• To understand epigenetic regulation by long noncoding RNAs (lncRNA)
  • To understand how lncRNAs enable allelic and locus-specific control (X-inactivation, imprinting)
  • To determine what and how lncRNAs interact with chromatin-modifying complexes to change gene expression
  • To investigate chromosome "counting", "pairing", and allelic choice as RNA-mediated phenomena
  • To develop techniques to investigate interactions at the RNA-protein interface
  • To translate basic mechanisms to disease and therapeutics


X-chromosome inactivation (XCI) equalizes gene expression between male (XY) and female (XX) mammals by silencing one X-chromosome in the female embryo. In this way, genes are expressed from the two female X-chromosomes at the same level as from the single male X-chromosome. XCI is an excellent model in which to study lncRNA because the epigenetic process is controlled by the "X-inactivation center" (Xic), a region on the X-chromosome that harbors many lncRNA. These transcripts interact with protein factors to control the initiation, spread, establishment, and maintenance of silencing on a 150 megabase scale. Some examples include:

  • Xist RNA: 17-kb transcript, coats the X, targets and spreads PRC2 to initiate silencing.
  • Tsix RNA: Antisense transcript that controls Xist.
  • Jpx RNA: Activates Xist by evicting CTCF.
  • Xite: eRNA for Tsix, controls allelic choice & pairing.
  • RepA RNA: Repeat RNA, targets PRC2 to the Xist.

Many aspects of XCI remain poorly understood. Current lab projects focus on (1) how "counting" works, (2) how X-chromosome pairing is regulated and how pairing is central to allelic choice, (3) how Xist spreads and targets silencing factors on a chromosome-wide scale, (4) how Tsix prevents this inactivation cascade, and (5) how imprinting might be controlled by mechanisms involving transgenerational inheritance. We suspect that RNA will be central to these problems.


CLICK HERE to view VIDEO: Jpx evicts CTCF.


Xist RNA coats the inactive X chromosome


Lessons from the X: LncRNA as guides and tethers

Two properties of mammalian lncRNAs render them excellent vehicles by which to deliver epigenetic control:

(1) Cis-regulation and allelic-specific control: Long transcripts are naturally tethered to the site of synthesis via the act of being transcribed. LncRNAs can therefore function as allele-specific tags and offer the possibility of recruiting chromatin complexes in cis. This property may explain their prominence within the Xic and imprinted regions. Proteins do not retain allelic memory, as their transcriptional origin is lost when mRNA is shuttled to the cytoplasm for translation to protein.

(2) Locus-specific targeting: Long transcripts can also direct chromatin complexes to a unique location in the genome. Transcription factors (proteins) generally recognize short DNA motifs that occur thousands of times in the genome. They therefore regulate expression of multiple genes at once. RNA's potential for locus-specific targeting may account for why so much of the mammalian genome is transcribed.


Many chromatin-associated factors are now known to interact with RNA. An established example is Polycomb repressive complex 2 (PRC2). In addition to Xist RNA, PRC2 associates with thousands of other transcripts, as shown by our RIP-seq analysis. Members of this "transcriptome" are candidate biomarkers and therapeutic targets in human disease. It is likely that other chromatin factors will associate with a large transcriptome as well. We would like to uncover such networks of RNA-protein interactions. Such efforts will facilitate understanding of chromosomal control and open up new ways of treating human diseases such as Rett Syndrome, muscular dystrophy, and cancer. CLICK HERE for an example. An example of the importance of lncRNA in disease can be found HERE (Xist).

CLICK HERE. Right panel: Xist RNA is tethered to the inactive X nucleation center via YY1 protein. Left panel: Xist RNA directs spreading of PRC2 via defined Polycomb stations.

CLICK HERE. Allele-specific CHART-seq shows that Xist RNA spreads across the X-chromosome in a two-step fashion, targeting active genes first as it spreads.

Copyright © 2016 The Massachusetts General Hospital