| | Category | CBIO | L09 | Measuring Expression for Novel Variations in Enhancers using |
| | STARR-seq Data |
| | Abstract | Enhancers, although not translated, help give rise to the variety of |
| | unique cell types discoverable throughout the body. Enhancers |
| | function through elevating transcription in both the forward and reverse |
| | orientations in conjunction with transcription factors. Single Nucleotide |
| | Polymorphisms (SNPs) have been statistically linked through Genome |
| | Wide Association Studies (GWAS) to Type 2 Diabetes (T2D), although |
| | the effect of other allelic differences surrounding such risk alleles has |
| | yet to be investigated. As such, data gathered from a modified STARR- |
| | seq assay will be used to determine the allelic effects of modifications |
| | around a known risk SNP within +/- 10 base pairs of the risk allele to |
| | better understand the specific differences in transcription caused by |
| | personal mutations around risk SNPs. Specifically, count data from the |
| | assay will be used to detect subtle differences in transcription by |
| | counting the number of transcripts generated by each enhancer within |
| | the input library. After initial QC, the creation of position weight matrices |
| | will help highlight the allelic binding preferences of transcription factors |
| | to improve the understanding of the significance of specific base pairs |
| | in TF binding. Further statistical analyses will then adjust the counts of |
| | transcripts to account for random variations and more accurately reflect |
| | the transcription levels induced by the enhancers. The project will |
| | advance understanding of genomic regulation by helping explore the |
| | binding preferences of transcription factors through the analysis of |
| | transcript count data and statistical association of transcription levels |
| | with allelic differences within the count data. |
| | Bibliography | Buenrostro, Jason D., et al. "Transposition of native chromatin for fast |
| | and sensitive epigenomic profiling of open chromatin, DNA-binding |
| | proteins and nucleosome position." Nature Methods, vol. 10, no. 12, |
| | 2013, doi:10.1038/nmeth.2770. Accessed 17 January 2017. |
| | Raj, Anil, and Graham McVicker. "The Genome Shows Its Sensitive |
| | Side." Nature Methods, vol. 11, no. 1, Jan. 2014, |
| | doi:10.1038/nmeth.2770. Accessed 17 January 2017. |