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Mapping the Genome

  • Carsten Carlberg
  • Ferdinand Molnár
Chapter

Abstract

The recent availability of the complete genome sequences of humans and other species allows comparative genomics approaches, such as phylogenetic footprinting, in order to detect transcription factor-binding sites that are under evolutionary constraint. However, only in combination with experimental data, for example, obtained by the ENCODE consortium, such in silico approaches are effective. The rapidly increasing amount of ChIP-seq data on transcription factor locations and multiple histone modifications significantly changes our understanding of gene regulation. The integration of these new sources of information has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome.

Many transcription factors are far more flexible in the way of recognizing their genomic target sequences than initially assumed. They often recognize a larger number of interacting nuclear proteins and may not always directly contact DNA. This new insight has also consequences on the question, which transcription factor is assigned to the regulation of which gene, i.e. not always the approach applies that sites in rather close vicinity to TSS regions are the main regions for regulation.

In this chapter, we are discussing a number of different approaches for a genome-wide identification of transcription factor-binding sites ranging from in silico comparative genomics over integrating large ChIP-seq data set to assays for a three-dimensional analysis of chromatin looping. Insight obtained from these novel methods provides helps to develop a new model of gene regulation.

Keywords

ENCODE Phylogenetic footprinting FAIRE-seq DNAse hypersensitivity site ChIP-seq Transcription factor-binding site Chromosome conformation capture assay Evolutionary constrain Regulatory sequence Genome-wide view MYOD1 

Further Reading

  1. Bell O, Tiwari VK, Thomä NH, Schübeler D (2011) Determinants and dynamics of genome accessibility. Nat Rev Genet 12:554–564PubMedCrossRefGoogle Scholar
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  5. Hardison RC, Taylor J (2012) Genomic approaches towards finding cis-regulatory modules in animals. Nat Rev Genet 13:469–483PubMedCrossRefGoogle Scholar
  6. The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project. Nature 447:799–816CrossRefGoogle Scholar
  7. The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74CrossRefGoogle Scholar
  8. Wasserman WW, Sandelin A (2004) Applied bioinformatics for he identification of regulatory elements. Nat Rev Genet 5:276–287PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Institute of Biomedicine, School of MedicineUniversity of Eastern FinlandKuopioFinland
  2. 2.Institute of Biopharmacy School of PharmacyUniversity of Eastern FinlandKuopioFinland

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