding yeast genome.
Ramachandran S, Zentner GE, Henikoff S. Ramachandran S, et al. Genome Res. 2015 Mar;25(3):381-90. doi: 10.1101/gr.182618.114. Epub 2014 Dec 9. Genome Res. 2015. PMID: 25491770 Free PMC article.
Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase.
Weber CM, Ramachandran S, Henikoff S. Weber CM, et al. Mol Cell. 2014 Mar 6;53(5):819-30. doi: 10.1016/j.molcel.2014.02.014. Mol Cell. 2014. PMID: 24606920
The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo.
Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang JP, Henikoff JG. Henikoff S, et al. Elife. 2014 Apr 15;3:e01861. doi: 10.7554/eLife.01861. Elife. 2014. PMID: 24737863 Free PMC article.
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