ed down onto the microarray slide, which was mounted into the AgilentTM Microarray Hybridization Chamber Kit. The hybridization was carried out in an 19276073 oven set to 65uC for 17 hours. After, microarray slides were washed according to Agilent’s instruction and scanned using GenePixH 4000B microarray scanner. Gene Expression Analysis The extraction of data from TIFF images generated through scanning of microarray slides were performed by using Agilent Feature Extraction Software version 9.5.3.1, using Linear Lowess algorithm to obtain background subtracted and normalized intensity values. The dye-normalyzed values generated in the Feature Extraction data files were used to upload the software Express Converter., which conveniently converts the Agilent file format to mev file format compatible to the TM4 softwares for microarray analysis. The mev files were then uploaded in the MIDAS software, where the resulting data were averaged from replicated genes on each array, from three biological replicates of each treatment. The generated mev files were finally analyzed by using TIGR MeV, where differentially expressed genes was statistically identified using one-class t test. Significantly different genes were those whose mean log2 expression ratio over all included samples was statistically different from 0, which indicates the absence of gene modulation. Acknowledgments We thank the Fundacao de Amparo a Pesquisa do Estado de Sao Paulo ~ ~ and Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Brazil for financial support. We also thank Dr. Vicky Sophianopoulou for providing the PilA::GFP and PilB::GFP strains. We would like to thank the reviewers for their suggestions and comments. Supporting lnformation hierarchal clusters of genes identified as being differentially expressed in the alcA::ypkA strain under repression and overexpression conditions when compared to the wild-type strain. Many studies have shown that a transcriptionally active structure can be formed when genes express actively. Several assays including 3C, ChIP-3C/Loop assay, DamID and other approaches have been applied to show that the chromatin looping events can bring distal regulatory elements and related gene promoters into close proximity and provide such a transcriptionally active 
structure. The looping events have been documented on several gene loci such as HBB, Igf2-H19, Igk, Dlx5/Dlx6, HoxB1, and TH2 loci. During exploring the possible formation mechanisms of spatial organization of chromatin in the nucleus, the Matrix/scaffold attachment regions have been suggested to be the important players for the complex packaging of eukaryotic chromosomes in nuclei. MARs are IC261 biological activity originally identified as genomic DNA fragments that remain tightly associated with high saltextracted and DNase Idigested nuclei, and have been postulated to be localized at the base of chromatin loops. The MARs help to form the chromatin loops by attaching to the nuclear matrix. MARs identified by such criteria often contain base-unpairing regions which become continuously unpaired when subjected to negative super helical strain. SATB1, which has been characterized as a MAR-binding protein, can bind to the BUR sequences and regulates higher order chromatin loop 10604956 structures in T-cell. Kumar et al also showed that SATB1 can recruit a regulatory complex that manages transcription by orchestrating dynamic chromatin-loop architecture in MHC class I locus. The intensive studies in the b-globin locus have
