Scientists cut ‘Gordian knot’ in human genome

A team of researchers co-led by Erez Lieberman Aiden of Rice University and Baylor College of Medicine has discovered how mysterious, inactive genes in females hold sway over the superloops that connect DNA sequences at opposite ends of the chromosome.

The work by Aiden and colleagues at Florida State University and the Broad Institute of MIT and Harvard University sheds light on female development in mammals

Females have two X chromosomes in each of their cells. Fully unfolded, each copy is 2 inches long. One of these two X chromosomes is inactive — its genes are turned off. This copy folds into a structure called the Barr body, a mysterious configuration that was discovered in 1949.

Recently, scientists have shown that the Barr body contains massive superloops that bring DNA sequences at opposite ends of the chromosome together inside the nucleus of a cell.

The researchers determined which part of the DNA code is responsible for these superloops and have shown that it is possible to use this information to change the structure of the Barr body as a whole.

The Hi-C method measures how frequently two loci in the genome make physical contact in the nucleus of the cell. Here, a Hi-C contact map is rendered as a three-dimensional surface. Strong proximity between nearby genomic loci creates a ‘wall’ bisecting the landscape. Peaks in the contact map correspond to loops in the genome. Courtesy of Ido Machol and Erez Lieberman Aiden. Rendered by Ido Machol

PNAS – Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture

“X inactivation is fundamentally important for female development,” said Miriam Huntley, co-first author on the study. “Without it, females would generate too much of every gene product of the X chromosome.”


In human females, one of the two X chromosomes is inactive (Xi) and adopts an unusual 3D conformation. The Xi chromosome contains superloops, large chromatin loops that are often anchored at the macrosatellite repeat DXZ4, and is partitioned into two large intervals, called superdomains, whose boundary lies at DXZ4. Here, we use spatial proximity mapping, microscopy, and genome editing to study the Xi. We find that superloops and superdomains are conserved across humans, macaque, and mouse. By mapping proximity between three or more loci, we show that superloops tend to occur simultaneously. Deletion of DXZ4 from the human Xi disrupts superloops, eliminates superdomains, and alters chromatin modifications. Finally, we show that a model in which CCCTC-binding factor (CTCF) and cohesin extrude chromatin can explain the formation of superloops and superdomains.

During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the “Barr body.” Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called “superdomains,” such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called “superloops.” DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4. We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.

SOURCES- Rice university, Proceedings of national academy of science