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

Question

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

Article:

Article contd:

Question:

Figure 1a:

DNase I cleavage patterns using empirically derived intrinsic DNA position, and is expected to provide a quantitative measure of factor cleavage propensities for DNase I showed that only a miniscule frac- occu pancy .To examine this relationship for a well-studied sequence- tion (0.24%) of discovered 1% FDR footprints from cell and tissue specific regulator (NRF1: ref. 12), we plotted DNase I cleavage pat samples could be caused by inherent DNase I sequence specificity terns surrounding all 4,262 NRF1 motifs contained within DHSs and (Supplementary Methods. ranked these by FOS. Whereas only a subset of these motif instances DNase I footprints were distributed throughout the genome, indud- (2351) coincided with high-confidence footprints, the vast majority (45.7%), introns (37.7%,upstream of transcrip- of NRFI motif instances ing intergenic regions in DNase l footprints (899% overlapped tional start sites (TSSs, 8.9%), and in 5' and 3' untranslated regions reproducible sites ofNRFI occupancy identified by chromatinimmu Fig.2a, b. DNase I (UTRs, 1.4% and 1.3%, respectively Supplementary noprecipitation followed by high-throughput sequencing (ChlP-seq) footprints were enriched in promoters (.6-fold, P

Explanation / Answer

DHSs or DNase I hypersensitivity sites are are some particular regions of chromatin that are sensitive to cleavage by the enzyme DNase I. These sites raise the probability of degradation of DNA by enzymes such as DNase I. This state is necessary for the binding if transcription factors and thus, these are functionally related to transcriptional activity. These areas are areas of chromatin and are specific to each cell type . These are also found in transcrptional start sites .

The foot printing of the transcription factors suggested that even within these hypersensitivity sites, the DNase I cleavage is not uniforms and there are sequence specific regulatory factors where the cutting of these fragments is not allowed. They identified short stretches of genomic sequence compartments, that encoded for the conserved recognition sequence of DNA binding proteins . These no cut regions present within the hypersensitivity regions are sheltered from methylation by DNA and certain allelic chromatin states remain conserved and concentrated within these regions. This also hints for a nucleotide level evolutionary conservation , which gives a basis for evolution also suggesting that the human genome structure had always had certain recognition motifs and transcription factors and these had always been imprinted in the human genome thus , conserved evolution.

Related Questions

Navigate

• Browse (All)
• Browse R
• Subjects

---

---

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.