Answer questions for the abstract

Optimization of DNase Hypersensitivity Site Detection Protocols for Genome-wide Mapping of Regulatory DNA Regions

ABSTRACT

Chromatin accessibility is closely associated with fundamental biological processes such as gene expression, replication, and genome organization. Chromatin regions that are actively involved in regulation of transcription assume an open confirmation, thus become hypersensitive to DNase I digestion. Using the recently developed massive parallel sequencing approach, it is possible to map DNase I hypersensitive sites (DHS) genome wide, allowing genome-wide assessment of regulatory regions. To study DHS in different tissues, cells or organisms, it is necessary to optimize the protocols for nucleus isolation, DNase digestion and DNA sequencing.

We are developing and optimizing protocols to be applied in the analysis of regulatory DNA elements in the chicken. Nuclei are isolated from liver and spleen tissue, digested with DNase I at various concentration and time. After digestion, DNA is isolated and examined by gel electrophoresis. DNase Hypersensitivity sites are validated by quantitative PCR assay. Optimized protocols will be applied in genome wide mapping of regulatory features in chickens.

From the Abstract Answer the following questions .

1. What unknown question is the scientist/author addressing or attempting to answer and or understand?

2. From reading the abstract, what do you propose the hypothesis to be?

3. What model was used?

4. Give at least one outcome or result of the study.

5. Name one experimental tool that was used to achieve the above outcome.

6. What is the importance of the study?

7. Does this study provide any broader impact for mankind? Why or why not?

8. What protein(s) or cell type is (are) the target(s) of this study? What other protein or cell type might be used to address the problem?