User:Jiayingcai/sandbox

DNA Methylation Article Evaluation

All of the information presented in this article seemed relevant to the article topic. It covered methylation in mammals, plants, fungi, insects, bacteria, as well as lower eukaryotes. In a neutral tone, it discussed how DNA methylation worked in suppressing gene transcription as well as how it worked in suppressing many other components in the DNA. There were no information that distracted me in any way.

Certain subtopics seemed to be up-to-date with the current findings in the scientific community as of 2017, whereas some date as far back as 2000, although no sources were from the 1990's There was no citation for the leading paragraph which stated the "big idea" for this topic. However, there were citations after each paragraph after the first one. The citations lead to links that worked and checked out as legitimate sources. Most of the sources for this topic came from scientific journals, and some came from websites that references other scientific journals.

In the Talk page of the article, there were no warning banners which is always a good sign. This article is apart of two projects. It is rated as a B-class in WikiProject Genetics and a Start-class in WikiProject Molecular and Cell biology. Although there is not much discussion, an important discussion topic was brought up regarding the need for more visual aids in the article. For an article that is considered B-class, it is definitely expected that this article should contain more visual aids. A total of 5 were seen and most subtopics did not have a visual aid, which would be "uninteresting" for some readers. There was a tag in 2008 stating that the page is to technical for most readers but has since then been removed. However I feel that the page is still too technical for the general public who may be interested in finding out more about the topic.

This topic is more extensively discussed in this article compared to the way we have talked about it in class. We have learned so far the role DNA methylation plays in suppressing gene transcription but its many other functions have not yet been explored. In both cases, a neutral tone was used to convey the information to the public and students.

Potential Articles

1. TATA Box - https://en.wikipedia.org/wiki/TATA_box
2. XXXY Syndrome - https://en.wikipedia.org/wiki/XXXY_syndrome
3. Geneticist - https://en.wikipedia.org/wiki/Geneticist

Looks good. Keep it up! AdamCF87 (talk) 15:24, 17 October 2017 (UTC)

Brainstorming for TATA Box Wikiproject for Bio3595A

• Info box
• Lead section
• Add: Genes containing TATA are correlated with high levels of transcription activation (cite: Characterization of TATA containing genes and TATA-less genes in S. cerevisiae…)
• Gene
• Add: TATA box is found in the core promoters of genes that code for the actin cytoskeleton and contractile apparatus in cells 
• In housekeeping genes, TATA is less conserved (second mode of TBP binding) (PMID 25789498)
• The type of core promoter affects level of transcription and expression
• SAGA recruitment of TBP vs.TFIID recruitment of TBP
• SAGA is a general cofactor for RNA pol II transcription (PMID 28918903)
• SAGA promoter/TATA box together are more highly regulated and display higher expression than promotors using TFIID and TBP mode of recruitment (cite: TFIID or not TFIID, a continuing transcriptional SAGA)
• Species, tissues, sub cellular distribution
• Add: The TATA box in metazoans is located 3-bp upstream of the TSS 
• Bound by the TATA-binding protein subunit of the TFIID complex (all above cite: Core promoter-specific gene regulation: ….)
• 20% of yeast genes have TATA elements
• TATA containing genes are subtelomeric, expressed at extremely high or low levels, and also stress induced (PMID 25451177)
• Function
• Add: Gene transcription by RNA polymerase II depends on the core promoter which contains sequences such as the TATA box
• The core promoter is regulated by long-range regulatory elements (e.g. enhancers, silencers) as well as promoter proximal elements
• Without proper regulation of transcription, euk organisms would not be able to properly respond to their environment--> all above cite Core promoter-specific gene regulation: TATA box selectivity and Initiator-dependent bi-directionality of serum response factor-activated transcription
• What correlates to the TATA box:
• Stress-response  functions for cellular defense
• Highly variable expression patterns between species (cite: Characterization of TATA-containing genes and TATA-less genes in S. cerevisiae…)
• Interactions
• Add: Interactions with a variety of activators or repressors can influence transcription
• Enhancers (Core promoter-specific gene regulation: TATA box selectivity and Initiator-dependent bi-directionality of serum response factor-activated transcription)
• Rearrange the information in "role in transcription initiation"
• Have a step by step "mechanism" section for transcription involving the TATA box
• Clinical significance
• Tech:
• Core promoter-specific mechanisms for transcription initiation by the canonical TBP/TFIID-dependent basal transcription machinery have remained poorly documented in vivo
• Recent studies have been done to demonstrate in vivo activation by the SRF-dependent UAS  of the human ACTB gene involved in TATA-binding
• Recent reports of a TATA box-selective activating sequence ( all info above cite: Core promoter-specific gene regulation: …..)
• Genetic engineering:
• Adaptation of apple trees to iron deficiency by inserting a TATA box in the promoter upstream the Iron-regulated transporter 1 (IRT1) gene
• Plants have an iron deficiency due to the development of Earth's aerobic atmosphere
• The insertion of the TATA box enhances expression by increasing promoter activity
• Increase in TFIID activity
• Increased iron uptake (all above cite: TATA box insertion provide a selected mechanism…)
• Disease:
• Gastric cancer w/ TATA box polymorphism (cite: INTERFERENCE OF PG2 TATA BOX REGION WITH THE SERUM PG2 LEVEL IN GASTRIC CANCER)
• PG2 gene produces PGII serum
• PGII level is used as a marker for tumors in gastric cancer
• TATA box has a binding site for the transcription factor for the PG2 gene
• Results: Found that longer TATA box sequences does correlate with a higher level of sPG2, which is indicative of gastric cancer conditions; while carriers with shorter TATA box may produce lower sPG2 levels
• Neurodegenerative disorders such as
• Spinocerebellar ataxia - Expansion of the polyglutamine repeat in the TBP, Accumulation of these polyglutamine-TBP cells, Shown by protein aggregates of TBP in brain sections in patients, Loss of neurons
• Huntington's disease - Protein aggregates also formed that contain TBP (all above cite: microRNA dysregulation in polyglutamine toxicity of TATA-box binding protein….) 
• Blindness due to cataract formation
• MicroRNAs target 3'UTR and bind to TATA box to regulate oxidative stress genes
• When bound to TATA box, miRNAs act to active transcription
• Increase in levels of pro-oxidative genes can lead increased cataract formation (all above cite: MiRNAs regulate oxidative stress related genes via binding to the 3′ UTR and TATA-box regions…..)
• SNPs in TATA boxes are associated with B-thalassemia, immunosuppression, and neurological disorders
• The rate at which TBP will associate with the TATA box significantly decreases in the presence of SNPs
• SNPs destabilize the TBP/TATA complex, which leads to lower levels of transcription
• Has been confirmed in vitro but results sufficient to display the interactions similar to that in vivo
• At a molecular level, the rate at which TBP binds to TATA affects the severity of diseases (all above PMID 24616209)
• Gilbert's syndrome
• UTG1A1 TATA box polymorphism is a molecular model
• Risk factor for developing jaundice in newborns (all above PMID 23981182)
• HIV-1
• miRNAs play a role in replicating viruses such as HIV-1
• Novel HIV-1-encoded miRNA enhances the production of the virus and activates HIV-1 latency by targeting the TATA box (cite PMID 24620741)
• History