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. 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.