Transcriptional regulation: connecting the dots from base pairs to nuclear architecture


Giacomo Cavalli, Xavier Darzacq, Bart Deplancke, Claude Desplan, Nathalie Dostatni, Eileen Furlong, Nicolas Gompel (organizer), Alexander (Sandy) Johnson, James Kadonaga, Patrick Lemaire, Mathilde Paris, Anasthasios (Tassos) Pavlopoulos, BenjaminPrud’homme (organizer), Filippo Rijli, François Spitz, Angela Stathopoulos


Bart Deplancke Sandy Johnson Claude Desplan Eileen Furlong Xavier Darzacq Benjamin Prud'homme François Spitz Patrick Lemaire James Kadonaga Mathilde Paris Filippo Rijli Nicolas Gompel (Anasthasios) Tassos Pavlopoulos Giacomo Cavalli Angela Stathopoulos Nathalie Dostatni Transcriptional regulation: connecting the dots from base pairs to nuclear architecture - Fondation des Treilles










Abstract. This seminar examined the process of gene transcription and its regulation at different levels of biological complexity, from DNA base pairs to nuclear organisation, and to the production and evolution of phenotypes. The outcome of this meeting clearly highlighted the need to superimpose the approaches to study this complex biological phenomenon, to reach a dynamic and integrative picture of gene transcription. 

Key words: transcription; gene expression; gene regulation; enhancer; core promoter; chromatin; nucleus;

The expression of genes is a central process in biology, relevant to all levels of biological complexity, from the clockwork of a cell to the development of an organism and to the formation of specific organs and tissues. It is also at the heart of several diseases and species evolution, when mutations modify the expression of particular genes. The first step in the process of gene expression is the transcription, whereby a particular molecular machinery of the cell uses a defined portion of nuclear DNA as a template to assemble a messenger molecule, the mRNA. This process is tightly controlled both by a myriad of proteins and by the DNA sequence itself. The regulation of this process has been at the center of attention in biological research for nearly five decades. The complexity of this regulation has given rise to many fields that have progressively evolved on their own over time, making it sometimes difficult to capture the essence of the biological process as a whole. More than a progress report of the research on transcriptional regulation, the goal of this meeting was to gather scientists studying various aspects of gene transcription, and attempt to integrate the progress obtained by different perspectives into a unifying framework.

The 16 participants to the meeting approached the question of transcriptional regulation from different angles, and at different molecular levels, covering the entire process, from the organization of DNA inside the nucleus, to the packaging of the chromatin, the local modulation of transcription by cis-regulatory elements and finally the nature of the gene core promoter. Moreover, the different participants use different animal model systems and different contexts in which changes in transcription lead to biological diversity (yeast metabolism, animal embryonic development, variation within populations, morphological variations between closely related species). These very different situations proved to be an interesting filter to identify general features of the process of transcription.

Three main, transversal themes have emerged from the participants’ presentations:   (1) how do regulatory sequences control gene expression? (2) how are the regulatory sequences structured and to what extent does this organization impact gene regulation? (3) how do changes in gene regulatory sequences contribute to gene expression and species evolution? Remarkably, these three themes intersected quite often in several presentations and across participants, showing how artificial it is to separate these three biological levels. This distinction is used here only to organize the participants’ communications.

1. Function of gene regulatory sequencesC. Desplan and F. Rijli explained how the functions of transcriptional regulatory systems contribute to the development of the brain, the diversity and the connectivity of the neurons. C. Desplan showed how the regulatory sequences of the Spineless locus can switch from a deterministic mode to a stochastic mode of gene expression activation, to control photoreceptor subtype diversity in the fly retina. F. Rijli explained how genes controlling chromatin state and gene expression affect neuronal guidance and connectivity to particular areas of the developing mouse brain. N. Dostatni discussed how precision in gene transcription is achieved in response to a morphogen gradient in the context of the syncitial Drosophila embryo. The visualization of nascent transcript and the response dynamics across cell divisions suggests the existence of a memorization process of the morphogen gradient transmitted through nuclei divisions. J. Kadonaga presented an analysis of the diversity of core promoter motifs, and suggested that this diversity plays a role in gene-specific modes of transcription and regulation. The binding of the RNA polymerase II to the core promoter is a rate-limiting step of transcription activation. X. Darzacq presented a set-up developed in this lab allowing to video-track transcription and transcription factors in living cells. This experimental system informs on the properties of transcription, the kinetics of RNA polymerase clustering and movement, that together describes the very dynamic behavior of this essential molecule.

2. Organization of gene regulatory sequences

Using different approaches on different model systems, F. Spitz, E. Furlong, G. Cavalli exposed how the genome is organized in space. F. Spitz showed the extent to which regulatory sequences acting on a particular gene are broadly distributed along mouse chromosomes, forming complex regulatory landscapes. These functional domains seem to overlap with physical domains of chromosomal organization. A related observation was presented by G. Cavalli who studies 3-dimensional folding and functional organization of the Drosophila genome in relation with epigenetic contexts. These presentations suggest that chromosomal domains reflect genomic and functional compartmentalization that impact gene regulation and function. Focusing on multiple, functionally-defined regulatory sequences involved in mesoderm formation in the fly embryo, E. Furlong exposed how these sequences integrate transcription factor inputs, how chromatin marks are changed in response to these inputs, and how regulatory sequences make short and long range contacts. A. Stathopoulos further showed how distinct regulatory sequences can compete over time to contact the promoter and activate gene expression and how this complex temporal dynamic is functionally relevant for the Drosophila mesoderm development.

3. Evolution of gene regulatory sequences

A. Pavlopoulos explained how changes in transcriptional regulation were involved in hindwing reduction during Dipteran evolution. To illustrate how transcriptional regulation evolves, A. Johnson presented multiple cases of gene regulatory rewiring involved in yeast metabolism. B. Prud’homme discussed what a functional regulatory sequence is made of and how novel regulatory functions can evolve. M. Paris and P. Lemaire discussed how embryonic gene expression can be conserved, among Drosophila species or ascidian species, despite tremendous genomic divergence. Conversely, B. Deplancke illustrated the extant of gene expression variations caused by genomic variations that exist in natural populations of adult flies and human cell lines. These presentations led to the seemingly paradoxical conclusion that transcriptional regulation can be extremely robust to mutations, and yet is extremely plastic and contributes predominantly to phenotypic evolution.


Many technical progresses have been made recently that reveal unknown levels of regulation and organization. These insights are forcing us to reconsider our operational definition of what is a regulatory element, the classical definition appearing now too limited. This seminar, and in particular the confrontation of different perspectives on transcriptional regulation, has reinforced the notion that an understanding of transcriptional regulation will only stem from an integrated approach, encompassing structure, function and evolution.

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