JUL 19, 2016 12:27 PM PDT

Researchers Reveal Functions of an Inactive Chromosome

WRITTEN BY: Carmen Leitch
In a report published in the Proceedings of the National Academy of Sciences, researchers working at Florida State University (FSU), Baylor College of Medicine and the Broad Institute of Harvard and MIT have shown that an unusual DNA repeat element located on an inactive X chromosome is actually critical to the resulting three-dimensional structure of this genetic phenomenon.
Concatemers produced by proximity ligation indicate simultaneous colocation of three or more loci: a modified in situ Hi-C protocol, dubbed
Breaking ground in a little-understood area of human genetics, it's what FSU Associate Professor of Biological Science Brian Chadwick, one of the authors of the paper, describes as the "black box of genome biology."

"These repeat elements are one of the unknowns in our genome," Chadwick explained. "Nobody knows where they originated from or why we have retained them, but typically this points to them performing some as of yet unknown important function. The repeats on the X chromosome are particularly intriguing, because they don't behave the way other DNA sequences do."

Virtually all female mammals have two X chromosomes, but one of the chromosomes is basically inactivated, in other words it’s thought that most genes there aren’t performing any functions. Silencing that chromosome is vital for proper female development, and scientists have long attempted to understand the underlying processes.

It’s been found that though the majority of the chromosome is shut down, there are some parts that are not. Interestingly, these parts feature unusual sequences of repetitive DNA, and at one location, the extensive tandem repeat named DXZ4.

These long repeats are not unusual in the genome. Several exist on other chromosomes, and at least one has been directly linked to the onset of a common form of muscular dystrophy, and another has been associated with schizophrenia. The repeats on the X chromosome however, are a complete mystery and studying them can be incredibly challenging.

The research teams involved in this study had completed earlier, independent work demonstrating that these repeat elements make contact with one another frequently, and exclusively on the inactive chromosome, creating what Erez Lieberman Aiden, Baylor Assistant Professor and Director of The Center for Genome Architecture, coined "superloops."

Upon learning of Aiden’s research, Chadwick suggested they work together to learn more about the function of these superloops. The investigators now also report that DXZ4 is involved in forming superloops on the inactive X chromosome in mice and rhesus monkeys.

"In principle, the presence of DXZ4 at one end of the human superloops could have been a coincidence," said Aiden. "But the fact the DXZ4 lies at the site of superloops in all three species was a critical clue."
Contact triples visualized as a 3D contact tensor. Details of chromosome organization are seen inside this tensor as n-dimensional shapes. Here, the bright diagonal seen in 2D contact matrices naturally creates an n-dimensional hyperstar. / Credit: PNAS Darrow et al
Chadwick and Aiden utilized cutting-edge genetic engineering methods to excise DXZ4 from the inactive X, resulting in one of the largest engineered deletions in human cells ever. They observed that the deletion caused a major, disruptive formation change in the chromosome; the three-dimensional structure of the inactive X DNA collapsed.
Deletion of DX4 disrupts compartmentalization, distribution of histone marks, and replication timing. Immunofluorescence shows the distribution of H3 lysine 9 trimethylation (green, indirect immunofluorescence) and histone H3 lysine 27 trimethylation (red, direct immunofluorescence) in wild-type RPE1 cells at interphase. White arrowheads indicate the location of the Xi chromosome that is expanded in the panels to the right, showing the corresponding nuclei./ Credit: PNAS Darrow et al
"In the absence of this repeat, it significantly alters the folding and organization of the X chromosome," Chadwick explained. "It showed for the first time that it was essential for the correct three-dimensional structure of the human chromosome."

"We're entering an exciting new era of genomics," Chadwick continued. "We know a lot about basic gene expression and gene structure. But what we don't know is how everything works three dimensionally in the nucleus. Armed with these new genome engineering resources and the state-of-the-art high-throughput genomic analysis tools pioneered by labs such as Dr. Aiden's, we're just starting to pick away at that."

Sources: PNAS, AAAS/Euerkalert! via FSU
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