X-Chromosome Silencing Depends on Antisense RNA

    Think of the silencing of the X chromosome as a construction project. Then, imagine you hear the beeping of heavy machinery operating in reverse. That’s the sound of the Xist gene being transcribed in the backwards, or antisense, direction. The Xist gene is read in the forward direction too, otherwise it wouldn’t generate a long, noncoding RNA that physically coats the X chromosome at the outset of X inactivation. But it turns out that the reverse transcription of the Xist gene is necessary, too.

    This finding emerged from research conducted by scientists at the University of Michigan Medical School. These researchers, led by geneticist Sundeep Kalantry, Ph.D., couldn’t simply listen for beeps, as though they were at a real construction site. Instead, they had to develop a new kind of test to detect antisense RNA strands, which cells make in much smaller amounts than the forward-reading kind.

    Dr. Kalantry’s team described its work October 19 in the journal Nature Communications, in an article entitled, “An Xist-activating antisense RNA required for X-chromosome inactivation.” The article detailed how the team developed ways to “tag” antisense strands to make them detectable. It also presented results suggesting that the Xist gene carries within its coding sequence an antisense RNA that drives Xist expression.

    “Here we discover an Xist antisense long non-coding RNA, XistAR (Xist Activating RNA), which is encoded within exon 1 of the mouse Xist gene and is transcribed only from the inactive X chromosome,” the authors wrote. “Selective truncation of XistAR, while sparing the overlapping Xist RNA, leads to a deficiency in Xist RNA expression in cis during the initiation of X inactivation.”

    Essentially, the scientists investigated what would happen if they kept cells in live mice from making XistAR. Without it, the cells couldn’t silence one X chromosome effectively, and they made too much of the X-chromosome gene products in females.

    If the discovery translates to humans—and XistAR seems to also be present in humans—Dr. Kalantry believes that XistAR may provide a convenient handle to manipulate X chromosome genes. For example, it could be possible to boost proteins generated by the X chromosome’s genes by stopping XistAR from working.

    “This work sheds light into how lncRNAs function, how genes and even an entire chromosome can be quieted. XistAR provides a molecular target to control gene expression—how to ‘wake the genes up’ or reduce their activity,” said Dr. Kalantry. “Exploring how the X chromosome becomes inactivated lets us know how to selectively activate it. Turning on the healthy copy of an X chromosome gene maybe a way to minimize disease risks associated with the X chromosome.”

    “The control of genes by lncRNAs, often via epigenetic means, is now appreciated to occur in a wide variety of contexts, from normal physiology to diseases. On a fundamental level, it controverts the central dogma of DNA begetting RNA, which then makes proteins,” continued Dr. Kalantry. “The techniques we’ve developed facilitate the discovery of rare RNA species in a cell. Such RNAs have been missed by high-throughput sequencing approaches, but they may be essential for cell function.”