Ansuman T. Satpathy

1 month ago | nature.com | Michael Scherer |Indranil Singh |Martina Braun |Pedro Sanchez |Pedro Sánchez |Dominik Lindenhofer | +13 more

AbstractCurrent approaches used to track stem cell clones through differentiation require genetic engineering1,2 or rely on sparse somatic DNA variants3,4, which limits their wide application. Here we discover that DNA methylation of a subset of CpG sites reflects cellular differentiation, whereas another subset undergoes stochastic epimutations and can serve as digital barcodes of clonal identity.

Jan 8, 2025 | nature.com | Robert R. Stickels |Zaki Abou-Mrad |Viviane Tabar |Brooke E. Howitt |Leif S. Ludwig |Ronan Chaligné | +1 more

AbstractSingle-cell genomics technologies have accelerated our understanding of cell-state heterogeneity in diverse contexts. Although single-cell RNA sequencing identifies rare populations that express specific marker transcript combinations, traditional flow sorting requires cell surface markers with high-fidelity antibodies, limiting our ability to interrogate these populations.

Dec 8, 2024 | cell.com | Jiaying Toh |Andrea J. Reitsma |Tetsuya Tajima |Sheren F. Younes |Chimere Ezeiruaku |Kayla Jenkins | +24 more

IntroductionEpstein-Barr virus (EBV) is a broadly disseminated gamma-1 herpesvirus estimated to infect 90%–95% of adults globally.1,2 EBV infection is mostly asymptomatic, with the virus proceeding through a complex life cycle including a productive lytic phase but ultimately establishing a latent infection in a subset of memory B cells.3 In this manner, EBV persists for the lifetime of the host, though periodic reactivation of EBV drives further lytic replication and viral transmission.

May 29, 2024 | nature.com | Jacob W. Freimer |Salvador Casaní-Galdón |Maya M. Arce |Bence Daniel |Katalin Sandor |Ralf Schmidt | +3 more

AbstractCis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity.

May 9, 2024 | nature.com | Arjun Nanda |Megan S. Ostrowski |Leanne C Sayles |Ansuman T. Satpathy |E. Alejandro Sweet-Cordero |Hani Goodarzi | +1 more

AbstractConcurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of California (PacBio) single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules.