Transcriptome activity of isochores during preimplantation process in human and mouse

Carl Barton, Costas S. Iliopoulos, Solon P. Pissis, Stilianos Arhondakis*

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review

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 languageEnglish
Pages (from-to)2297-2306
Number of pages10
JournalFEBS Letters
DOIs
Publication statusPublished - 1 Jul 2016
Externally publishedYes

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

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