6432 Nucleic Acids Research, 2011, Vol. 39, No. 15 Figure 2. Entire roX1 and roX2 mRNAs are associated with a complete or partial MSL complex. (A–C) In formaldehyde cross-linked extracts, actively transcribed RNAs are immunoprecipitated by chromatin-associated proteins. Comparison of a ChIP-chip proﬁle representing the MSL complex (MSL1-ChIP) and the MSL2 RIP-chip proﬁles from the native nuclear extract (MSL2 N6-RIP) and formaldehyde-cross-linked nuclear extract (MSL2 FA-RIP). Representative 400 kb regions from the X chromosome including roX1 (A) and roX2 (B) are compared to a representative (continued)