Talk:Primary transcript

Slj758 (talk) 19:56, 7 October 2013 (UTC). Kohw 19:59, 7 October 2013 (UTC)

Summary Version

An outline of a more complete rendition of this page could look as follows. First, by way of introduction, a definition of what the primary transcript is, supported by a picture and comments about its fundamental RNA characteristics and sequence details will be necessary. Second, it will be important to describe how the primary transcript is made, with attention given to the process of transcription and the various factors that effect production of primary transcripts (DNA template, RNA polymerase, transcription factors, etc.). Again, diagrams and visualizations to aid the reader in understanding the mechanism of primary transcript production would be helpful. Third, an emphasis on how the primary transcript is processed into mRNA. This would involve describing the fundamental differences between the primary transcript and mRNA transcripts, as well as the necessary splicing required to process the primary transcript. Fourth, a description of the regulatory factors contributing to activation and/or inhibition of primary transcript processing and production. Fifth, it would be informative to include a section on diseases that might result from mis-coded, erroneous primary transcripts. Fifth, there will be a section on experiments done regarding primary transcript (for example, it will include experiments on the factors affecting the formation of the primary transcript). Details and information of the experiments will be provided by the sources/bibliography we listed before.

Slj758 (talk) 21:05, 17 October 2013 (UTC). Kohw 23:53, 18 October 2013 (UTC)

Initial Bibliography

Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997. Available from: http://www.ncbi.nlm.nih.gov/books/NBK19441/

Griffiths AJF, Gelbart WM, Miller JH, et al. Modern Genetic Analysis. New York: W. H. Freeman; 1999. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21310/

Griffiths AJF, Miller JH, Suzuki DT, et al. An Introduction to Genetic Analysis. 7th edition. New York: W. H. Freeman; 2000. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21853/

Strachan T, Read AP. Human Molecular Genetics. 2nd edition. New York: Wiley-Liss; 1999. Available from: http://www.ncbi.nlm.nih.gov/books/NBK7585/

To be continued...

Slj758 (talk) 01:02, 11 October 2013 (UTC)

I am considering developing this page further as part of an educational assignment in Fall of 2013. If someone else is also working on this, please send me a message and let me know soon, so we donʼt duplicate initial efforts in page development. Kohw 09:58, 6 October 2013 (UTC) — Preceding unsigned comment added by Kohw (talk • contribs)

Possible suggestion to the article

This article only gives information that precursor mRNA as primary transcript becomes mRNA. This article may have many repetitive information with the other wikipedia article on precursor mRNA. However, this article could be improved to give better understanding in primary transcript. First of all, more information on how primary transcript is produced should be added (the process of transcription leading to production of primary transcript). It would help readers to understand the process better if visual of the steps is provided! In addition, informations on how regulations on transcription can affect the production of primary transcript through transcription. Such details may include silencer's job on repressing transcription of a particular gene, the job of transcription factors, and etc. Then, a light explanation on how primary transcript becomes mature mRNA through RNA processing could be added to give insight of a bigger picture. The information above are provided in many web pages and texts. The text Developmental Biology, 10th edition by Scott F. Gilbert provides a clear and detailed explanation on the topics above. Kohw 03:37, 7 October 2013 (UTC) — Preceding unsigned comment added by Kohw (talk • contribs)

Additional Bibliography

Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. RNA Processing and Turnover. Available from: http://www.ncbi.nlm.nih.gov/books/NBK9864/)

Will CL, Dolnick BJ. 5-Fluorouracil inhibits dihydrofolate reductase precursor mRNA processing and/or nuclear mRNA stability in methotrexate-resistant KB cells. J Biol Chem. 1989 Dec 15;264(35):21413-21. PMID 2592384

Ferro P, Forlani A, Muselli M, Pfeffer U. Alternative splicing of the human estrogen receptor alpha primary transcript: mechanisms of exon skipping. Int J Mol Med. 2003 Sep;12(3):355-63. PMID 12883652

Darnell JE Jr. Reflections on the history of pre-mRNA processing and highlights of current knowledge: a unified picture. RNA. 2013 Apr;19(4):443-60. doi: 10.1261/rna.038596.113. Epub 2013 Feb 25. Review. PMID 23440351; PMC 3677254

Poss ZC, Ebmeier CC, Taatjes DJ. The Mediator complex and transcription regulation. Crit Rev Biochem Mol Biol. 2013 Oct 3. [Epub ahead of print] PMID 24088064. — Preceding unsigned comment added by Kohw (talk • contribs) 23:42, 14 October 2013 (UTC)

More Additional Bibliography

Mattick, J.S. (2004). The Hidden Genetic Program of Complex Organism, Scientific American.

Alberts B, Bray D, Lewis J, et al. Molecular Biology of the Cell. 3rd edition. New York: Garland Science; 1994. RNA Synthesis and RNA Processing. Available from: http://www.ncbi.nlm.nih.gov/books/NBK28319/

hnRNA size and processing as related to different DNA content in two dipterans: Drosophila and Aedes. Lengyel J, Penman S. Cell. 1975 Jul;5(3):281-90. PMID 807333 [PubMed - indexed for MEDLINE]

Prespliceosomal Assembly on Microinjected Precursor mRNA Takes Place in Nuclear Speckles Ivo Melčák, Štěpánka Melčáková, Vojtěch Kopsky, Jaromíra Večeřová, Ivan Raška Mol Biol Cell. 2001 February; 12(2): 393–406. PMC 30951

E9P2 (talk) 03:32, 15 October 2013 (UTC)

Developmental Biology group additions (11/15/13)

This page contained virtually no information on primary transcripts before our group took up the task to expand the article. One of us added the sections "Production of the Primary Transcript" and "Regulation of Primary Transcript Production" along with the figures depicting the processes described in both sections. These sections include multiple wikilinks to alternative, related material on wikipedia and citations for books and web sources alike. Slj758 (talk) 22:15, 14 November 2013 (UTC)

One of us included sections that were about experiments performed centered around primary transcripts, as well as specific diseases that stem from it, either by changes to it or the processing of it. Also, a picture of what a primary transcript actually looks like. E9P2 (talk) 04:05, 16 November 2013 (UTC)

One of us included sections that were centered on different modifications that primary transcripts go through after production such as RNA processing. Also, initial few sentences on introducing primary transcripts were added and initial pictures were added. Kohw 04:08, 16 November 2013 (UTC) — Preceding unsigned comment added by Kohw (talk • contribs)

Peer Review

• Introduction
  • “Based on the needs of a given cell, certain DNA sequences are transcribed to produce a variety of RNA products to be translated into functional proteins for cellular use.” --- Perhaps you could delve a bit as to what specific needs would target the production the certain DNA sequences
• Production of the Primary Transcript
  • “One strand of this DNA template to be used for transcription of the single-stranded primary transcript mRNA is then bound by an RNA polymerase at the promoter region of the DNA – The syntax of this sentence takes away from the meaning the writer is trying to convey. Are you trying to say that one strand of the DNA template is used for transcription during which mRNA and bound by an RNA polymerase, etc.? If so, it would be best to word it as such.
  • RNA polymerase II should be linked
  • “RNA polymerase II of eukaryotes transcribes the primary transcript mRNA from the antisense DNA template in the 5' to 3' direction, and the newly synthesized mRNA is complimentary to this antisense strand of DNA (see Figure)”. --- Complimentary should be complementary. Remove "see figure"
  • “RNA polymerase II constructs the primary transcript using a set of four specific ribonucleoside monophosphate residues (AMP, CMP, GMP, and UMP) ….” -- Ribonucleoside should be hyperlinked; include the meanings for the acronyms AMP, CMP, etc.
  • “Inclusion of the exon and intron RNA sequences within primary transcripts explains the size disparity between larger primary transcripts and smaller, modified mRNA ready for translation into protein.” – remove the italicized “and”; consider starting the sentence with “the”
• Regulation of Primary Transcript Production
  • Add\skip a line between “A number of factors contribute ...” and the bolded “activation”
  • It’s good that enhancers, transcription factors and nucleosomes are mentioned because they are key aspects to the process of transcription; however, I think it’s noteworthy to mention their significance in transcription or what they are; what key roles do they play or what actually happens to the nucleosome when they function together? What is an enhancer? Etc. This portion needs a bit more tweaking in terms of content.
  • Consider linking transcription elongation complex
• Primary Transcript and RNA Processing
  • “However, this step involved in the production of primary transcripts is only the first step that should be followed by many modifications and processing to yield functional forms of RNAs.” – this could use some rewording; perhaps, “This step should only be followed by …”
• Processing of Primary Transcripts
  • “On the other hand, precursor mRNAs (mRNA primary transcripts) of eukaryotic cells undergo wide range of modifications prior to their transport from nucleus to cytoplasm of the cell.” -- consider using another transition phase other than “On the other hand, …” since it was used in a sentence or two above this one
• 5’ Capping
  • Consider linking GTP, G residue
• Polyadenylation
  • Consider removing “ the reaction called” and changing the sentence to “In eukaryotes, polyadenylation …”
  • Consider linking pre-mRNA
• Alternative Splicing
  • Do not capitalize linked words; example, “Alternative splicing takes place in a large protein complex of Spliceosome. “ --- spliceosome should not be capitalized
• Experiments Involving Primary Transcripts
  • “For example, one article by Cindy L. Wills and Bruce J. Dolnick from the Department of Experimental Therapeutics at the Roswell Park Memorial Institute in Buffalo, New York and from the Cell and Molecular Biology Program at University of Wisconsin in Madison, Wisconsin….” This entire part is unnecessary; just create a citation and go straight into discussing the study done; this same idea applies for the other two studies discussed below this.
  • “The experiment explained whether 5-Fluorouracil inhibits dihydrofolate reductase precursor mRNA processing and or nuclear mRNA stability in methotrexate-resistant KB cells.” – yes, but delve into why it’s relevant to primary transcripts explicitly
  • Link and write out what hnRNA is
  • Link dipterans
  • What is an hnRNA and its correlation to a primary transcript??
  • “Ivo Melcak, Stepanka Melcakova, Vojtech Kopsky, Jaromıra Vecerova and Ivan Raska from the department of Cell Biology at the Institute of Experimental Medicine, at the Academy of Sciences of Czech Republic in Prague studied the influences of nuclear speckles on pre-cursor mRNA.” --- create a citation for this; don’t just list out the authors and those involved; look at the first comment I made about citations in the first bullet
  • Link splicing factors
  • “ We conclude that the (pre)spliceosomal complexes on microinjected pre-mRNA are formed inside the speckles.” – who is we? The wiki authors, those involved in the study, etc.??
  • If you would like to keep the experiment section, do not go over procedures included in the studies, “…microinjection of splicing competent and mutant adenovirus pre-mRNAs with differential splicing factor binding, which form different…”
  • I don’t think the experiment section is necessary unless you tie the experiments to how they are specifically relevant to primary transcripts. I feel that this section gets quite a bit muddy in terms of its focus. What is the main goal that are you trying to get across to readers with this section?
• Related Diseases Involving Primary Transcripts
  • “The article describing the procedure was entitled, "Alternative splicing of the human estrogen receptor alpha primary transcript: mechanisms of exon skipping" by Paola Ferro, Alessandra Forlani, Marco Muselli and Ulrich Pfeffer from the laboratory of Molecular Oncology at National Cancer Research Institute in Genova, Italy. “ --- remove this! Create a citation
  • Keep this, “It explained that 1785 nucleotides of the coding region of the estrogen receptor alpha (ER-alpha) are dispersed over a region of more than 300,000 nucleotides in the primary transcript. “ --- Instead, just go straight to the main point and leave out “It explained”
  • Have “Splicing of this precursor RNA …” be its own paragraph

Overall: This is good as a very basic wiki article, however, I think you should include more information as to what triggers the formation of primary transcripts and where exactly the process takes place. This information should probably be included in the beginning summary of the article whereas the information about triggers should be scattered throughout the article in their respective places. For example, you mention that there are several factors that contribute to the activation and transcription but never actually delve into what these factors are in terms of their effects on primary transcripts. You need to flesh out the article more with details. At times the structure of your sentences or certain phrases can seem redundant or somewhat difficult to grasp. Try to keep your article to the point, use the K.I.S.S. principle! Keep working on improving the article as a whole. Remember, citations are your friends. Good luck! Mbeez (talk) —Preceding undated comment added 18:18, 22 November 2013 (UTC)

Another Review

The article has a wealth of great information regarding not only the primary transcript, but other elements that it is involved with. However, much of the grammar needs to be tightened and polished. Also, some of the information presented is either misleading or bogged down in bad grammar. Consider linking more of your words as there are many things which should be linked. Below are various edits which may be considered:

• Introduction
  • Overall grammar check should be done.
  • "A primary transcript is the single-stranded RNA product synthesized by transcription of DNA, and processed in many ways to yield various functional RNAs such as mRNAs, tRNAs, and rRNAs to be used in translation" - your opening sentence is misleading. There are many primary transcripts, including rRNA and tRNA, that are never translated.
    • The sentence needs overall work. Consider breaking it into two sentences as the and is combining two unrelated thoughts.
  • You make want to consider merging precursor mRNA into your article.
  • You refer to the primary transcript being in the cell's nucleus. This is incorrect as bacteria also have primary transcript which undergo processing such as alternative splicing.
  • "Of all of these, alternative splicing is the factor that directly contributes to the diversity of mRNA found in cells" - I would consider removing this sentence. It is misleading.
• Production of the Primary Transcript
  • Again, nucleus and translation usage must be watched.
  • There should be a link to the main transcription page as most of this material is covered. i.e put Main Article : Transcription at the top of the section.
  • "RNA polymerase II of eukaryotes transcribes the primary transcript mRNA from the antisense DNA template in the 5' to 3' direction, and the newly synthesized mRNA is complimentary to this antisense strand of DNA (see Figure)." is extremely confusing. "primary transcript mRNA" has no meaning. I believe you are trying to say "transcribes a transcript destined to be processed into an mRNA.
• Regulation of primary transcript production
  • "Factors that lead to histone acetylation activate transcription while factors that lead to histone deacetylation inhibit transcription" is not necessarily true. Consider H3K4AC, which can repressive.
• Primary transcript and RNA processing
  • "For example, in bacteria, mRNAs serve as templates for synthesis of protein as they are being transcribed." is not necessarily correct. Also, it seems odd to have this here.
  • Again, these all have main pages that should be linked to.
• Experiments involving primary transcripts
  • "Several experiments have been performed to better understand what results stem from manipulation of the formation of different RNA from a primary transcript at several steps. For example, one article by Cindy L. Wills and Bruce J. Dolnick from the Department of Experimental Therapeutics at the Roswell Park Memorial Institute in Buffalo, New York and from the Cell and Molecular Biology Program at University of Wisconsin in Madison, Wisconsin was made to understand the procedure for it's experiment involving precursor mRNA" remove and get into the topic.
  • An overall rework of this section should be done. It feels as though your group is presenting papers rather than the topic. I would suggest an integration of the results into the main article.
• Related diseases involving primary transcripts
  • Cite your sources.

DSKireai (talk) 20:30, 22 November 2013 (UTC)

Peer Review

Overall your page has a really great flow. Each of the sections make sense and moves nicely into the next one, and the writing is both scientifically accurate and easy for everyone to understand at the same time. I think that the introduction is good in terms of the material that it contains, but there are sections where it could be written a little more concisely. It is important to include the information there, however you don’t want to have the introduction be too wordy when you are going to cover all that material again later. The first section is pretty well written, it explains the processes, but doesn’t go into too much detail, which if good because that topic has its own page. The only think I would say is that in the second paragraph on the production of the primary transcript section, the first sentence talks about the kinds of RNAs produced by different polymerases in prokaryotes and eukaryotes, but then you only go on to talk about eukaryotes. Maybe you could add information about the prokaryotes, or change it so that you aren’t talking about prokaryotes in the middle of talking about eukaryotes, because that could be a little confusing. The section about experiments involving primary transcripts was really interesting to read and I think that it was a great idea to add it, so that people can learn about how primary transcripts are used/studied in the lab, but it was a little dense and could be overwhelming for the layperson. There were lots of areas in the page where you guys could have linked out to other wikipedia pages, as I found myself wanting to click around in certain sections to make sure that I knew what was going on still and there were no links. The writing was well done, however there were areas, for example in the introduction, where the sentence structure was wordy, too fragmented, or redundant. Heykei1 (talk) 21:40, 8 December 2013 (UTC)

Merge proposal

Primary transcript and pre-mRNA are near-identical concepts. Given that primary transcript is the longer article, the stub should be merged in. However pre-mRNA is by far the more common term, so conceivably the final merged article should be hosted on that page? T.Shafee(Evo&Evo)^talk 10:57, 7 October 2016 (UTC)

  Y Merger complete. Klbrain (talk) 19:43, 1 July 2018 (UTC)