About the Project
The goal of the project is to understand transcriptional processes leading to neuro-developmental disorder known as Prader-Willi syndrome (PWS). In particular, to investigate how non-coding RNAs transcribed from the PWS locus control transcriptome of the human cell.
Deregulation of non-coding RNA (ncRNA) synthesis has been observed in many conditions including viral infections, cancer and autism [1-3]. One of the frequent genetic disorders directly associated with ncRNA is Prader-Willi syndrome (PWS). PWS patients display broad pathological spectrum including dysmorphic changes, behavioural problems and mild intellectual disabilities. In their early childhood, patients develop hyperphagia which leads to severe obesity. As PWS has a birth incidence rate of 1:10000 to 1:25000, it is the most common syndromal cause of life-threatening obesity in humans [4].
Prader-Willi syndrome results from the loss of the “PWS locus” from paternally inherited chromosome 15. The PWS locus contains several transcription units, including a noncoding region which hosts multiple genes encoding small nucleolar RNAs (snoRNA). Recent studies revealed that snoRNAs transcribed from the PWS region form unusual snoRNA -long ncRNA species (called sno-lncRNA and SPA lncRNA) which are associated with chromatin [5, 6]. Moreover, spliced exons of the host ncRNA also accumulate close to their transcription sites [7]. Current findings suggest that such chromatin-associated ncRNAs may act to maintain higher-order chromatin structure [2, 8]. Such three-dimensional organization of the chromatin plays crucial role in the regulation of gene expression [9]. Thus, the aim of this project is to employ a wide range of high-throughput analysis to investigate how ncRNAs transcribed from the PWS locus affect global transcription, chromatin organization and consequently, gene expression. Elucidating of molecular mechanisms of Prader-Willi syndrome will help to better understand roles for non-coding RNA in the development of the human body.
Experimental methods that will be undertaken during the project.
- Genome editing (CRISPR-cas9)
- High-throughput RNA analyses (4sU-seq, chrRNA-seq, and RNA-seq)
- Bioinformatics
- Chromosome conformation capture techniques (3C)
- RNA and protein visualization in situ (FISH, IF)
- Quantitative PCR
- Western blotting
- Standard molecular biology techniques (cloning, PCR, RT-PCR, etc.)
Person Specification
Applicants should have a strong background in molecular biology and hold or expect to obtain at least an Upper Second Class Honours Degree (or equivalent) in genetics/molecular biology/medicine or relevant field.
To apply please complete the application form at https://www.birmingham.ac.uk/schools/mds-graduate-school/scholarships/mrc-impact/index.aspx
References
1. Kwok, Z.H. and Y. Tay, Long noncoding RNAs: lincs between human health and disease. Biochem Soc Trans, 2017. 45(3): p. 805-812.
2. Rutkowski, A.J., et al., Widespread disruption of host transcription termination in HSV-1 infection. Nat Commun, 2015. 6: p. 7126.
3. Parikshak, N.N., et al., Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature, 2016. 540(7633): p. 423-427.
4. Angulo, M.A., M.G. Butler, and M.E. Cataletto, Prader-Willi syndrome: a review of clinical, genetic, and endocrine findings. J Endocrinol Invest, 2015. 38(12): p. 1249-63.
5. Yin, Q.F., et al., Long noncoding RNAs with snoRNA ends. Mol Cell, 2012. 48(2): p. 219-30.
6. Wu, H., et al., Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins. Mol Cell, 2016. 64(3): p. 534-548.
7. Vitali, P., et al., Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays. J Cell Sci, 2010. 123(Pt 1): p. 70-83.
8. Vilborg, A., et al., Widespread Inducible Transcription Downstream of Human Genes. Mol Cell, 2015. 59(3): p. 449-61.
9. Bonev, B. and G. Cavalli, Organization and function of the 3D genome. Nat Rev Genet, 2016. 17(12): p. 772.
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