Growth Conditions for SMC Proteins v1

A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through protein–DNA interactions. A powerful method for investigating proteins within a native chromatin environment in the cell is chromatin immunoprecipitation (ChIP). Combined with the recent technological advancement in next generation sequencing, the ChIP assay can map the exact binding sites of a protein of interest across the entire genome. Here we describe a-step-by step protocol for ChIP followed by library preparation for ChIP-seq from yeast cells. Chromatin immunoprecipitation (ChIP) is a powerful method for assaying protein–DNA binding in vivo and is broadly used to estimate the density of DNA-bound proteins at specific sites in the genome. ChIP is a multistep assay and every step needs to be optimized for consistent results. Briefly, protein–DNA associations are immobilized by cross-linking with formaldehyde [1,2,3] before shearing the chromatin, either mechanically [4] or by enzymatic digestion [5] into DNA fragments of average size 200–500bp. Specific cross-linked protein–DNA complexes are then isolated by immunoprecipitation using an antibody to the protein of interest. Finally, the cross-links are reversed, and the retrieved DNA is analyzed to determine the sequences bound by the protein. ChIP followed by quantitative real-time PCR (ChIP-qPCR), using specific primers, can be used to measure protein association and relative abundance at a particular genomic locus. Alternatively, ChIP can be combined with next generation sequencing (ChIP-seq) to provide a genome-wide view of protein occupancy. While ChIP-seq allows for relative protein abundance at distinct chromosomal addresses to be compared within a sample, differences between samples cannot be quantified without introducing a method to normalize. Typically, this involves “spike in” of a known amount of DNA or cross-linked cells from a different species, with sufficient sequence divergence from the organism of interest to allow sequencing reads to be confidently distinguished bioinformatically [6,7,8]. This technique, referred to as calibrated ChIP-seq, makes it possible to quantitate genome-wide changes in the distribution of an epitope tagged protein and allows for quantification of differences in occupancy between experimental samples [8]. Calibrated ChIP-seq requires that both calibration and experimental organisms carry the same epitope tag and can be immunoprecipitated by the same protocol. For this protocol we use S. pombe to calibrate S. cerevisiae, a combination that also allows us to invert the roles, that is, calibrate S. pombe with S. cerevisiae. The ChIP method described here has been optimized for use with chromatin from two species of yeast,S. cerevisiae and S. pombe; however, it should be easy to adapt it for use with other chromatin sources. To demonstrate the robustness of our ChIP and library preparation protocols we performed ChIP against the Scc1 subunit of the cohesin multiprotein complex, tagged with the 6HA epitope [9,10,11] . We have also used a similar protocol for the condensin subunit Brn1 [12] and for the meiotic counterpart of cohesin, Rec8 [13]. Here, we outline in detail an optimized protocol for cross-linking and harvesting cells, fragmenting chromatin, immunoprecipitating the desired protein–DNA complexes, and preparing the library for sequencing on the Illumina MiniSeq platform. A schematic stepwise representation of the method is illustrated in Fig.1. References: Solomon MJ, Varshavsky A (1985) Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. 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Nat Methods 5(10):887–893.https://doi.org/10.1038/nmeth.1251 Ford E, Nikopoulou C, Kokkalis A, Thanos D (2014) A method for generating highly multiplexed ChIP-seq libraries. BMC Res Notes 7:312. https://doi.org/10.1186/1756-0500-7-312 Acknowledgements: We are grateful to Manu Shukla for discussions and comments on the ChIP-seq library preparation and for kindly providing a representative Bioanalyzer image, Nicholas Toda, Jesus Torres-Garcia, and Flora Paldi for sharing tips on the ChIP-seq library protocol and Stefan Galangher and Lesley Clayton for general comments on the manuscript. This work was funded by Wellcome through a Senior Research Fellowship to AM and a Wellcome Centre core grant [107827 and 203149].