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Literature DB >> 32857856

IsoXpressor: A Tool to Assess Transcriptional Activity within Isochores.

Lorraine A K Ayad¹, Athanasia-Maria Dourou², Stilianos Arhondakis², Solon P Pissis^3,4.

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).

Entities: Species

Keywords: GC level; RNA-Seq; isochores; preimplantation; transcription

Year: 2020 PMID： 32857856 PMCID： PMC7523728 DOI： 10.1093/gbe/evaa171

Source DB: PubMed Journal: Genome Biol Evol ISSN： 1759-6653 Impact factor: 3.416

18 in total

1. The Genomic Code: A Pervasive Encoding/Molding of Chromatin Structures and a Solution of the "Non-Coding DNA" Mystery.

Authors: Giorgio Bernardi
Journal: Bioessays Date: 2019-11-08 Impact factor: 4.345

2. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.

Authors: Zhigang Xue; Kevin Huang; Chaochao Cai; Lingbo Cai; Chun-yan Jiang; Yun Feng; Zhenshan Liu; Qiao Zeng; Liming Cheng; Yi E Sun; Jia-yin Liu; Steve Horvath; Guoping Fan
Journal: Nature Date: 2013-07-28 Impact factor: 49.962

3. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Authors: Bo Li; Colin N Dewey
Journal: BMC Bioinformatics Date: 2011-08-04 Impact factor: 3.307

4. Isochores and the regulation of gene expression in the human genome.

Authors: Stilianos Arhondakis; Fabio Auletta; Giorgio Bernardi
Journal: Genome Biol Evol Date: 2011 Impact factor: 3.416

5. Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos.

Authors: Xinyi Wang; Denghui Liu; Dajian He; Shengbao Suo; Xian Xia; Xiechao He; Jing-Dong J Han; Ping Zheng
Journal: Genome Res Date: 2017-02-21 Impact factor: 9.043

1. 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.

Authors: Dan Graur
Journal: Int J Mol Sci Date: 2022-06-12 Impact factor: 6.208

1 in total

IsoXpressor: A Tool to Assess Transcriptional Activity within Isochores.

1. The Genomic Code: A Pervasive Encoding/Molding of Chromatin Structures and a Solution of the "Non-Coding DNA" Mystery.

2. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.

3. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

4. Isochores and the regulation of gene expression in the human genome.

5. Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos.

6. An Isochore Framework Underlies Chromatin Architecture.

7. The formation of chromatin domains involves a primary step based on the 3-D structure of DNA.

8. DNA sequence-dependent chromatin architecture and nuclear hubs formation.

9. Chromosome Architecture and Genome Organization.

Review 10. Recent evidence that TADs and chromatin loops are dynamic structures.

1. 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.