The light-responsive chromatin accessibility landscape in rice

Here, we show that light greatly altered chromatin accessibility during the switches from skotomorphogenesis to photomorphogenesis Overall design: Freshly collected seedlings were immediately chopped with a razor blade for 5 min in 100 µL lysis buffer (20 mM MES, pH 5.7, 0.6M Mannitol, 10 mM MgCl2, 10 mM KCl, 0.1% 2-mercaptoethanol and 0.2% Triton X-100, 1x PI (protease inhibitor)) on ice (two biological replicates were performed) according to our previous work(10) . Thereafter the chopped slurry was washed into 1 ml lysis buffer in a 1.5ml tube and incubated for 5 min on ice with gentle shaking. The mixture was filtered through a 40-µm filter into a new tube, followed by centrifugation at 500 g for 8 min (4 °C). Then, we resuspended the precipitation with 150 µl wash buffer (20 mM Tris-HCl pH 7.8, 10 mM MgCl2, 60 mM KAc pH 5.6). The above washed 50,000 nuclei were then tagged with TS-Tn5 at 37ºC for 30 min following the kit's instructions (Vazyme, TD501). After tagging, the integration products were purified using DNA Purification Kit (ZYMO, D4004) and then amplified using Q5 high fidelity DNA polymerase (New England Biolabs, M0491S) for 10-15 cycles. The libraries were sequenced on Illumina HiSeq X Ten with paired-end reads of 150-bp