Graphical Abstract Bonev et al 2017, Cell


  • Ultra-deep Hi-C during mouse neural differentiation, both in vitro and in vivo
  • Transcription is correlated with, but not sufficient for, local chromatin insulation
  • Polycomb network is disrupted, while novel contacts between neural TF sites appear
  • Dynamic contacts among exon-rich gene bodies, enhancer-promoters, and TF sites


Chromosome conformation capture technologies have revealed important insights into genome folding. Yet, how spatial genome architecture is related to gene expression and cell fate remains unclear. We comprehensively mapped 3D chromatin organization during mouse neural differentiation in vitro and in vivo, generating the highest-resolution Hi-C maps available to date. We found that transcription is correlated with chromatin insulation and long-range interactions, but dCas9-mediated activation is insufficient for creating TAD boundaries de novo. Additionally, we discovered long-range contacts between gene bodies of exon-rich, active genes in all cell types. During neural differentiation, contacts between active TADs become less pronounced while inactive TADs interact more strongly. An extensive Polycomb network in stem cells is disrupted, while dynamic interactions between neural transcription factors appear in vivo. Finally, cell type-specific enhancer-promoter contacts are established concomitant to gene expression. This work shows that multiple factors influence the dynamics of chromatin interactions in development.

The paper can be found here
Fig1 of Review of Bonev et al, 2017


Understanding how chromatin is organized within the nucleus and how this 3D architecture influences gene regulation, cell fate decisions and evolution are major questions in cell biology. Despite spectacular progress in this field, we still know remarkably little about the mechanisms underlying chromatin structure and how it can be established, reset and maintained. In this Review, we discuss the insights into chromatin architecture that have been gained through recent technological developments in quantitative biology, genomics and cell and molecular biology approaches and explain how these new concepts have been used to address important biological questions in development and disease.

The Review can be found here
Graphical Abstract of Bonev et al, 2012


  • miR-9 controls Hes1 oscillations by regulating Hes1 mRNA stability in NPCs
  • Hes1 represses miR-9 transcription, giving rise to antiphase oscillations
  • The accumulation of mature miR-9 dampens Hes1 oscillations
  • The double-negative feedback loop serves as a self-limiting oscillator


Short-period (ultradian) oscillations of Hes1, a Notch signaling effector, are essential for maintaining neural progenitors in a proliferative state, while constitutive downregulation of Hes1 leads to neuronal differentiation. Hes1 oscillations are driven by autorepression, coupled with high instability of the protein and mRNA. It is unknown how Hes1 mRNA stability is controlled and furthermore, how cells exit oscillations in order to differentiate. Here, we identify a microRNA, miR-9, as a component of ultradian oscillations. We show that miR-9 controls the stability of Hes1 mRNA and that both miR-9 overexpression and lack of miR-9 dampens Hes1 oscillations. Reciprocally, Hes1 represses the transcription of miR-9, resulting in out-of-phase oscillations. However, unlike the primary transcript, mature miR-9 is very stable and thus accumulates over time. Given that raising miR-9 levels leads to dampening of oscillations, these findings provide support for a self-limiting mechanism whereby cells might terminate Hes1 oscillations and differentiate.

The Paper can be found here
Fig1 of Bonev et al, 2011


  • miR-9 function in neural progenitors is context dependent
  • miR-9 loss induces proliferation in the hindbrain and apoptosis in the forebrain
  • The primary function of miR-9 in neurogenesis is to downregulate hairy1 mRNA levels
  • miR-9/hairy1 affects proliferation via cyclinD/p27 and apoptosis via p53


Neural progenitors self-renew and generate neurons throughout the central nervous system. Here, we uncover an unexpected regional specificity in the properties of neural progenitor cells, revealed by the function of a microRNA—miR-9. miR-9 is expressed in neural progenitors, and its knockdown results in an inhibition of neurogenesis along the anterior-posterior axis. However, the underlying mechanism differs—in the hindbrain, progenitors fail to exit the cell cycle, whereas in the forebrain they undergo apoptosis, counteracting the proliferative effect. Among several targets, we functionally identify hairy1 as a primary target of miR-9, regulated at the mRNA level. hairy1 mediates the effects of miR-9 on proliferation, through Fgf8 signaling in the forebrain and Wnt signaling in the hindbrain, but affects apoptosis only in the forebrain, via the p53 pathway. Our findings show a positional difference in the responsiveness of progenitors to miR-9 depletion, revealing an underlying divergence of their properties.

The Paper can be found here

TADs are 3D structural units of higher-order chromosome organization in Drosophila.
Szabo Q., Jost D., Chang JM., Cattoni D., Papadopoulos G., Bonev B., Sexton T., Gurgo J., Jacquier C., Nollmann M., Bantignies F. & Cavalli G.
Science Advances (2018) 4, eaar8082.

Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila.
Ciabrelli F., Comoglio F., Fellous S., Bonev B., Ninova M., Szabo Q., Xuéreb A., Klopp C., Aravin A., Paro R., Bantignies F. & Cavalli G.
Nature Genetics (2017) 49, 876–886.

Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development.
Loubiere V., Delest A., Thomas A., Bonev B., Schuettengruber B., Sati S., Martinez, AM & Cavalli, G.
Nature Genetics (2016) 48, 1436–1442.

Multiple knockout mouse models reveal lincRNAs are required for life and brain development.
Sauvageau M., Goff LA, Lodato S., Bonev B., Groff AF, Gerhardinger C., Sanchez-Gomez DB., Hacisuleyman E., Li E., Spence M., et al. & Arlotta P., Rinn J.
Elife (2013) e01749.

microRNA-9 regulates axon extension and branching by targeting Map1b in mouse cortical neurons
Dajas-Bailador F., Bonev B., Garcez P. Stanley P., Guillemot F. & Papalopulu N.
Nature Neuroscience (2012) 15, 697–699.

Methods to analyze microRNA expression and function during Xenopus development.
Bonev B. & Papalopulu N.
Methods in molecular biology (2012) 917: 445-459.

Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration.
Love NR., Chen Y., Bonev B., Gilchrist MJ, Fairclough L., Lea R., Mohun TJ, Paredes R., Zeef LA, & Amaya E.
BMC Dev Biol (2011) 11, 70.

FoxG1 and TLE2 act cooperatively to regulate ventral telencephalon formation.
Roth M., Bonev B., Lindsay J., Lea R., Panagiotaki N., Houart C. & Papalopulu N.
Development (2010) 137, 1553-62.