The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting

Abstract

Pluripotency of embryonic stem (ES) cells is controlled by defined transcription factors1,2. During differentiation, mouse ES cells undergo global epigenetic reprogramming, as exemplified by X-chromosome inactivation (XCI) whereby one female X-chromosome is silenced to achieve gene dosage parity between the sexes3-5. Somatic XCI is regulated by homologous X-chromosome pairing6,7, counting8-10, and random choice of future active X (Xa) and inactive X’s. XCI and cell differentiation are tightly coupled11, as blocking one process compromises the other8,12 and dedifferentiation of somatic cells to induced pluripotent stem (iPS) cells is accompanied by X-reactivation2. Recent evidence suggests coupling of Xist expression to pluripotency factors13, but how the two are interconnected remains unknown. Here, we show that the Oct414 lies at the top of the XCI hierarchy and regulates XCI by triggering X-chromosome pairing and counting. Oct4 directly binds Tsix and Xite, two regulatory ncRNA genes of the X-inactivation center15,16, and also complexes with XCI trans-factors, Ctcf and Yy117, through protein-protein interactions. Depletion of Oct4 blocks homologous X-chromosome pairing and results in inactivation of both Xs in female cells. Thus, we have identified the first trans-factor that regulates counting and ascribed novel functions to Oct4 during X-chromosome reprogramming.

Single molecule detection of direct, homologous, DNA/DNA pairing

“…Recombinational double-strand break repair and programmed homologous recombination during meiosis all involve complex series of biochemical reactions in which single-stranded DNA (ssDNA) plays a prominent role. There also exist homologous pairing reactions that seem to involve interactions between chromosomal regions whose DNAs are chemically intact double-stranded DNA (dsDNA) (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). In some instances, whole chromosomes pair via multiple interactions all along their lengths (1)(2)(3)(4)(5)(6)(7)(8)(9) or via any region present in duplicate copies (10).…”

“…In some instances, whole chromosomes pair via multiple interactions all along their lengths (1)(2)(3)(4)(5)(6)(7)(8)(9) or via any region present in duplicate copies (10). In other cases, pairing occurs preferentially or exclusively in particular localized regions (''pairing sites''), which tend to involve repeated sequences, specific proteins (for establishment and/or maintenance of pairing) and/or heterochromatic regions (characterized by a paucity of genes and a less ''open'' chromatin structure) (1,(11)(12)(13)(14)(15).…”

“…In some instances, whole chromosomes pair via multiple interactions all along their lengths (1-9) or via any region present in duplicate copies (10). In other cases, pairing occurs preferentially or exclusively in particular localized regions (''pairing sites''), which tend to involve repeated sequences, specific proteins (for establishment and/or maintenance of pairing) and/or heterochromatic regions (characterized by a paucity of genes and a less ''open'' chromatin structure) (1,(11)(12)(13)(14)(15).In contrast to recombination-related processes that are known to involve protein-mediated Watson-Crick basepairing interactions between a ssDNA and a ssDNA or dsDNA partner, the fundamental basis for ''recombination-independent'' pairing remains mysterious. The most obvious possibility is direct DNA/DNA interactions.…”

Mechanistic concepts in X inactivation underlying dosage compensation in mammals

“…Recently, the stem cell transcription factor Oct4 has been implicated in the regulation of Xist expression in mice (Navarro et al, 2008;Donohoe et al, 2009). Oct4 has been shown to bind DNA sequences within Xist intron 1 and around the promoter and enhancer sequences of Tsix (Figure 2b).…”

Advances in understanding chromosome silencing by the long non-coding RNA Xist

“…Recent studies further propose that the differential expression of Xist is spatio-temporally regulated between two X chromosomes prior to the onset of X-inactivation by a physical association of the Xic region referred to as 'pairing', suggesting a means by which two X chromosomes may communicate with one another prior to selecting a single X chromosome for silencing [19,20]. Other studies have suggested that pluripotency factors, which bind their recognition sequences present in potential regulatory regions of Xist and Tsix, balance their expression to suppress or induce X-inactivation in a developmentally regulated manner [21][22][23]. More recently, an X-linked factor, Rnf12, has been shown to have a role in ensuring that Xist is activated only on a single X chromosome in female cells [24].…”