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Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
- Gage S. Black,
- Xiaomeng Huang,
- Yi Qiao,
- Philip Moos,
- Deepa Sampath,
- Deborah M. Stephens,
- Jennifer A. Woyach,
- and Gabor T. Marth
Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
..., Columbus, Ohio 43210, USA ↵6 These authors contributed equally to this work. Corresponding author: gmarth@genetics.utah.eduAbstractBruton tyrosine kinase (BTK) inhibitors are effective for the treatment of chronic lymphocytic leukemia (CLL) due to BTK's role in B cell survival and proliferation. Treatment...
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Research: Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
- Lili Wang,
- Jean Fan,
- Joshua M. Francis,
- George Georghiou,
- Sarah Hergert,
- Shuqiang Li,
- Rutendo Gambe,
- Chensheng W. Zhou,
- Chunxiao Yang,
- Sheng Xiao,
- Paola Dal Cin,
- Michaela Bowden,
- Dylan Kotliar,
- Sachet A. Shukla,
- Jennifer R. Brown,
- Donna Neuberg,
- Dario R. Alessi,
- Cheng-Zhong Zhang,
- Peter V. Kharchenko,
- Kenneth J. Livak,
- and Catherine J. Wu
Genome Res. August 2017 27: 1300-1311; Published in Advance July 5, 2017, doi:10.1101/gr.217331.116
...and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA; 11Fluidigm Corporation, South San Francisco, California 94080, USA Intra-tumoral genetic heterogeneity has been characterized across cancers by sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
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Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
- Benjamin Morledge-Hampton,
- Kathiresan Selvam,
- Manish Chauhan,
- Alan G. Goodman,
- and John J. Wyrick
Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
...susceptible to disruption or repositioning in response to the cellular stress and ongoing repair activity induced by UV damage. For example, a previous study has shown that the SWI/SNF complex can remodel nucleosomes to accommodate the repair of UV damage (Gaillard et al. 2003). Such a mechanism may...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...sequences, both in UV-irradiated yeast cells and in human skin cancers. CPD deamination is suppressed near the transcription start and end sites of yeast genes, which may in part by mediated by DNA-bound transcription factors. Finally, we show that the wrapping of DNA in nucleosomes modulates CPD...
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Research: DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
- Brian Giacopelli,
- Min Wang,
- Ada Cleary,
- Yue-Zhong Wu,
- Anna Reister Schultz,
- Maximilian Schmutz,
- James S. Blachly,
- Ann-Kathrin Eisfeld,
- Bethany Mundy-Bosse,
- Sebastian Vosberg,
- Philipp A. Greif,
- Rainer Claus,
- Lars Bullinger,
- Ramiro Garzon,
- Kevin R. Coombes,
- Clara D. Bloomfield,
- Brian J. Druker,
- Jeffrey W. Tyner,
- John C. Byrd,
- and Christopher C. Oakes
Genome Res. May 2021 31: 747-761; Published in Advance March 11, 2021, doi:10.1101/gr.269233.120
...sequences, all cell types have distinct epigenetic patterns, thus patterns originating from normal counterparts must be accounted for when determining tumor cell–specific epigenetic changes. We have previously shown this to be important for deriving tumor-specific events in chronic lymphocytic leukemia (CLL...
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Method: Size-based expectation maximization for characterizing nucleosome positions and subtypes
- Jianyu Yang,
- Kuangyu Yen,
- and Shaun Mahony
Genome Res. September 2024 34: 1334-1343; Published in Advance June 17, 2024, doi:10.1101/gr.279138.124
...510515, China Corresponding authors: kuangyuyen@ihcams.ac.cn, mahony@psu.eduAbstractGenome-wide nucleosome profiles are predominantly characterized using MNase-seq, which involves extensive MNase digestion and size selection to enrich for mononucleosome-sized fragments. Most available MNase-seq analysis...
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Research: Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
- Pedro G. Ferreira,
- Pedro Jares,
- Daniel Rico,
- Gonzalo Gómez-López,
- Alejandra Martínez-Trillos,
- Neus Villamor,
- Simone Ecker,
- Abel González-Pérez,
- David G. Knowles,
- Jean Monlong,
- Rory Johnson,
- Victor Quesada,
- Sarah Djebali,
- Panagiotis Papasaikas,
- Mónica López-Guerra,
- Dolors Colomer,
- Cristina Royo,
- Maite Cazorla,
- Magda Pinyol,
- Guillem Clot,
- Marta Aymerich,
- Maria Rozman,
- Marta Kulis,
- David Tamborero,
- Anaïs Gouin,
- Julie Blanc,
- Marta Gut,
- Ivo Gut,
- Xose S. Puente,
- David G. Pisano,
- José Ignacio Martin-Subero,
- Nuria López-Bigas,
- Armando López-Guillermo,
- Alfonso Valencia,
- Carlos López-Otín,
- Elías Campo,
- and Roderic Guigó
Genome Res. February 2014 24: 212-226; Published in Advance November 21, 2013, doi:10.1101/gr.152132.112
...Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia Pedro G. Ferreira 1 , 2 , 12 , Pedro Jares 3 , 13 , Daniel Rico 4 , 13 , Gonzalo Gómez-López 4...
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Research: Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites
- Patrick D. Wilson,
- Xinyang Yu,
- Christopher R. Handelmann,
- and Michael J. Buck
Genome Res. March 2025 35: 404-416; Published in Advance February 10, 2025, doi:10.1101/gr.279541.124
...—the three members of the TP53 family—regulate gene expression by binding to their DNA binding sites, many of which are situated within nucleosomes. To thoroughly examine the nucleosome-binding abilities of the TP53 family, we used Pioneer-seq, a technique that assesses a transcription factor's binding...
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Research: Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development
- Vladimir B. Teif,
- Daria A. Beshnova,
- Yevhen Vainshtein,
- Caroline Marth,
- Jan-Philipp Mallm,
- Thomas Höfer,
- and Karsten Rippe
Genome Res. August 2014 24: 1285-1295; Published in Advance May 8, 2014, doi:10.1101/gr.164418.113
...(5hmC), nucleosome repositioning, and binding of the transcription factor CTCF during this process. By integrating MNase-seq and ChIP-seq experiments in mouse embryonic stem cells (ESC) and their differentiated counterparts with biophysical modeling, we found that the interplay between these factors...

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