After fertilization, to initiate development, gametes are reprogramed to become totipotent. Approximately half of the mammalian genome consists of repetitive elements, including retrotransposons, some of which are transcribed after fertilization. Retrotransposon activation is generally assumed to be a side effect of the extensive chromatin remodeling underlying the epigenetic reprogramming of gametes. Here, we used a targeted epigenomic approach to address whether specific retrotransposon families play a direct role in chromatin organization and developmental progression. We demonstrate that premature silencing of LINE-1 elements decreases chromatin accessibility, whereas prolonged activation prevents the gradual chromatin compaction that occurs naturally in developmental progression. Preventing LINE-1 activation and interfering with its silencing decreases developmental rates independently of the coding nature of the LINE-1 transcript, thus suggesting that LINE-1 functions primarily at the chromatin level. Our data suggest that activation of LINE-1 regulates global chromatin accessibility at the beginning of development and indicate that retrotransposon activation is integral to the developmental program.

In mammals, the emergence of totipotency after fertilization involves extensive rearrangements of the spatial positioning of the genome1,2. However, the contribution of spatial genome organization to the regulation of developmental programs is unclear3. Here, we have generated high-resolution maps in mouse pre-implantation embryos of genomic interactions with the nuclear lamina, a filamentous meshwork that lines the inner-nuclear membrane. We find that nuclear organisation is not inherited from the maternal germline but is instead established de novo rapidly after fertilisation. The two parental genomes establish lamina-associated domains (LADs4) with different features that converge after the 8-cell stage. We find that the mechanism of LAD establishment is unrelated to DNA replication. Instead, we show that paternal LAD formation in zygotes is prevented by ectopic expression of Kdm5b, suggesting that LAD establishment may be dependent upon remodelling of H3K4 methylation. Together, our data suggest a step-wise assembly model whereby early LAD formation precedes consolidation of Topologically Associating Domains (TADs).

The fusion of the gametes upon fertilization results in the formation of a totipotent cell. Embryonic chromatin is expected to be able to support a large degree of plasticity. However, whether this plasticity relies on a particular conformation of the embryonic chromatin is unknown. Moreover, whether chromatin plasticity is functionally linked to cellular potency has not been addressed. Here, we adapted fluorescence recovery after photobleaching (FRAP) in the developing mouse embryo and show that mobility of the core histones H2A, H3.1, and H3.2 is unusually high in two-cell stage embryos and decreases as development proceeds. The transition toward pluripotency is accompanied by a decrease in histone mobility, and, upon lineage allocation, pluripotent cells retain higher mobility than the differentiated trophectoderm. Importantly, totipotent two-cell-like embryonic stem cells also display high core histone mobility, implying that reprogramming toward totipotency entails changes in chromatin mobility. Our data suggest that changes in chromatin dynamics underlie the transitions in cellular plasticity and that higher chromatin mobility is at the nuclear foundations of totipotency.Supplemental material is available for this article.Received January 25, 2014; revised version accepted April 16, 2014. Embryonic cells are characterized by a large degree of plasticity, which is the ability to generate different cell types upon differentiation and is necessary to start a full developmental program. After fertilization, the mouse embryo has the transient capacity to generate both embryonic and extraembryonic cell types, a feature that is referred to as totipotency (Tarkowski 1959;Ishiuchi and Torres-Padilla 2013). This is in contrast to pluripotent cells, which contribute to all three germ layers of the embryo proper, but not to extraembryonic lineages, and therefore have a more restricted potential than totipotent cells. In mice, only the zygote and two-cell stage blastomeres are, strictly speaking, totipotent, since they have the ability to develop into a full organism without the need of carrier cells (Tarkowski 1959;Tarkowski and Wroblewska 1967;Kelly et al. 1978;Ishiuchi and Torres-Padilla 2013). As development progresses, pluripotent cells form in the inner cell mass (ICM) of the blastocyst, accompanied by the activation of pluripotency-associated transcription factors like Nanog and Pou5f1/Oct4 (Nichols et al. 1998;Chambers et al. 2003). The first differentiated embryonic tissue, the trophectoderm (TE), appears morphologically distinguishable and surrounds the ICM in the blastocyst. Thus, during the early stages of development, the mouse embryo undergoes dramatic changes in cellular plasticity.Upon fertilization, embryonic chromatin undergoes intense chromatin remodeling. Indeed, this epigenetic reprogramming of the gametes is thought to be essential to gain totipotency (Sado and Ferguson-Smith 2005;Surani et al. 2007;Hemberger et al. 2009). However, the precise conformation of embryonic chromatin and the way it...