Non-coding RNAs with gene regulatory functions are starting to be seen as a common feature of mammalian gene regulation with the discovery that most of the transcriptome is non-coding RNA. Given that a significant proportion of the genome encodes non-coding RNAs, relatively little is known about the regulatory mechanisms and functions of these RNAs. Thus, new insights into how non-coding RNAs are regulated and how they regulate gene expression are essential for a complete understanding of mammalian gene expression. We employ X chromosome inactivation as a model system to study the regulation and function of non-coding RNAs. X-inactivation is the developmentally regulated transcriptional silencing of one X chromosome in female cells, used to equalize X-linked gene dosage with male cells. An antisense pair of non-coding RNAs, Xist and Tsix RNA, are central in the regulation of X-inactivation. X-inactivation is random - the X chromosome from each parent is silenced with equal frequency. Xist and Tsix RNA are expressed before the onset of X chromosome silencing and are necessary for X-inactivation to occur randomly. In Xist or Tsix mutant cells, X-inactivation is non-random and the fates of the mutant and the wild-type X chromosomes are fixed. Xist and Tsix mutations have opposite effects on X chromosome fate: an Xist mutant chromosome is always chosen as the active X and a Tsix mutant X chromosome is always chosen as the inactive X. Xist and Tsix also negatively regulate each other's expression, forming a feedback loop. In this proposal we dissect the Xist/Tsix feedback loop and explore how it is used to ensure that each X chromosome has an equal frequency of being silenced.

Public Health Relevance

Project Narrative (Public Health Relevance) Non-coding RNAs play critical roles in regulating DNA structure, RNA expression, and translation, and thus affect normal development. While non-coding RNAs are already being identified as markers for cancer and associated with other complex diseases such as coronary disease and diabetes, little is understood about their regulation and function. A better understanding of non-coding RNAs will undoubtedly be important in the diagnosis and treatment of these conditions. We use X-inactivation as a model system to study the regulation and function of non-coding RNAs. In mammalian female cells, one X chromosome is silenced. This silencing ensures that X-linked gene dosage in XX female cells is equivalent to that in XY male cells. This process is essential for the survival of females. A pair of non- coding RNAs, Xist and Tsix RNA, is central in the regulation of X-inactivation. In this submission, we propose to study the regulation and function of Xist and Tsix RNA. What we learn will undoubtedly contribute to our understanding of X-inactivation, and more generally to the function of non-coding RNAs.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics B Study Section (MGB)
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Carter, Anthony D
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University of California San Francisco
Schools of Medicine
San Francisco
United States
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Miri, Kamelia; Latham, Keith; Panning, Barbara et al. (2013) The imprinted polycomb group gene Sfmbt2 is required for trophoblast maintenance and placenta development. Development 140:4480-9
Royce-Tolland, Morgan E; Andersen, Angela A; Koyfman, Hannah R et al. (2010) The A-repeat links ASF/SF2-dependent Xist RNA processing with random choice during X inactivation. Nat Struct Mol Biol 17:948-54