Search

Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor α (ER-α) in the human genome. We found that most high-confidence remote ER-α-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-α functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes. © 2009 Macmillan Publishers Limited. All rights reserved.

Simulations have been performed for signal reproduction from a read‐only super resolution optical disk using a beam splitting method, in which a collimated laser beam generated by a laser diode is split into two beams with orthogonal polarizations and then recombined using polarizing beamsplitters. The beam with a higher power is used to raise the temperature of the mask layer, while the one with a lower power is employed to reproduce the recorded data. Tilting one of the laser beams against the other results in two laser spots partially overlapped at the focal plane, and the distance between the center of the two spots can be controlled by a galvanomirror. This allows signal readout with maximum resolution independent of the disk rotation speed.

ChIA-PET Tool can be used to process long-range chromatin interaction data. Results are visualized on a user-friendly genome browser., Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source (available at http://chiapet.gis.a-star.edu.sg).