IsoXpressor: A Tool to Assess Transcriptional Activity Within Isochores

Overview

Journal Genome Biol Evol

Publisher Oxford University Press

Specialties Biology
Genetics
Molecular Biology

Date 2020 Aug 29

PMID 32857856

Citations 2

Authors

Lorraine A K Ayad

Athanasia-Maria Dourou

Stilianos Arhondakis

Solon P Pissis

Affiliations

Soon will be listed here.

Abstract

Genomes are characterized by large regions of homogeneous base compositions known as isochores. The latter are divided into GC-poor and GC-rich classes linked to distinct functional and structural properties. Several studies have addressed how isochores shape function and structure. To aid in this important subject, we present IsoXpressor, a tool designed for the analysis of the functional property of transcription within isochores. IsoXpressor allows users to process RNA-Seq data in relation to the isochores, and it can be employed to investigate any biological question of interest for any species. The results presented herein as proof of concept are focused on the preimplantation process in Homo sapiens (human) and Macaca mulatta (rhesus monkey).

Citing Articles

Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish.

Vohnoutova M, Sedlakova A, Symonova R Int J Mol Sci. 2023; 24(17).

PMID: 37685974 PMC: 10487504. DOI: 10.3390/ijms241713167.

Slaying (Yet Again) the Brain-Eating Zombie Called the "Isochore Theory": A Segmentation Algorithm Used to "Confirm" the Existence of Isochores Creates "Isochores" Where None Exist.

Graur D Int J Mol Sci. 2022; 23(12).

PMID: 35743002 PMC: 9224211. DOI: 10.3390/ijms23126558.

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