scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells

Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We developed scTAM-seq, a targeted bisulfite-free method for profiling up to 650 CpGs in up to 10,000 cells per experiment, with a dropout rate as low as 7%. We demonstrate that scTAM-seq can resolve DNA methylation dynamics across B-cell differentiation in blood and bone marrow, identifying intermediate differentiation states that were previously masked. scTAM-seq additionally queries surface-protein expression, thus enabling integration of single-cell DNA methylation information with cell atlas data. In summary, scTAM-seq is a high-throughput, high-confidence method for analyzing DNA methylation at single-CpG resolution across thousands of single cells.We acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme/Generalitat de Catalunya. We acknowledge support from the CRG/CNAG/UPF core facilities (cytometry and genomics unit). A.B. was supported by an FPI fellowship from the Spanish Ministry of Science and Innovation (PRE2019-087574), R.B. was supported by a Junior Leader Fellowship from the la Caixa foundation. M.S. was supported through the Walter Benjamin Fellowship funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 493935791. This work was supported by grants from the Spanish Ministry of Science and Innovation (RTI2018-096359-A-I00) and the European Hematology Association (EHA, Advanced Research Grants to L.V. and R.B.)

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

Chromosome conformation capture (3 C) techniques have captured largescale 3D genome architecture. Here the authors present their “Tiled-MCC” approach for generation of 3 C data across megabase-scale loci at very high (up to 20 bp) resolution, which allowed them to observe nano-scale chromatin structures and investigate how these structures depend on cohesin and CTCF