Read beginning through the end of section in the article titled: \"Footprints ar

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Read beginning through the end of section in the article titled: "Footprints are quantitative markers of factor occupancy" Answer questions in your own words.

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

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Figure 1a:

Questions on transcription factor footprints paper is motif is a DNA sequence pattern in this context, in the case here a sequence pattern that characteristic for some transcription factor binding site. "Lexicon" basically means words of a language. In this case it would apply to the "language" used in human genome sequences to specify transcription factor binding sites. 6. (4 points) This paper looks at a method of determining transcription factor footprints by looking at areas within DNase I hyspersensitive sites that are actually not cut. So it is a small area of no cutting within a larger area where there is a lot of cutting by DNase L See Figure la What is this footprint of no cutting is representing compared to the overall DNase hypersensitive site? Think about nucleosomes, chromatin, DNA binding proteins like transcription factors, and what you have learned so far about DHSs. Describe in your own words.

Explanation / Answer

Dnase I cleaves the DNA at specific sites in the DNA causing breakage of the specific region from the DNA. Dnase I has the endonuclease activity. If the region of DNA protected by any factor then the DNA cannot be cleaved by DNase I . Here the DNA is protected by transcription factor and hence it cannot be cleaved ie the DNA is protected by the transcription factor binding to nucleosomes. These nucleosomes are flanking nucleosomes from the DNA which are present while remodelling the DNA as chromatin. Here in the promoter region of MTPN gene in Fig 1a. you can see no waves in a particular region . This region is were the DNA is bound by transcription factor . This is what it implies from the fig 1a.

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