Transcription Regulation in Eukaryotes Molecular Biology

Exam 2

What is ENCODE?

encyclopedia of DNA Elements, a multi-laboratory international project to explore the structure and expression of the human genome. It has made use
of the total human genome sequence and sophisticated data analysis algorithms to probe transcriptional functional elements and their regulation in depth

What are the seven major classes of elements?

transcribed genes, their TSSs and promoters, two classes of predicted enhancers (strong and weak enhancers), CTCF-binding sites, and transcriptionally repressed regions

What does DHSs stand for?

DNase I hypersensitive sites

What do DHSs indicate?

open chromatin structures, correlate with TSSs, promoters, transcribed genes, enhancers

Are most DHSs empty or occupied by transcription factors (TFs)?

almost all DHSs are occupied by at least one TF, many by multiple at each site

Do open chromatin regions come first, followed by TFs binding?

No. In most cases,TFs binding induces open chromatin region

Are there two nucleosomes equally likely positioned flanking the nucleosome free region?

No, a nucleosome is either placed closely 5’ or 3’ to the TSS, but not equally on both sides