"lncRNA-directed neural stem cell regulation in the developing and aging brain (2017-11-SHKUMATAVA)" project details

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Long noncoding RNAs, Neural stem cells, Regeneration, Zebrafish

lncRNA-directed neural stem cell regulation in the developing and aging brain

Director(s) and team

Alena Shkumatava

lincRNAs in Vertebrate Development


Description of the PhD thesis project
The human genome generates thousands of long noncoding RNAs (lncRNAs), which are RNA polymerase II transcripts longer than 200 nucleotides that do not encode proteins. Whereas some examples of well-studied lncRNAs indicate that they act as key regulators of important biological processes with their dysregulation being associated with several human diseases including cancers and neurological disorders, the function of the majority of lncRNAs remains enigmatic. To identify the in vivo functions of lncRNAs and, in particular, their potential role in brain development and neurogenesis, we use zebrafish. One of the distinguishing features of the zebrafish brain when compared to mammals is its widespread neurogenesis that is maintained at adult stages in several brain regions.

Neural stem cells (NSCs) have the capacity to generate neurons and glia in the intact and injured brain. Because the exhaustion of the NSC pool is associated with aging, defining the mechanisms underlying the survival, behaviour and the regenerative properties of NSCs is key to counteract neurodegeneration and premature aging of the brain. We recently discovered a lncRNA with implications in NSC integrity in zebrafish. We found that zebrafish mutants lacking this lncRNA have a significantly reduced number of NSCs in the embryonic and adult brain. We aim to identify how this lncRNA impacts NSC quantity in the brain and to determine its potential role during neural regeneration following mechanical brain injury. As the sequence of the lncRNA is conserved throughout vertebrate evolution, its biological function and the mechanism of action could be conserved to mammals and will be explored in this project.

Together, we will characterize the biological and molecular functions of a conserved lncRNA that impacts NSC number in the developing and adult brain. Importantly, our project has the potential to uncover a functional link between NSC number and the regenerative capacity of the brain.

International, interdisciplinary & intersectoral aspects of the project
The project proposed here is based on interdisciplinary approaches at the forefront of RNA biology, stem cell biology, regeneration and advanced biochemical methods. The student will develop specific skills in all mentioned above disciplines. In particular, the regenerative capacity of the injured brain will be tested by in vivo imaging that will be performed by the student at the Helmholtz Zentrum München, Germany. He/she will develop basic programming skills, which will be necessary to analyze the in vivo imaging data. In addition, the successful accomplishment of the project will require the development of advanced Crispr-Cas9-based genetic tools that will be done in collaboration with a biotech company based in Versailles, France.

Recent publications
1. Bitetti, A*, Mallory AC*, Carrieri C, Golini E, Carreño Gutierrez H, Perlas E, Pérez-Rico YA, Tocchini-Valentini GP, Enright AJ, Norton WHJ, Mandillo S, O’Carroll D, Shkumatava A. MicroRNA degradation by a conserved target RNA regulates animal behavior (in revision at Nat Struct & Mol Biol).
2. Davis MP, Carrieri C, Saini HK, van Dongen S, Leonardi T, Bussotti G, Monahan JM, Auchynnikava T, Bitetti A, Rappsilber J, Allshire RC, Shkumatava A, O'Carroll D, Enright AJ.
Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution.
EMBO Reports. 2017 Jul;18(7): 1231-1247.
3. Pérez Rico YA, Boeva V, Mallory AC, Bitetti A, Majello S, Barillot E, Shkumatava A. Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. Genome Research. 2017 Feb;27 (2):259-268.
4. Mallory AC, Shkumatava A.
LncRNAs in vertebrates: Advances and challenges.
Biochimie. 2015 Oct; 117:3-14.
5. Ulitsky I*, Shkumatava A*, Jan C, Sive H, Bartel DP (2011).
Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution.
Cell. 2011 Dec 23;147(7):1537-1550.
*denotes equally contributing authors

Requirements to apply for the PhD thesis project

Highly motivated students interested in regulatory noncoding RNA biology in an in vivo context are encouraged to apply. Successful candidates should have a strong background in one or more of the following areas: cell biology, developmental biology and/or stem cell biology. Background in bioinformatics is a plus but not compulsory. The project highly relies on confocal microscopy and live imaging techniques, for which the applicant should have either experience or a strong motivation to learn.