Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos

Abstract

Upon fertilization, the genome of animal embryos remains transcriptionally inactive until the maternal-to-zygotic transition. At this time, the embryo takes control of its development and transcription begins. How the onset of zygotic transcription is regulated remains unclear. Here, we show that a dynamic competition for DNA binding between nucleosome-forming histones and transcription factors regulates zebrafish genome activation. Taking a quantitative approach, we found that the concentration of non-DNA-bound core histones sets the time for the onset of transcription. The reduction in nuclear histone concentration that coincides with genome activation does not affect nucleosome density on DNA, but allows transcription factors to compete successfully for DNA binding. In agreement with this, transcription factor binding is sensitive to histone levels and the concentration of transcription factors also affects the time of transcription. Our results demonstrate that the relative levels of histones and transcription factors regulate the onset of transcription in the embryo.DOI: http://dx.doi.org/10.7554/eLife.23326.001

Zygotic Genome Activation in Vertebrates

“…Interestingly, these replication factors are specifically degraded near the MBT, suggesting that the effects on replication may be downstream of an earlier MBT trigger, which might target replication factors for degradation to elongate S-phase. However, the effects on zygotic transcription were moderate (Collart et al, 2013), consistent with the likely existence of multiple titrated molecules, with some having greater influence on replication and others—such as histones—perhaps having greater influence on transcription (Amodeo et al, 2015; Joseph et al, 2017). In addition to histones and replication factors, other candidate titrated molecules include the phosphatase PP2A-B55 (Murphy and Michael, 2013), maternal histone variants (Yue et al, 2013), the DNA methyl transferase xDnmt1 (Dunican et al, 2008), and dNTPs (Landström et al, 1975; Vastag et al, 2011).…”

“…One possibility is that transcriptional onset is determined by the competition of free histones and specific transcription factors at gene loci (Joseph et al, 2017). Consistent with this model, in zebrafish, addition of histones delays transcription, while addition of activating transcription factors advances transcription.…”

“…Consistent with this model, in zebrafish, addition of histones delays transcription, while addition of activating transcription factors advances transcription. Moreover, reducing the concentration of free histones advances transcription of several tested genes (Joseph et al, 2017; Pálfy et al, 2017). Thus, critical activation thresholds could be reached at different times for different genes depending on the concentrations and DNA binding kinetics of the specific activator.…”

Transcription organizes euchromatin similar to an active microemulsion

“…Fixed whole embryos were prepared, fluorescently stained, and imaged using a Zeiss Z1 light sheet microscope exactly as described by us in a previous publication (Joseph et al, 2017). Pol II Ser2Phos was labeled by immunofluorescence, using mouse IgM anti-Pol II Ser2Phos primary antibody (1:500) and anti-mouse IgM secondary antibody (conjugated with Alexa 488, dilution 1:1000).…”

“…15, 2017; fluorescence in the cytoplasm is determined and subtracted from the total nuclear. The cytoplasmic intensity is determined using a segmentation shell that is created by an outward dilation of the nuclear segmentation mask (Stasevich, Sato, et al, 2014;Joseph et al, 2017).…”