Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis

PloS One
Nicolas BuisineLaurent M Sachs

Abstract

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...Continue Reading

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Citations

Jul 26, 2016·Frontiers in Endocrinology·Frédéric Flamant
Jan 18, 2017·Genesis : the Journal of Genetics and Development·Amy K Sater, Sally A Moody
Jan 22, 2017·Genesis : the Journal of Genetics and Development·Laurent M Sachs, Daniel R Buchholz
May 18, 2018·Cold Spring Harbor Protocols·Daniel R Buchholz, Yun-Bo Shi
May 31, 2019·Frontiers in Endocrinology·Laurent M Sachs, Daniel R Buchholz
Jun 14, 2018·Cold Spring Harbor Protocols·Nicolas BuisineLaurent M Sachs
Jun 4, 2019·Frontiers in Endocrinology·Anita A ThambirajahCaren C Helbing
Apr 3, 2020·Developmental Biology·Yasuhiro KyonoRobert J Denver

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Methods Mentioned

BETA
ChIP-Seq
RNA-Seq
PCR
dissection
electrophoresis
ChIP
immunoprecipitation

Software Mentioned

cython
SOLiD Corona - Lite
Ensembl
TOPHAT
Prism 7300
Cufflinks
RNA
Bioscope
ChIA
bowtie

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