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Comparative Genomics of Transcription Factor Binding in Drosophila

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Book cover Short Views on Insect Genomics and Proteomics

Part of the book series: Entomology in Focus ((ENFO,volume 3))

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Abstract

While the number of genome-wide, in vivo transcription factor binding datasets is growing, yielding greater insight into the role of regulatory DNA in development, evolution and disease, it is difficult to tease apart signal from noise and identify truly functional binding events. Comparative studies of transcription factor binding between closely related species offer one way to combat this problem, as functionally important aspects of enhancer architecture tend to be constrained by natural selection. Here we review the current field in the area of in vivo transcription factor binding in Drosophila, illustrating how evolutionary studies within the drosophilids are helping to unravel the complexity of the genomic regulatory code. A number of techniques exist for studying transcription factor binding on a genome-wide scale, including ChIP-chip, ChIP-seq and DamID; we touch on these and address the challenges and advantages of each with regard to working on non-model species. We also describe major findings in the field so far, focusing on comparative studies of the developmental regulatory network, the logic of combinatorial binding and the evolutionary properties of noncoding DNA. Finally, we examine how insights from Drosophila compare with similar studies in the vertebrates and address some open questions that have been raised by studies conducted thus far.

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Abbreviations

A-P:

Anterior-posterior

ChIP:

Chromatin immunoprecipitation

ChIP-chip:

Chromatin immunoprecipitation combined with the use of microarray chips

ChIP-seq:

Chromatin immunoprecipitation combined with parallel array sequencing

Dam:

DNA adenine methyltransferase

DamID:

DNA adenine methyltransferase identification

DamID-seq:

DNA adenine methyltransferase identification combined with parallel array sequencing

eQTL:

Expression quantitative trait locus

FWOB:

Four-way orthologous binding

GFP:

Green fluorescent protein

GO:

Gene ontology

modENCODE:

Model Organism Encyclopedia of DNA Elements

ORF:

Open reading frame

PCA:

Principle component analysis

PWM:

Positional weight matrix

RNA-seq:

RNA sequencing

TF:

Transcription factor

TWOB:

Two-way orthologous binding

UCSC:

University of California, Santa Cruz

UAS:

Upstream activating sequence

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Authors and Affiliations

  1. Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK

    Sarah Carl & Steven Russell

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  1. Sarah Carl
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  2. Steven Russell
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Correspondence to Steven Russell .

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Editors and Affiliations

  1. Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA

    Chandrasekar Raman

  2. Biological Sciences Department Center for Biotech. and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA

    Marian R. Goldsmith

  3. Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA

    Tolulope A. Agunbiade

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Carl, S., Russell, S. (2015). Comparative Genomics of Transcription Factor Binding in Drosophila . In: Raman, C., Goldsmith, M., Agunbiade, T. (eds) Short Views on Insect Genomics and Proteomics. Entomology in Focus, vol 3. Springer, Cham. https://doi.org/10.1007/978-3-319-24235-4_7

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