Transcriptome activity of isochores during preimplantation process in human and mouse

Carl Barton; Costas S. Iliopoulos; Solon P. Pissis; Stilianos Arhondakis

doi:10.1002/1873-3468.12245

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 Journal › Article › Academic › peer-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 language	English
Pages (from-to)	2297-2306
Number of pages	10
Journal	FEBS Letters
DOIs	https://doi.org/10.1002/1873-3468.12245
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

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title = "Transcriptome activity of isochores during preimplantation process in human and mouse",

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.",

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doi = "10.1002/1873-3468.12245",

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AU - Barton, Carl

AU - Iliopoulos, Costas S.

AU - Pissis, Solon P.

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PY - 2016/7/1

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N2 - 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.

AB - 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.

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KW - expression

KW - GC level

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KW - preimplantation

KW - RNA-seq

KW - transcriptome

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Transcriptome activity of isochores during preimplantation process in human and mouse

Abstract

Funding

Keywords

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