The development of an adult multi-cellular organism from a single fertilized egg requires the proliferation and differentiation of a large number of cells. In many species, the early post-fertilization divisions occur rapidly and synchronously without growth phases and cell cycle checkpoints. These early embryos are almost entirely transcriptionally inactive and therefore driven by maternally supplied RNAs. At the Mid-Blastula Transition (MBT), the embryo initiates large-scale transcription from the zygotic genome and cells gain growth phases and checkpoints. Previous work suggested that the MBT is initiated by the increased DNA-to-cytoplasmic ratio resulting from repeated rounds of DNA replication and cell division without cell growth. This led to the hypothesis that the progressive titration of an inhibitory factor present in the embryo allows the initiation of zygotic transcription. Using a cel free system that recapitulates zygotic genome activation in vitro, we purified the transcriptional inhibitory activity present in the Xenopus egg cytoplasm and identified histones H3/H4 as DNA-titrated inhibitors of the MBT. Manipulating histone levels quantitatively shifts the onset of zygotic transcription and cell cycle lengthening in vivo, demonstrating a specific role for chromatin state in MBT initiation. This raises the question as to how histone titration and chromatin state are mechanistically linked to transcription and cell cycle duration. To address this, we will measure zygotic transcription and nucleosome occupancy genome wide at unprecedented temporal resolution through early development in control and histone manipulated embryos. We will determine mechanism linking DNA replication and histone levels. Successful completion of these aims will identify the mechanism through which global histone levels can be used to coordinate transcription and cell division with development. Since activating zygotic transcription is the first major transition after fertilization in human embryos our work determining how chromatin based mechanisms regulate the initiation of transcription will also provide insight global gene regulation and developmental reprogramming in the early vertebrate embryo.

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At the Mid-Blastula Transition (MBT), the frog embryos initiate large-scale transcription from the zygotic genome and cells gain growth phases and checkpoints. We aim to determine the mechanisms through which the titration of histones by genomic DNA regulates MBT events.

National Institute of Health (NIH)
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Research Project (R01)
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Development - 2 Study Section (DEV2)
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Ravindranath, Neelakanta
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Stanford University
Schools of Arts and Sciences
United States
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Bell, Jason C; Jukam, David; Teran, Nicole A et al. (2018) Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts. Elife 7:
Jukam, David; Shariati, S Ali M; Skotheim, Jan M (2017) Zygotic Genome Activation in Vertebrates. Dev Cell 42:316-332