ÌìÃÀ´«Ã½

Abstract

Initial development of the embryo is exclusively under the control of maternally deposited proteins and RNAs. In externally developing metazoan embryos cycles of extremely fast and synchronous cell divisions precedes global zygotic genome activation (ZGA). The genome is activated when a threshold nucleo-cytoplasmic ratio is reached, which dilutes repressive maternal factors. This event coincides with the mid-blastula transition (MBT). However, the earliest expressed genes, which prepare the rest of the genome for activation escape global genome repression and are activated well before the MBT. How do these genes get transcribed during the short cell cycles, which are only 15 minutes and lack G phases, remains mostly unexplored. We have developed a native transcription imaging tool, which detected nascent transcripts accumulating in a transcription body during the minor wave of genome activation. We described the spatial and temporal dynamics of the first wave of genome activation and its cross-regulation by the cell cycle. We demonstrate that the transcription body forms at an excessively high copy number gene cluster, composed of the highest promoter density in the genome and which encodes miR430 microRNAs responsible for clearance of maternal mRNAs. While this transcription body represent the main sites of detectable transcription, we showed that minor wave genes can be independently transcribed due to their distinct promoter architecture and promoter features from that of the main wave of ZGA. These findings suggest distinct transcription mechanisms between the minor and major waves of genome activation.

To further explore mechanisms of zygotic genome activation and the contribution of parental information to this process we also focussed on the formation and specification of primordial germ cells, which are singled out by selective retention of maternal determinants. 4D imaging and epigenomic analysis of these cells have uncovered the role of cytoplasmic maternal determinants in distinct chromatin topology organisation for specific gene regulation of primordial germ cells during early development.

Selected references

1. Hadzhiev, Y Wheatley, L., Cooper, L., Ansaloni, F., Whalley, C., Chen, Z., Finaurini, S., Gustincich, S., Sanges, R., Burgess, S., Beggs, A. and Müller, F. (2022) The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation, in press

2. Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, … et al,…. Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B and Müller F. (2022) Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat Genet. 54(7):1037-1050.

3. D'Orazio FM, Balwierz PJ, González AJ, Guo Y, Hernández-Rodríguez B, Wheatley, L, Jasiulewicz A, Hadzhiev Y, Vaquerizas JM, Cairns B, Lenhard B, Müller F. (2021) Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization. Dev Cell. 56(5):641-656.e5.

4. Hadzhiev, Y., Qureshi, H., Wheatley, L., Cooper, L. Jasiulewicz, A., Wragg, J., Nguyen, H., Poovathumkadavil, D., Conic, S., Bajan, S., Sik, A., Hutvagner, G., Tora, L., Gambus, A., Fossey J. and Müller F. (2019) A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation Nature Communications 2019 Feb 11;10(1):691.

5. Haberle, V., Li, N., Hadzhiev, Y., Plessy, C., Previti, C., Nepal, C., Gehrig, J., Dong, X., Akalin, A., Suzuki, A-M., van IJcken, W., Armant, O., Ferg, M., Strähle, U., Carninci, P., Müller F.* and Lenhard B. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature, 507(7492):381-5, *co-corresponding author.