Read section in the article titled “Footprints are quantitative markers of facto

Question

Read section in the article titled “Footprints are quantitative markers of factor occupancy” and answer the question below.   

Article URL: http://www.nature.com/nature/journal/v489/n7414/full/nature11212.html

Question:

NRF1 I a specific regulatory transcription factor. Briefly define NRF1 (use outside resources, not in this paper). Then, in looking at Figure 1c, we find “heat maps” that show some relative relationships. There were 4,262 instances of the sequence “motif” where NRF1 is known to bind DNA across the genome. These 80 bp sites were compared with DNase cut sites and ChIP-seq derived sequences from highly repeated sequencing across the genome. Recall ChIP-seq would give us the sequence of DNA actually bound by the NRF1 protein in this cell line at the time it was sampled. Answer: focusing on the top of the heat maps (where there was higher overlap of sequences obtained by ChIP-seq and footprints) what is observed about the DNase I cutting at each of the 80 bp in the motif and the degree of conservation at each bp across vertebrate animals?

** The section and figure can be found in the article url above**

Explanation / Answer

NRF1 is nuclear respiratory factor 1 and it also known as a transcription factor which acts on the regulation of gene expression related to growth, respiration, mitochondrial gene replication etc. In the article the 80 bp sites were compared with DNA footprinting assay which give the exact location of where the transcription factors bind in the DNA and the DNAse I digestion will digest only those DNA sequence which is not bound by Transcription factors. Footprint occupancy and nucleotide-level conservation correlation for 80% of all transcription factor motifs is shown in the assay.

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