The Myc-Associated Zinc Finger Protein (MAZ) Works Both Independently and Together with CTCF to Control Cohesin Positioning and Genome Organization

Purpose: The objectives of this study are to evaluate the roles of MAZ in cellular processes using the NGS-deriveed ChIP-seq, RNA-seq and Hi-C profiles in K562 wild type and siRNA MAZ knockdown cells Methods: ChIP-Seq and Hi-C profiles of K562 wild-type (WT) and siRNA MAZ knockdown cells were generated by deep sequencing in duplicate or triplicate using Illumina GAIIx. The ChIP-seq sequence reads were analyzed with Burrows–Wheeler Aligner (BWA) followed by MACS software; The Hi-C sequence reads were analyzed with Juicer and HiC-Pro software. Results: Comparative analysis of the ChIP-seq, RNA-seq and Hi-C data between K562 wild type and siRNA MAZ knockdown cells indicates that 1.MAZ colocalizes with CTCF in the genome, and helps stabilize CTCF binding; 2. MAZ is able to arrest the cohesin complex independently of CTCF and contributes additively to cohesin localization when it is associated with CTCF; 3. MAZ, similarly to CTCF, acts as an insulator protein to block interaction between promoter and enhancer ; 4. MAZ can pause the elongating form of RNA Pol II; and 5. MAZ helps control local chromatin organization and some aspects of TAD structure. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: K562 wild type and siRNA MAZ knocking down cells were used to generate ChIP-Seq and Hi-C libraries. The libraries were deep sequenced using Illumina GAIIx.