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Fig. 5 | Epigenetics & Chromatin

Fig. 5

From: In vivo chromatin organization on native yeast telomeric regions is independent of a cis-telomere loopback conformation

Fig. 5

Chromatin organization of the X element on TEL05R (XY’ context). a Schematic drawing of the X–Y’ junction area on TEL05R with the positions of the PvuI sites. The TEL05R-specific probe used in b is represented by a solid black line. AF: Analyzed Fragment. b In vivo ChEC experiments with GBD-MN, NLS-MN and MN-RAP1 analyzed on the TEL05R X–Y’ junction fragment. Southern blot with PvuI-digested genomic DNA hybridized to the TEL05R-specific probe. Time of MNase activity in minutes is indicated on top of gel. Arrowheads with solid line show detectable cutting common to all MNase-fused proteins, whereas the arrowhead with dotted line corresponds to cutting observable predominately with MN-RAP1, and black arrowheads indicate cutting not detected with MN-RAP1. Band labelled AF is the full-length fragment, and dotted lines indicate two very weak cross-hybridizing non-specific bands. M: DNA size marker with DNA marker sizes indicated on left of gel (kb). c Same as in b with H2A-MN and MN-Rap1 strains. d Averaged fragment sizes ± standard deviation of MNase-induced cuttings from indicated MN-fused proteins determined from at least 2 independent experiments is plotted with respect to the telomere distal PvuI site. Location of features (ACS, Abf1, Tbf1 and Reb1 potential binding sites) is included. Only cutting sites on X element (X–I, X–II, X–III, X–IV) and Y’–I and Y’–II are displayed. e Rap1 ChIP analysis on Y’, HMRE, X(05R)–Y’ junction (X(05R)) and X(16R)–Y’ junction (X(16R)). Percent of input DNA recovered from ChIP performed with anti-Rap1 antibody (+ Ab) or without (− Ab) from SIR4 (W3749-1a) or sir4Δ (EPY031) strains. Data are mean ± standard deviation from two biological duplicates. *P value < 0.05 (unpaired t-test). Note that the differences of IP values between the SIR4 vs sir4Δ strains on the X(05R)–Y’ and X(16R)–Y’ loci are not significant

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