Question

The precise coordination of gene expression in humans is complex, and requires lots of events to ‘align’ to produce a protein from DNA sequence in the genome. Please answer all of the questions below, keeping answers brief and to the point (e.g., 3 lines or so per answer).

1. Describe what is required at the epigenetic level for gene expression, and give one example of a currently popular method we discussed to survey the epigenome (chromatin state) for evidence that a gene may be capable of being expressed.
2. To be expressed, most eukaryotic genes require not only RNA polymerase and other core transcription factors to bind to the promoter region, but also require the stabilization of activator proteins bound to enhancer sequences. Describe the 3D characteristics required for expression of a gene, and describe 2 methods we discussed that can provide information about these processes.
3. Even after transcription, in eukaryotes there are several steps required for an mRNA to be exported from the nucleus (so it can be translated into a protein). What are these steps? Describe a technique for using next-generation sequencing to estimate how many mature mRNA transcripts have been made (including how you have decided to make sure you will only sequence mature mRNA, and not other RNAs).  

Answer 1

1. Describe what is required at the epigenetic level for gene expression, and give one example of a currently popular method we discussed to survey the epigenome (chromatin state) for evidence that a gene may be capable of being expressed.

Answer: Epigenetic processes, including DNA methylation and histone modification, are thought to influence gene expression chiefly at the level of transcription. Chromatin state plays a major role in controlling gene expression, and comparative analysis of ChIP-seq data is key to understanding epigenetic regulation. We present chrome switch, an R/Bioconductor package to integrate epigenomic data in a defined window of interest to detect an overall switch in chromatin state.

2. To be expressed, most eukaryotic genes require not only RNA polymerase and other core transcription factors to bind to the promoter region but also require the stabilization of activator proteins bound to enhancer sequences. Describe the 3D characteristics required for expression of a gene, and describe 2 methods we discussed that can provide information about these processes.

as transcription factors preferentially bind to open chromatin, techniques that detect these regions, such as ATAC-seq or DNAse-seq