Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis.
Genome-wide functional analyses require high-resolution genome assembly and annotation. We applied ChIA-PET to analyze gene regulatory networks, including 3D chromosome interactions, underlying thyroid hormone (TH) signaling in the frog Xenopus tropicalis. As the available versions of Xenopus tropicalis assembly and annotation lacked the resolution required for ChIA-PET we improve the genome assembly version 4.1 and annotations using data derived from the paired end tag (PET) sequencing technologies and approaches (e.g., DNA-PET [gPET], RNA-PET etc.). The large insert (~10 Kb, ~17 Kb) paired end DNA-PET with high throughput NGS sequencing not only significantly improved genome assembly quality, but also strongly reduced genome "fragmentation", reducing total scaffold numbers by ~60%. Next, RNA-PET technology, designed and developed for the detection of full-length transcripts and fusion mRNA in whole transcriptome studies (ENCODE consortia), was applied to capture the 5' and 3' ends of transcripts. These amendments in assembly and annotation were essential prerequisites for the ChIA-PET analysis of TH transcription regulation. Their application revealed complex regulatory configurations of target genes and the structures of the regulatory networks underlying physiological responses. Our work allowed us to improve the quality of Xenopus tropicalis genomic resources, reaching the standard required for ChIA-PET analysis of transcriptional networks. We consider that the workflow proposed offers useful conceptual and methodological guidance and can readily be applied to other non-conventional models that have low-resolution genome data.
UMR CNRS 7221, Muséum National d'Histoire Naturelle, Paris, France.
Nicolas
N
Buisine
The Jackson Laboratory of Genomic Medicine, Farmington, Connecticut, United States of America; Department of Genetics and Developmental Biology, University of Connecticut, Farmington, Connecticut, United States of America; Genome Institute of Singapore, Singapore, Singapore.
Xiaoan
X
Ruan
UMR CNRS 7221, Muséum National d'Histoire Naturelle, Paris, France; Watchfrog S.A.S., Evry, France.
Patrice
P
Bilesimo
UMR CNRS 7221, Muséum National d'Histoire Naturelle, Paris, France.
Alexis
A
Grimaldi
UMR CNRS 7221, Muséum National d'Histoire Naturelle, Paris, France.
Gladys
G
Alfama
Genome Institute of Singapore, Singapore, Singapore.
Pramila
P
Ariyaratne
Genome Institute of Singapore, Singapore, Singapore.
Fabianus
F
Mulawadi
Genome Institute of Singapore, Singapore, Singapore.
Jieqi
J
Chen
Genome Institute of Singapore, Singapore, Singapore.
Wing-Kin
WK
Sung
The Jackson Laboratory of Genomic Medicine, Farmington, Connecticut, United States of America; Department of Genetics and Developmental Biology, University of Connecticut, Farmington, Connecticut, United States of America; Genome Institute of Singapore, Singapore, Singapore.
Edison T
ET
Liu
UMR CNRS 7221, Muséum National d'Histoire Naturelle, Paris, France.
Barbara A
BA
Demeneix
The Jackson Laboratory of Genomic Medicine, Farmington, Connecticut, United States of America; Department of Genetics and Developmental Biology, University of Connecticut, Farmington, Connecticut, United States of America; Genome Institute of Singapore, Singapore, Singapore.
Yijun
Y
Ruan
UMR CNRS 7221, Muséum National d'Histoire Naturelle, Paris, France.
Laurent M
LM
Sachs
D000818:Animals; D002843:Chromatin / Q000235:genetics; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks / Q000235:genetics; D016678:Genome; D006801:Humans; D058977:Molecular Sequence Annotation; D012313:RNA / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D017422:Sequence Analysis, DNA; D013963:Thyroid Hormones / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D014981:Xenopus / Q000235:genetics*
D002843:Chromatin; D012333:RNA, Messenger; D013963:Thyroid Hormones; D012313:RNA