Biology Reference
In-Depth Information
CHAPTER TEN
High-Throughput Sequencing Will
Metamorphose the Analysis of
Thyroid Hormone Receptor
Function During Amphibian
Development
Alexis G. Grimaldi
*
, Nicolas Buisine
*
, Patrice Bilesimo
*
,1
,
Laurent M. Sachs
*
,2
*
Laboratoire d'Evolution des Regulations Endocrinienne, Mus´um National d'Histoire Naturelle,
D´partement R´gulation, D´veloppement et Diversit´ Mol´culaire, UMR 7221 CNRS, Paris, France
1
Present address: Translational Research Center, Perelman School of Medicine, University of Pennsylvania,
Philadelphia, Pennsylvania, USA
2
Corresponding author: e-mail address: sachs@mnhn.fr
Contents
1.
Introduction
278
2. Xenopus tropicalis Genomic Sequence and Annotation: Current State
280
2.1 A fragmented genome assembly
280
2.2 An incomplete annotation
283
3. TH and TR Regulating Network Using NGS-Based Transcriptome Analysis
287
3.1 Toward a better annotation
287
3.2 NGS provides functional data to analyze TH-induced differential expression
291
4. TR Interactome
292
4.1 Whole genome TR mapping
292
4.2 A need for 3D analysis
296
5. Conclusion
299
Acknowledgments
300
References
300
Abstract
Amphibian metamorphosis is marked by dramatic thyroid hormone (T
3
)-induced
changes including de novo morphogenesis, tissue remodeling, and organ resorption
through programmed cell death. These changes involve cascades of gene regulation
initiated by thyroid hormone (TH). TH functions by regulating gene expression through
TH receptors (TR). TR are DNA-binding transcription factors that belong to the steroid
hormone receptor superfamily. In the absence of ligand, TR can repress gene expression
by recruiting a corepressor complex, whereas liganded TR recruits a coactivator
