Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues

by Kai Fu, Giancarlo Bonora, Matteo Pellegrini
Published 2020-03-01

DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS).

by Giancarlo Bonora, Liudmilla Rubbi, Marco Morselli, Feiyang Ma, Constantinos Chronis, Kathrin Plath, Matteo Pellegrini
Published 2019-01-01

Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming

by Kai Fu, Constantinos Chronis, Abdenour Soufi, Giancarlo Bonora, Miguel Edwards, Stephen T. Smale, Kenneth S. Zaret, Kathrin Plath, Matteo Pellegrini
Published 2018-12-01

X Chromosome Dosage Influences DNA Methylation Dynamics during Reprogramming to Mouse iPSCs

by Vincent Pasque, Rahul Karnik, Constantinos Chronis, Paula Petrella, Justin Langerman, Giancarlo Bonora, Juan Song, Lotte Vanheer, Anupama Sadhu Dimashkie, Alexander Meissner, Kathrin Plath
Published 2018-05-01

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory

by Alessandro Bertero, Paul A. Fields, Vijay Ramani, Giancarlo Bonora, Galip G. Yardimci, Hans Reinecke, Lil Pabon, William S. Noble, Jay Shendure, Charles E. Murry
Published 2019-04-01

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse

by Marco Morselli, William A Pastor, Barbara Montanini, Kevin Nee, Roberto Ferrari, Kai Fu, Giancarlo Bonora, Liudmilla Rubbi, Amander T Clark, Simone Ottonello, Steven E Jacobsen, Matteo Pellegrini
Published 2015-04-01

Correction: In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse

by Marco Morselli, William A Pastor, Barbara Montanini, Kevin Nee, Roberto Ferrari, Kai Fu, Giancarlo Bonora, Liudmilla Rubbi, Amander T Clark, Simone Ottonello, Steven E Jacobsen, Matteo Pellegrini
Published 2017-08-01

Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome

by He Fang, Giancarlo Bonora, Jordan P. Lewandowski, Jitendra Thakur, Galina N. Filippova, Steven Henikoff, Jay Shendure, Zhijun Duan, John L. Rinn, Xinxian Deng, William S. Noble, Christine M. Disteche
Published 2020-11-01

Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation

by Kris G. Alavattam, Katie A. Mitzelfelt, Giancarlo Bonora, Paul A. Fields, Xiulan Yang, Han Sheng Chiu, Lil Pabon, Alessandro Bertero, Nathan J. Palpant, William S. Noble, Charles E. Murry
Published 2023-01-01

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.

by Hyeon-Jin Kim, Galip Gürkan Yardımcı, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B Ware, Jay Shendure, Zhijun Duan, William Stafford Noble
Published 2020-09-01

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

by Giancarlo Bonora, Vijay Ramani, Ritambhara Singh, He Fang, Dana L. Jackson, Sanjay Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure, Zhijun Duan, Xinxian Deng, William S. Noble, Christine M. Disteche
Published 2021-09-01