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). I already did #1, please I need help with 2 & 3. The article is super confusing. COPY THE BELOW LINK AND PASTE IN YOUR BROWSER

https://www.researchgate.net/publication/50596700_A_long_noncoding_RNA_maintains_active_chromatin_to_coordinate_homeotic_gene_expression

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

2. Methods used by researchers

a. High throughput chromosome confirmation capture (5C) was used to study the spatial organization in a cell of a specific structure called chromatin .

b. siRNA knockdown experiments were performed to know the function of HOTTIP RNA

c. qPCR were performed to get the amplification of interested DNA at specific interval of time.

d. ChIP-chip was performed to know the interaction between protein and DNA

e. Single-molecule RNA-fluorescent in situ hybridization (FISH) was performed to know the quantification of HOTTIP RNA

f. RNA-immunoprecipitation with WDR5 used to see the interaction of HOTTIP RNA with protein of interest.

3. Strength of paper: The researchers are successfully HOTTIP(linc RNA), organizes the activation of 59 HOXA genes in vivo and HOTTIP RNA is required to activate 5’ HOXA genes.

Weakness of the paper: In figure 4, reserachers include some more and other acontrol (negative or positive) for inferring the interaction between RNA and protein.