MSymond1 Week 12

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1. A list of biological terms from the paper I did not know the definitions for when I first read the article
   • transcription regulator activity: A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons. https://amigo.geneontology.org/amigo/term/GO:0140110
   • transcription cis-regulatory region binding: Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. https://amigo.geneontology.org/amigo/term/GO:0000976
   • respiratory electron transport chain: A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient. https://amigo.geneontology.org/amigo/term/GO:0022904
   • Lysis: The disintegration or rupture of the cell membrane, resulting in the release of cell contents or the subsequent death of the cell. https://www.biologyonline.com/dictionary/lysis
   • immunoprecipitate: the precipitate formed in an antigen‐antibody reaction. https://www.oxfordreference.com/display/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-9850?rskey=ZIIfXn&result=1
   • DNA ligation: The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase. https://amigo.geneontology.org/amigo/term/GO:0006266
   • Phylogeny: the scientific study of phylogeny. It studies evolutionary relationships among various groups of organisms based on evolutionary history, similarities, and differences. It makes use of molecular sequencing data (such as homologous sequences, protein sequences, nucleotide sequences, etc.) and morphological data matrices to understand and analyze the protein and gene evolutions of genetically-related groups of organisms https://www.biologyonline.com/dictionary/phylogenetics
   • PCR: A laboratory method used to make many copies of a specific piece of DNA from a sample that contains very tiny amounts of that DNA. PCR allows these pieces of DNA to be amplified so they can be detected. PCR may be used to look for certain changes in a gene or chromosome, which may help find and diagnose a genetic condition or a disease, such as cancer. It may also be used to look at pieces of the DNA of certain bacteria, viruses, or other microorganisms to help diagnose an infection. Also called polymerase chain reaction. https://www.cancer.gov/publications/dictionaries/cancer-terms/def/pcr
2. The main Findings of the paper are that the architecture of the promoter, meaning the arrangements of the DNA binding site, change depending on environmental conditions and can be predicted with confidence what the binding arrangement will be depending on the promoter and the environmental conditions.
3. The significance of these findings is the fact that they combine genome-wide location data with phylogenetic conservation data. Using both these types of data allowed to cluster all significant results from the genome wide data location based upon their conservation data.
4. The limitations of prior studies is the fact that it cannot be determined what the location is for the recognition sites of transcriptional regulators with phylogenetic sequence data alone, or with any other prior knowledge from any previous study. The fact that the sequences have been conserved through evolution indicates that they can be regulated, but does not reveal information about the binding process, or the conditions, or the architecture of such binding.
5. They treated the Yeast cells by using PCR and they printed about 6000 DNA fragments to represent nearly all regions in the yeast genome.
6. They used Saccharomyces cerevisiae yeast.
7. They grew them in microarrays with PCR products. The article does not specify temperature or time, in the supplementary methods section, it does list that the times varies for each of the conditions. it is as low as 20 minutes for certain conditions (namely the moderately hypertonic condition). And the time is as high as 14 hours (namely the filamentation inducing condition). It does not specify the temperature for most of the conditions, except for the elevated temperature condition in which it specifies that it begins at 30 degrees celsius and is shifted to 37 degrees celsius.
8. The controls group they used was an unenriched microarray to compare with the immunoprecipitated samples.
9. They ran each program 50 times on a randomly selected set of sequences.
10. The study conducted their genome wide location analysis by cross linking the proteins to the DNA, which then created precipitate which separated the DNA from the protein. These precipitates were then went through PCR procedures to hybridize them to a microarray of spotted PCR products, each representing a different location of the yeast genome. Such locations were used to compare the probabilities of binding interactions.
11. They used an Axon 200B scanner to scan the microarrays, they compared the immunoprecipitated sample with the unenriched sample. They found the median of each channel to calculate a normalization factor. They then calculated the log ratio of the intensity of the test channel to the control channel. The log ratios were normalized by subracting the average log ratio of every spot across all arrays. Finally, they calculated an error model by calculating the significance of enrichment on each chip, and combining the data for all replicates to calculate an average ratio and significance of enrichment for every region in the genome.
12. their supplementary tables are available to the public for download on nature.com and these tables have the results that they were able to calculate from their data, but their raw data and calculations are not to be found available to the public.
13. The list of figures from the article
    • Figure 1 has 2 parts, part a essentially states that the conclusions from this study, regarding the identification of transcription factor binding site specificities, could only be concluded when using the three kinds of data they have. They had their genome-wide location data, their phylogenetic sequence conservation data, and other previous work. Part b shows the sequence specificities of some of the regulators. There are 2 columns, one of the columns displays sequences that had already been discovered and were rediscovered with this study, and the other column shows sequences that were newly discovered by this study. Each of the letters in the sequence have a size proportional to the product of their frequency and their information content
    • Figure 2 has three parts, part a displays the different chromosomes, as well as certain genes located on said chromosomes with , it also shows the locations of certain DNA sequences that are bound by transcriptional regulators. They obtained this information by mapping on the yeast genome sequences the motifs that they found to be bound by regulators at high confidence that were also conserved. The functions of the specific transcriptional regulators had already been previously established. Part b of the figure combines binding data with sequence conservation data. This part of the graph is in 3 parts, the first shows all sequence matches to DNA binding specificities. The second part shows all of the sequence matches to conserved sequences, and the third part shows all sequences that match with conserved sequences that are bound by regulators. Part c of the figure is a graph that shows the frequency of binding sites in relation to the distance from translational start site on the DNA sequence. The x axis is the distance from translational start site, and the y axis is the number of binding sites.

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