![]() MACS was originally designed to give robust and high resolution peak identification for ChIP-Seq data with two main features ( Zhang, et al., 2008). The enriched DNA fragments are then sequenced using massively parallel DNA sequencing technology, with outputs called sequencing reads or tags. Briefly, in the ChIP step, DNA sequences are fragmentized into hundreds of base pairs, and fragments with certain TF binding are enriched through immunoprecipitation. To uncover the regulation mechanisms, one promising approach is to identify all cis-acting targets, or called binding sites, for a given TF in the genome scale, which is defined as the TF’s cistrome ( Carroll, et al., 2006 Lupien, et al., 2008), and the popular technology to study cistrome is Chromatin Immunoprecipitation coupled with sequencing (ChIP-Seq) ( Johnson, et al., 2007). One type of special proteins, called transcription factors (TFs), performs important functions by regulating the transcription of genes via physically interaction with certain DNA sequence patterns, or called motifs.
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