Team
SnorDmiR
Team manager: Cavaille Jérôme
Our team is committed to advancing the understanding of antisense small non-coding RNAs, with a particular emphasis on two key families: small nucleolar RNAs of the C/D box family (SNORDs) and microRNAs (miRNAs). Both SNORDs and miRNAs are extensively characterized with respect to their structure, associated protein partners, and the molecular mechanisms through which they regulate gene expression. Briefly, these small regulatory RNAs function as antisense RNAs by forming base-pairing interactions with other cellular RNAs – mRNAs, rRNAs, tRNAs and U-snRNAs – thereby playing a critical role in the fine-tuning of post-transcriptional gene expression. SNORDs direct the site-specific modification of rRNAs, U-snRNAs, and tRNAs, primarily through 2′-O-ribose methylation and N4-acetylcytidine modifications. miRNAs regulate gene expression by inhibiting mRNA translation and/or promoting the degradation of target mRNAs
A major challenge in understanding miRNA function arises from their short and imperfect base-pairing interactions with mRNAs. This implies that a single miRNA can theoretically regulate dozens, if not hundreds, of different mRNAs. Conversely, a single mRNA may be targeted by multiple miRNAs. As a result, the vast number of potential combinatorial interactions makes it challenging to identify which miRNA-mRNA pairs are biologically significant, complicating efforts to fully understand the precise regulatory roles of miRNAs in gene expression. SNORD-directed 2’-O-methylations and N4-acetylcytidine modifications are believed to fine-tune the secondary and tertiary structures of rRNAs, U-snRNAs, or tRNAs, thereby influencing processes such as pre-mRNA splicing and mRNA translation. However, the functional impact of individual RNA modifications is often subtle, as the loss of a single modification typically does not result in overt phenotypic changes in multicellular organisms.
To explore the biological and evolutionary significance of SNORD- and miRNA-mediated regulation, we employ a multidisciplinary approach that integrates gene knockouts, genome-wide techniques based on next-generation sequencing, and comprehensive phenotypic analyses (encompassing physiology, behavior, and metabolism). This approach is applied across various model systems, including mice, cultured human cells, zebrafish, and Drosophila. We are particularly interested in studying atypical miRNAs and SNORDs whose gene expression is regulated by genomic imprinting, an epigenetic mechanism that results in monoallelic expression based on the parental origin of the alleles. In this context, our research specifically focuses on brain function and placentation.
Our ongoing investigations are organized into three primary research axes, which are outlined below:
Project 1
The chromatin domain on human chromosome 15q11-q13 (syntenic to mouse chromosome 7c) contains many neuronally expressed, paternally expressed SNORD genes, with most of them organized into two large repeated arrays: SNORD116 and SNORD115. Unlike other ubiquitously expressed SNORDs that display biallelic expression, the cellular RNA targets of these brain-specific SNORDs are still unknown in vivo. However, SNORD115 is believed to target the htr2c mRNA for 2’-O-methylation (alternative splicing and/or A-to-I RNA editing). Deficiencies in SNORDs, particularly the loss of the SNORD116 gene array, are believed to play a significant role in the pathophysiology of Prader-Willi syndrome (PWS), a rare genetic disorder characterized by hormonal and behavioral abnormalities, with hyperphagia being a notable feature. This uncontrolled appetite can lead to severe obesity and various related health complications. To investigate the regulatory functions of these SNORDs in brain function, we are utilizing three knockout mouse models: SNORD116-KO, SNORD115-KO and SNORD116/115-KO. Not only may a deeper understanding of these SNORDs unveil unexpected novel regulatory roles in neural process, but it may also provide valuable insights into the underlying mechanisms of PWS and help identify potential therapeutic targets for managing its symptoms.
Project 2
The Chromosome 19 MicroRNA Cluster (C19MC) represents a recent gene innovation found exclusively in primates. This cluster comprises an approximately 100 kb-long non-coding array of tandemly repeated, paternally expressed miRNA genes (n = 46), which are specifically and massively expressed in the placenta, contributing to 20-30% of the total miRNA population in this tissue. To better understand the function of the C19MC in placental cells, we are now developing a range of molecular and cellular approaches to identify the complete repertoire of mRNA targeted by C19MC-derived miRNAs. This research opens new avenues for exploring how recently evolved miRNA-mediated gene regulation may have influenced the development and functions of the placenta within the primate lineage.
Project 3
The highly conserved N4-acetylcytidine (ac4C) in helix 45 of 18S rRNA is directed by SNORD13 (formerly known as U13). SNORD13 establishes two imperfect base-pairing interactions near the target cytidine, which likely facilitates the recruitment of the N-acetyltransferase NAT10. This enzyme catalyzes the acetylation of cytidine, although the precise mechanisms involved in this process remain poorly understood. Surprisingly, our recent findings indicate that SNORD13-dependent ac4C is largely dispensable for human cell growth, ribosome biogenesis, global translation, and zebrafish development. Our ongoing research aims to elucidate how SNORD13 specifically targets helix 45 and to investigate the role of N4-acetylcytidine in shaping the structure and function of ribosomes, particularly under challenging conditions.
– Antisense pairing and SNORD13 structure guide RNA cytidine acetylation. Thalalla Gamage S, Bortolin-Cavaillé ML, Link C, Bryson K, Sas-Chen A, Schwartz S, Cavaillé J, Meier JL. RNA. 2022 Dec;28(12):1582-1596.
– Deleting Snord115 genes in mice remodels monoaminergic systems activity in the brain toward cortico-subcortical imbalances. Marty V, Butler JJ, Coutens B, Chargui O, Chagraoui A, Guiard BP, De Deurwaerdère P, Cavaillé J. Hum Mol Genet. 2023 Jan 6;32(2):244-261.
– The microRNA cluster C19MC confers differentiation potential into trophoblast lineages upon human pluripotent stem cells. Kobayashi N, Okae H, Hiura H, Kubota N, Kobayashi EH, Shibata S, Oike A, Hori T, Kikutake C, Hamada H, Kaji H, Suyama M, Bortolin-Cavaillé ML, Cavaillé J, Arima T. Nat Commun. 2022 Jun 2;13(1):3071.
– Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution. Bortolin-Cavaillé ML, Quillien A, Thalalla Gamage S, Thomas JM, Sas-Chen A, Sharma S, Plisson-Chastang C, Vandel L, Blader P, Lafontaine DLJ, Schwartz S, Meier JL, Cavaillé J. Nucleic Acids Res. 2022 Jun 24;50(11):6284-6299.
– Reassessment of the involvement of Snord115 in the serotonin 2c receptor pathway in a genetically relevant mouse model. Hebras J, Marty V, Personnaz J, Mercier P, Krogh N, Nielsen H, Aguirrebengoa M, Seitz H, Pradere JP, Guiard BP, Cavaille J. Elife. 2020 Oct 5;9:e60862.
– Developmental changes of rRNA ribose methylations in the mouse. Hebras J, Krogh N, Marty V, Nielsen H, Cavaillé J. RNA Biol. 2020 Jan;17(1):150-164.
Funding
Affiliation
