Question

Read the article (link is below) and answer the questions that follow in a paper format. (Paper has to be 1-page, 11-inch font- single-spaced). COPY THE BELOW LINK AND PASTE IN YOUR BROWSER.

https://www.sciencedirect.com/science/article/pii/S1097276513001329

Primary Paper HW assignment guidelines

Your primary paper consists of three parts:

1. In your own words, state the essential take home message of the paper assigned.

-Here you should briefly mention what was known about this topic before this paper was published

-Then state what the aim/goal/purpose of this published study was. In other words, what did the authors set out to do?

-Also describe why this research is important (if you think it is important)/ what are the researchers hoping to contribute to the existing knowledge.

2. State how the authors demonstrated the essential point of the paper: what experiments and what methods they used to prove the point

-In this section you should link how a particular approach/method was used to obtain a particular result and why it would be important/relevant. For example:

-Authors used method A to get/show result B. Result B is important because (it supports their original hypothesis in the following way/describe how/ or it provides novel findings regarding mechanism X

-Continue the bulleted list to correlate specific method with specific result and how it supports the claims made in the paper.

3. Discuss the strengths and significance of the paper and also the weaknesses and indicate additional lines of investigation that you think would be worth pursuing that were opened up by the paper.

-Here I want you to critique the experimental approach and author’s conclusions, not their writing style or format of the paper. Also, keep in mind that these are primary research articles published in scientific journals, so they are intended for a scientific, not general audience. Hence the language could be a bit dense.

-I want you to be very specific here. Do not write general and vague statements. Instead, refer to specific data in the paper (in figure X, or table Y) and indicate any possible flaws or limitations of the experiment.

-Propose possible future directions or follow up studies. You can look up papers that cited this research or follow up on the last author’s subsequent research.

-Explain if this paper contributed anything new to the field and if it enabled better understanding of the subject

Answer 1

1. In your own words……

• Earlier information about structure and function of eukaryotic genomes was known. All information related to linear maps of genomic information focusing on the regulation of DNA-dependent processes.
• But actual impact of structural arrangement of DNA on DNA-dependent processes was not known.
• The purpose/ aim of study was to determine the mechanisms by which the Isw2 chromatin remodeling enzyme is targeted to specific loci across the S. cerevisiae genome. To study mechanism for targeting a chromatin remodeling factor and identifies a physiological role for DNA looping.
• Importance of research: This research provides evidence suggesting that Ume6- dependent DNA looping mediates chromatin remodeling and transcriptional repression. It shows mechanism by which the 3D spatial organization of genomes affects chromatin structure and DNA-dependent processes on a genome-wide scale.

2. State how the authors demonstrated……

A total of 5,642 intergenic regions upstream of nondubious genes was used to determine the hypergeometric distribution of 1,020 intergenic regions upstream of genes with Isw2 enrichment at the 50 end and containing at least one annotated binding site for a particular TF. Isw2 and Ume6 ChIP-chip was performed using 3x-FLAG-tagged Isw2 or 3x-FLAG-tagged Ume6. It is important to use this method because partially the result of chromosomal duplications and/or deletions, as previously reported

Changes in Isw2 enrichment were measured using LIMMA. DNA loops were analyzed by a modified version of 3C. It is important because it can be done by using the restriction enzyme MspI

3. Discuss the strengths and significance…….

Significance of the paper is it gives detailed information about how TF-dependent recruitment plays the important role in Isw2 targeting through at least two distinct mechanisms as given in Figure 7. This paper contributed new thing to this field and enable better understanding of model which provides mechanism by which the three-dimensional folding of chromatin fiber affects DNA dependent processes.

Weakness is paper does not gave idea about unidentified mechanisms for Ume6-dependent targeting of Isw2 to these loci.

Possible future directions of research in this field are to find out other unidentified TFs may be involved in this process.