Abstract
This work investigates the role of isochores during preimplantation process. Using RNA-seq data from human and mouse preimplantation stages, we created the spatio-temporal transcriptional profiles of the isochores during preimplantation. We found that from early to late stages, GC-rich isochores increase their expression while GC-poor ones decrease it. Network analysis revealed that modules with few coexpressed isochores are GC-poorer than medium-large ones, characterized by an opposite expression as preimplantation advances, decreasing and increasing respectively. Our results reveal a functional contribution of the isochores, supporting the presence of structural-functional interactions during maturation and early-embryonic development.
Original language | English |
---|---|
Pages (from-to) | 2297-2306 |
Number of pages | 10 |
Journal | FEBS Letters |
DOIs | |
Publication status | Published - 1 Jul 2016 |
Externally published | Yes |
Funding
The authors would like to thank the anonymous reviewers for the valuable comments. We thank Giorgio Bernardi (Universita di Roma III), Oliver Clay (Universidad del Rosario, Bogota, Colombia & CIB, Medellin) and Tapash Gosh (Centre for Excellence in Bionformatics) for their valuable suggestions and constructive criticisms. Finally, we thank Fatima Vayani and Lorraine Ayad (Algorithms & Bioinformatics Group, King's College) for their comments and effort in editing. SA during the preparation of this work was supported by SYNERGASIA 2009 programme from ITE/FORTH. CB is supported by an EPSRC grant (Doctoral Training Grant #EP/J500252/1). SPP is supported by a Research Grant (#RG130720) awarded by the Royal Society.
Keywords
- base composition
- expression
- GC level
- isochores
- preimplantation
- RNA-seq
- transcriptome