Crown Project Notebooks

Open-source investigation into ribosomal DNA/RNA variation in humans

Manuscripts:

Loss of macpΨ ribosomal RNA modification is a major feature of cancer.

Intra- and Inter-individual Genetic Variation in Human Ribosomal RNAs.

HYPOTHESIS

rDNA is variable across loci/copies rDNA is mutable in cancer rDNA mutations will result in altered ribosomal function Mutated rDNA represent a potential gain/loss of function onco-ribosomes mechanism

Content

./Crown/wiki/Home.md: Index file for notebooks

./Crown/scripts/: Analysis scripts for Crown

Research Files

• PROTOCOL: amino-carboxyl-propyl Reverse Transcriptase (aRT)-PCR
• 100 Genomes (GVCF) (XLS)
• 100 Genomes hgr1-aligned BAM
• hgr1 reference sequence (fasta) (annotation)

Open Questions

These are some of the open questions regarding rDNA variation. If you think you can take one on then join the project and give it a stab. Open and unrestricted collaboration.

Population / Evo-Genetics

1. How many distinct human haplotypes are there of RNA45S and the rDNA repeat? What's the phasing?
2. How does the human rDNA variation compare to other organisms?
3. What is the mode of inheritence of rDNA variation?
4. How rapid is the process of homogenization? Can resistence to homogenization then be measured?
5. How can purifying / balancing selection be measured within rDNA?

Medical Genetics + Molecular Biology

1. Does a persons distinct set of ribosomal variants influence how their cells interpret the genome?
2. Are there rare variants or allelic imbalances in variants leading to ribosomopathy in humans?
3. Are similar variants localized to the same molecule (cis), the same chromosome (trans) or ad-mixed?
4. Is there tissue-specific expression of certain rRNA variants?

Structural Biochemistry

1. What's the biochemical consequence of 28S.A59G? 1b. Do the A and G alleles segregate between monosomes and polysomes?
2. What's the biochemical consequence of the other variants within mature rRNA?

Computational Biology / Bioinformatics

1. How many distinct human haplotypes are there of RNA45S and the rDNA repeat? What's the phasing?
2. Will a variant-aware aligner increase sensitivity for alignment and variant calling?
3. How can the internet be leveraged to share and collaborate on data and experiments?

Contact + Community

email: ababaian [AT] bccrc [DOT] ca