ChIA-PET Study Demonstrates Effect of Genome Folding on Gene Expression

For a recent publication in Cell, scientists used the SageELF whole-sample fractionation platform to perform size selection prior to cDNA sequencing on the PacBio system. The Iso-Seq method allows PacBio users to generate full-length transcripts, and SageELF makes it easier to pool size fractions and include the exact size range of interest for the study.

In this paper, “CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription,” the PacBio data set complemented short-read sequence data. Lead authors Zhonghui Tang, Oscar Junhong Luo, and Xingwang Li, along with senior author Yijun Ruan, worked with collaborators at the Jackson Lab and several other institutes to better understand genome organization and its implications for transcription.

The scientists used ChIA-PET (a much-needed abbreviation for “chromatin interaction analysis by paired-end tag sequencing”) to perform 3D mapping of the genome in four types of human cells, focusing on interactions mediated by transcription catalyst RNAPII and CTCF, which is known to play a role in genome folding. Separately, they studied gene expression with long-read sequencing.

“We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation,” the authors report, “whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes toward CTCF foci for coordinated transcription.” They also show that changes in haplotype or allele interactions affect chromosomal configuration and alter gene expression.

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