This repo contains code I have written to analyze hundreds of local repeats found in the human genome. Primarily, I am interested in understanding the role of local repeats in human lncRNAs.
Summary of the main findings so far (Updated - 7/25/15):
- In both the mouse and human genome, local repeats are significantly enriched in lncRNAs compared to mRNAs. There is only LR that is same in human and mouse.
- Local repeat rich lncRNAs (LR lncRNAs) are longer, have more isoforms, exons, tandem repeats and transposable elements compared to other lncRNAs.
- LR lncRNAs are similarly tissue and cell type specific, but more highly expressed and more highly correlated in expression to their neighbors compared to other lncRNAs and protein coding genes.
- LR lncRNAs are significantly more nuclear than other lncRNAs only in H1-hESC. In all other cell lines, they are as nuclear as other lncRNAs.
- Local repeats found in lncRNAs (LRs) are significantly enriched at TAD boundaries and there is weak evidence for their colacalization in 3D.
- There is a sharp increase in signal for chromatin marks - H3K4Me1, H3K4Me3 and H3K27Ac concurrently only in H1-hESC. For a few LRs, the ratio of H3K4Me1/H3K4Me3 is greater than 3 suggesting potential enhancer like roles.
- There is a sharp increase in conservation scores (phyloP) across LRs compared to the neighboring regions.
- LR elncRNAs have more 3D contacts than other lncRNAs and protein coding genes
- LR elncRNAs are more correlated with their neighbors but have a similar expression and specificity profile as protein coding genes and other lncRNAs
Future things to Do (Updated - 7/25/15):
- Distribution of exonic LRs in lncRNA transcripts. Are there lncRNA transcripts with only exonic LRs?
- For each category have a pony and or named lncRNA
- Check LR lncRNA distribution in Sheq's fractionation data.
- What is the average distance form neighbor for LR vs non LR?
A lot of the scripts written here are built on the following publicly available software:
- [Segemehl] (http://www.bioinf.uni-leipzig.de/Software/segemehl/)
- [TopHat] (https://ccb.jhu.edu/software/tophat/index.shtml)
- [Cufflinks] (https://github.com/cole-trapnell-lab/cufflinks)
- [MUMmer] (http://mummer.sourceforge.net/)
- [DeepTools] (https://github.com/fidelram/deepTools)
- [RepeatScout] (http://bix.ucsd.edu/repeatscout/)
- [Jellyfish] (https://github.com/gmarcais/Jellyfish)
- [RepeatMasker] (http://www.repeatmasker.org/)
- [HyperBrowser] (https://hyperbrowser.uio.no/hb/)
- [GNU Parallel] (https://www.gnu.org/software/parallel/)
- [BedTools] (https://github.com/arq5x/bedtools2)
- [The Meme Suite] (http://meme-suite.org/index.html)