GSE108948
Fine Resolution Mapping of TF binding and Chromatin  Interactions
Monitoring the location of transcription factors (TFs) binding to DNA is key to understanding  transcriptional regulation. The main tool for mapping TF binding is ChIP-seq and its variants.  However, current ChIP-based methods are hampered by at least one of the following limitations:  large input requirements, low spatial resolution, and limited compatibility with high-throughput  automation. Here, we describe SLIM-ChIP (Short fragment enriched, Low input, Indexed,  MNase ChIP), which overcomes these challenges by combining enzymatic fragmentation of  chromatin and on-bead indexing of immobilized TF-DNA complexes. We show that SLIM-ChIP  reproduces high resolution binding map of yeast Reb1 similarly to the high-resolution TF  mapping methods ChIP-exo and ORGANIC. Yet, SLIM-ChIP requires substantially less input  material, and is fully compatible with high-throughput procedures. We further demonstrate the  robustness and flexibility of SLIM-ChIP by probing Abf1 and Rap1 in yeast and CTCF in mouse  embryonic stem cells. Finally, we show that the unique combination of high resolution and  preservation of DNA protection patterns by SLIM-ChIP provide an additional layer of information  on the chromatin landscape surrounding the bound TF. We used this information to identify a  class of Reb1 sites in which the proximal -1 nucleosome tightly interacts with Reb1 and unlike  in most Reb1 sites is refractory to remodeling by the RSC complex. Importantly, the interaction  of Reb1 with the -1 nucleosome prevents transcription initiation and can serve as a more  general mechanism for maintaining unidirectional transcription. Altogether, SLIM-ChIP is an  attractive solution for mapping DNA binding proteins in a more informative context regarding  their surrounding chromatin occupancy landscape at a single cell level. Overall design: The dataset includes several ChIP-Seq experiments of yeast and mouse ESCs transcription factors.  Reb1 (yeast) ChIP was performed in several Mnase levels and different numbers of input cells (five samples overall). Mouse CTCF ChIP was performed in several Mnase levels (five samples overall). Abf1 and Rap1 (yeast) were mapped using a mix of different Mnase levels (one sample each).