DS0401 - Etude des systèmes biologiques, de leur dynamique, des interactions et inter-conversions au niveau moléculaire

Principles of molecular recognition between Polycomb protein SCML2A and human long-non coding RNAs – lincRNPs

Submission summary

Polycomb repressive complexes 1 (PRC1) and 2 (PRC2) are evolutionary conserved regulators of embryogenesis and stem cell differentiation. They repress transcription by marking chromatin at key positions of target genes with chemical modifications, such as ubiquitination and methylation, respectively. The functions of PRC1 and PRC2 are regulated by long non-coding RNAs (lncRNAs), a vast class of RNAs longer than 200 nucleotides devoid of protein coding capacity and expressed in a time and tissue-specific manner through development. A prominent lncRNA that regulates PRC1 and PRC2 is HOTAIR, a 2200-nucleotide-long spliced and polyadenylated non-coding RNA. Via PRC1 and PRC2, HOTAIR represses transcription of homeotic genes in peripheral tissues of the body, thus regulating cell differentiation during epidermis maturation. In pathological conditions, HOTAIR promotes the development of cancers and metastases.
PRC1 and PRC2 associate to lncRNAs forming ribonucleoprotein complexes (lincRNPs), in which the RNA subunit allosterically modulates the enzymatic activity of the catalytic protein subunits. Such lincRNPs are thus key regulators of gene expression. However, molecular details on the interactions between Polycomb complexes and lncRNAs are poorly understood, partly because of lack of structural data.
In humans, a well-characterized Polycomb component that forms lincRNPs is SCML2A, a PRC1 subunit that interacts with various lncRNAs, including HOTAIR. SCML2A lincRNPs associate to specific sites on chromatin, particularly to genes that are also targeted by PRC2 and HOTAIR, like the HOXD8 gene and genes involved in neuronal differentiation and development. Therefore, SCML2A lincRNPs are at the center of an intricate and synergistic network of Polycomb-dependent gene silencing and not surprisingly they are implicated in various neurological disorders and cancers like medulloblastoma, a highly malignant brain tumor with high incidence in children.
SCML2A binds to lncRNAs via an RNA-binding region (RBR) of undetermined structure and such interaction enhances the PRC1 ubiquitination activity. Little is known so far about the molecular mechanism of SCML2A-lncRNA association, but remarkably and differently from other non-specific protein-lncRNA interactions, SCML2A-lncRNA interactions are tight and specific, which makes this lincRNP ideal for structural studies.
To shed light on the function of SCML2A-lncRNA complexes, in this work we will study the SCML2A- HOTAIR lincRNP and its association to PRC1 and chromatin. We will identify the minimal functional units of SCML2A, HOTAIR and PRC1 and we will determine their structures by multidisciplinary biophysical approaches, which include X-ray crystallography, nuclear magnetic resonance, electron microscopy and small angle X-ray and neutron scattering. Functional studies in vitro, in cells and in mice will complement the structural results and allow us to establish comprehensive structure-functional relationships. Specifically, our study will reveal how the different domains of SCML2A, PRC1 and HOTAIR communicate to exert their interrelated functions, including reciprocal recognition and reading and writing of histone marks. More broadly, our study will shed light onto a common and widespread paradigm that characterizes the association of Polycomb complexes and lncRNAs. Consequently, this project is of exceptional interest in the fields of structural biology, oncology, and medicinal chemistry, and it represents a much-needed pioneering study of lincRNP structures, many more of which are likely to be determined in the future.

Project coordination

Marco MARCIA (CNRS-UJF-EMBL International Unit (UMI 3265))

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


UVHCI-EMBL CNRS-UJF-EMBL International Unit (UMI 3265)

Help of the ANR 246,504 euros
Beginning and duration of the scientific project: September 2015 - 36 Months

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