Talk:Microsatellite

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Can someone add links to the Wiki article on "Satellite DNA" in the "Structure" section? Unfortunately I don't know how to do it. — Preceding unsigned comment added by Richard.F.Fowler (talk • contribs) 20:07, 15 December 2017 (UTC)

Phrasing issue

Says main mechanism for elongation of microsatellite sequences is replication slippage caused by mismatch between DNA strands while "being replicated in mitosis". DNA replication does not occur during mitosis, it occurs during inter-phase (specifically S phase). Am I missing something...?

- - my answer to you is that (as far as I understand) it means the whole cell cycle of the 4 stages, that result in two cells, here he gives the name of the part to the total just like when you say: yesterday was the day I met my friend, probably you did lot of other things but that part is interesting enough to call the whole day after it.

— Preceding unsigned comment added by 128.84.124.234 (talk) 20:57, 17 November 2013 (UTC) 

Developing this article

Ive had a bit of an overhaul... I am aware that I still need to sort out references. Hope to do this within the ext few days, unless someone can help! SEJohnston 00:42, 29 April 2006 (UTC)

The article is very vague,there is no mention of how you construct an enriched microsatellite library,i had listed the entire process in the previous edit with specific references for isolation. The standard definition of microsatellites and the classification system has been totally neglected. If you need to edit this page please do so in a manner so as to enable users to gain insight into a specific topic.

It seems to be less vague than when you last edited it. Can you help improve the article? David D. (Talk) 18:38, 19 May 2006 (UTC)

The article isnt as comprehensive as I have wished it to be, but I do intend to do a lot more work on it... also, there is nothing stopping you from contributing. What are specific parts of the article you feel need to be changed or improved? Criticism is encouraged. Let me know what you want to see added, and I can give it a good try. Hopefully now that my exams and holiday is over, I can really get stuck into it. SEJohnston 12:01, 21 May 2006 (UTC)

Thanks for asking for desired additions. What role(s) to microsatellites play in the organism — what good are they to the creature? Do microsatellites occur within coding regions (within genes) or within the promoter regions of genes or within exons? Or are they Junk DNA?

They're "Junk DNA" in the sense that they don't code for anything. I'm not sure about the benefits of satellite DNA. Perhaps because they easily expand the genome they offer possibilities on the formation of beneficial sequences.128.163.224.198 19:13, 27 July 2007 (UTC)

Satellite DNA says that microsatellites are repeats less than 15 basepairs long, but this says they are 1-4 basepairs in length. Which is correct? Also, that article says that " Microsatellites are often found in transcription units." What does that mean? Thanks again, David.Throop 21:06, 12 December 2006 (UTC)

In another book it says that microsatellites are 2-5 bps, just to let you know.128.163.224.198 19:14, 27 July 2007 (UTC)

I've generally heard 2-10bp, with a minisatellite being 10-100or200. A SNP is generally a 1bp polymorphism. —Preceding unsigned comment added by Mkayatta (talk • contribs) 14:04, 2 November 2007 (UTC)

It seems strange to open the Introduction with One rare example of a microsatellite is... Shouldn't the introduction provide general information? 87.112.90.98 (talk) 23:55, 12 October 2008 (UTC)

Should this article really link to the "polymorphism" article if that one talks about phenotypic polymorphism? From that article: "The term is also used somewhat differently by molecular biologists to describe certain point mutations in the genotype, such as SNPs (see also RFLPs). This usage is not discussed in this article." —Preceding unsigned comment added by 148.85.208.36 (talk) 20:38, 29 June 2009 (UTC)

I just added the section on evolutionary impact, as part of a class project for a class in evolutionary biology, here at Cornell. It's turning out that repetitive DNA is far from being junk! My guess is that most of it will turn out to be useful genetic data, just parsed differently. BTW is there an easy way to convert a list of references to the standard Wiki format? Dennismk (talk) 18:12, 6 November 2009 (UTC)

Difference with short tandem repeat?

I can't see the difference between "microsatellite" and "short tandem repeat" (STR). I would appreciate if anybody wrote it. A good way would include adding "short tandem repeat" somewhere in the neat assortment on Repeated sequence (DNA). Thank you. Mortsggah 16:38, 6 April 2007 (UTC)

They are basically the same thing.

Well, then I'll propose a merge between the articles. Mortsggah 14:24, 17 April 2007 (UTC)

Yes, they should be merged. According to the book I'm reading (Molecular Evolution: A Phylogenetic Approach) the two things are one and the same.128.163.224.198 19:17, 27 July 2007 (UTC)

In agreement here, SSRs (microsatellites) and STRs are in essence the same thing and could be covered under the same Wiki topic, both are co-dominant in nature and have similar functionality12.210.165.57 03:46, 8 August 2007 (UTC)Matt

Sounds like a fine idea to me! Coming from a forensic science background, we never call them minisats which is why I never even thought to look if there was such an article already in existence. But it's just another way to say the same thing, so a merge definitely makes sense. Sekiyu 04:22, 22 August 2007 (UTC)

Specifically, a microsatellite (as opposed to minisatellite) is a repetition of 1 to 6 nucleotides. The term short tandem repeat seems more vague. I think you guys should just remove the short tandem repeat article and move its contents to the microsatellite article. Genericforms 20:08, 19 September 2007 (UTC)

i was told that SSRs (micro-satellites) are a 1-5 nucleotide repeat structure, STRs are 5-10, and VNTRs are 10-100. obviously there is a bit of overlap in there, but they are definitely different in their frequency throughout the different genomes. larger repeats (STR and VNTR) seem to be used more heavily in human research, while the smaller repeats (SSRs) are used extensively in plant research. Dave C. —Preceding unsigned comment added by 69.233.131.125 (talk) 07:11, 2 October 2007 (UTC)

SSRs are not exactly microsatellite; actually they are composed of two types micrsatellite (1-5 kbp long, they are composed of 20-50 tandem repeat units and are found in centromere and telomeres) and minisatellites (can be up to 600 bp and are composed of tandem repeat units that are typically 1-4 bp in lenth). Minisatellites are sometimes found in transcriptional units. —Preceding unsigned comment added by TAKEN00 (talk • contribs) 22:54, 11 December 2007 (UTC)

It sounds like the concepts are very related. They belong in the same article; separate articles would either be confusing, or would repeat a lot of text to explain the difference; also it can be expected that their significance and methods of detection would overlap a lot. I support the idea to merge the articles and clearly explain the difference between the concepts in the various forms they are used in the literature. -Pgan002 (talk) 14:07, 24 February 2011 (UTC)

Co-dominance?

excuse me, why are you stating in this article that micro-satellites, SSRs etc. are co-dominant. Do they effect the phenotype in any way? Aren't they strongly evolving parts of the "junk"-DNA and thus can't have any real effect on the phenotype (unless they are randomly inserted within promotors, exons, TF-binding sites etc. -- what would be part of a transposon article). I may be wrong, but if you stat that fact, why don't you put in a reference to proof it?

-- my answer to you (as far as I understand) is that you just supposed something that is not correct, these repeats are not "junk", they are otherwise merely "REPEAT" regardless of where are they found, this means that they can exist in coding or non-coding areas .... in both cases they are just have the feature of being "a repeat"

—Preceding unsigned comment added by 134.95.83.94 (talk) 17:58, 18 April 2010 (UTC) 

Merge Discussion First

Discussions on merging between STR and microsatellites held at two places, Talk:Microsatellite(HERE) and Talk:Short tandem repeat. So we should merge discussions at first :) Also, we should discuss based on literatures, since there seems wide variety of what is microsatellite and what is STR. I have already picked up some literatures at Talk:Short tandem repeat. Please check it out.--Mzaki 06:19, 12 October 2007 (UTC)

Figures would be nice

and would make this easier to understand. 77.96.89.50 (talk) 14:34, 12 July 2010 (UTC)

Merge or make distinction clear

My reading of this talk page and of Talk:Short tandem repeat convinces me that the merger under discussion since at least 2007 should be undertaken by members of the wikiprojects interested in the topic. But if I am wrong, if the merger is really a bad idea, the articles should be changed to clarify the difference between the two topics and the template suggesting the merger should be removed. I have marked the article as needing attention for that reason. I would work on the article myself but I don't have the background to contribute effectively. 67.100.127.75 (talk) 04:06, 27 June 2011 (UTC)

Move?

The following discussion is an archived discussion of the proposal. Please do not modify it. Subsequent comments should be made in a new section on the talk page. No further edits should be made to this section.

The result of the proposal was move. Apparently the primary topic.Cúchullain ^t/c 14:31, 2 July 2012 (UTC)

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Microsatellite (genetics) → Microsatellite –

• Dab page only has two entries so they can be sorted quite easily by hatnotes (hatnote is already pesent on Microsatellite (genetics) article). The other topic is under a different name so this topic is the most logical to move. Relisted. Jenks24 (talk) 11:13, 22 June 2012 (UTC) AIRcorn (talk) 13:15, 14 June 2012 (UTC)
• Oppose I think it should redirect to the space satellite article, and not the genetics article. Microsats (space satellites) seem to be more prominent among regular people than the genetics concept. 70.24.251.208 (talk) 05:28, 15 June 2012 (UTC)

Maybe, although the stats seem to suggest that more people are looking for the genetic concept. Genetic page views vs Satellite page views. AIRcorn (talk) 06:23, 15 June 2012 (UTC)

In fact more people go to the DAB page [1] than the Miniaturized_satellite one. AIRcorn (talk) 06:32, 15 June 2012 (UTC)

Most of the Google News hits are for the space satellite concept, and not the genetics concept [2]. If you use the abbreviated form "microsat", all of the Gnews hits [3] are for the space satellite. 70.24.251.208 (talk) 03:44, 16 June 2012 (UTC)

Changed the microsat redirect to miniaturized satellites. Many of those Gnews hits use micro-satellite or micro satellite spellings and refer to the recent transit of venus. I have never heard the genetics concept referred to in those forms so it is probably safe to redirect them there to miniaturized satellites too. Searching for microsatellite in quotes and from the archive shows a different story [4], although many of them link to nature and other journals. AIRcorn (talk) 13:08, 16 June 2012 (UTC)

• Oppose. Just because the other article is titled under a different name doesn't make it any less notable. Both concepts are equally notable, so the current arrangement should be retained. --W. D. Graham 07:05, 15 June 2012 (UTC)

Notability has nothing to do with this. One being the WP:Primary Topic does however. The page stats give a pretty strong indication that most people are looking for the genetics term. A Google search [5] gives just seven mentions of the space satellites out of the first 50 hits. Google scholar is also convincing Microsatellite plus genetics vs microsatellite plus space (two of the instances in the first page refer to genetic microsatellite). Dictionary definitions mention [6][7][8][9] the genetic term and not the space satellite. Incoming links favors the Genetics version as well. I probably should have made a better argument when I first started, but this seemed like a pretty straight forward move (hence the technical request). AIRcorn (talk) 08:27, 15 June 2012 (UTC)

• Oppose. Classic case of needing a two-way DAB at the undisambiguated name. Andrewa (talk) 09:21, 22 June 2012 (UTC)

• Support per WP:TWODABS; IMO, the bar for primary topic can be lowered when there are only two options, especially so when only one of the articles is actually at the title in question. Powers ^T 17:44, 22 June 2012 (UTC)
  • Comment: Interesting thought, and it seems to indicate that lowering the bar is necessary in this case. And of course WP:TWODABS doesn't currently support doing this; Should it? No change of vote, for now at least. Andrewa (talk) 18:31, 22 June 2012 (UTC)

I am not even sure the bar really needs to be lowered that much. It can be difficult to show that an article is the clear Primary Topic, which is why there are such big arguments with some articles, but most of the evidence I have found suggests it is the genetics term (Google, page views, definitions). However, as the space term does get a reasonable number of mentions it might not meet some editors definition of being primary enough. From a readers point of view, if they were looking for the space satellite they would need to click twice whether it was a DAB page or a hatnote on the genetics page. Those looking for the genetics term would only have to enter the name. Going through a DAB page is a small inconvenience, but in this case it is one that happens about 180 times each day. AIRcorn (talk) 21:01, 22 June 2012 (UTC)

But if we are all unsure which is primary, or want the bar lowered, isn't this then exactly the case for which a two-way DAB is intended? Or do you think we should do away with two-way DABs althogether? That's what your argument suggests to me. Andrewa (talk) 23:25, 22 June 2012 (UTC)

I'm not a fan of two-way DABs. Sometimes they're necessary. Here, where only one of the articles actually uses the title being debated? I see no reason for one. Powers ^T 19:05, 23 June 2012 (UTC)

I am not unsure which is primary. In my opinion, and looking at the Ghits, page views etc, the genetics one is definatly primary. However, I have been here long enough to know that another reasonable editor can disagree with me. They usually provide evidence, but so far only the IP has made a case against the genetic microsatellites being Primary. AIRcorn (talk) 23:10, 23 June 2012 (UTC)

• Strong support for moving this article from Microsatellite (genetics) to Microsatellite, per obvious primary (even to this layman) and WP:TWODABS. Ask yourself: is a hatnote even needed at miniaturized satellite? Plainly, no (unless someone forced microsatellite to redirect there). --→gab 24dot grab← 16:44, 29 June 2012 (UTC)
• Support, per WP:PRIMARYTOPIC. stats.grok.se:

Microsatellite_(genetics) has been viewed 33948 times in the last 90 days.

Miniaturized_satellite has been viewed 8351 times in the last 90 days.

Might as well save some collective clicks by putting the evidently primary topic at the name. ENeville (talk) 18:59, 30 June 2012 (UTC)

The above discussion is preserved as an archive of the proposal. Please do not modify it. Subsequent comments should be made in a new section on this talk page. No further edits should be made to this section.

"Microsatellites are also known to be causative agents in human disease, especially neurodegenerative disorders and cancer." -This sentence is fundamentally wrong, in the part mentioning cancer. Microsatellite instability is only a consequence of faulty mismatch-repair machinery, which have other consequences leading to cancer, such as accelerated mutations in other genes. It should be modified accordingly. — Preceding unsigned comment added by 94.189.128.112 (talk) 22:43, 2 January 2013 (UTC)

Unreferenced section on arrays

The following subsection from the main article contains no citations, despite a request, dating from April 2012, to provide citations. Once the citations have been supplied, this section may be returned to the main article:

Global Microsatellite Content with microarrays

Using a CGH-style array manufactured by Nimblgen/Roche the entire microsatellite content of a genome can be measured quickly, inexpensively and en masse. It is important to note that this approach does not evaluate the genotype of any particular locus, but instead sums the contributions for a given repeated motif from the many positions in which that motif exists across the genome. This array evaluates all 1- to 6- mer repeats (and their cyclic permutations and complement). This approach has been used to place any species, sequenced or not, onto a taxonomic tree. That tree matched precisely the currently accepted phylogenic relationships. With this new platform technology it is possible to study the genomic variations within an individual for those genomic features that are most variable, microsatellites.

Using this global microsatellite content array approach, studies indicate that there are major new genomic destabilization mechanisms that globally modify microsatellites, thus potentially altering very large numbers of genes. These global scale variations in both the tumor and germline patient samples may have important roles in the cancer process, of potential value in diagnosis, prognosis and therapy judgments . This Global Microsatellite Content array revealed that for the cancers studied, especially breast cancer, that there were elevated amounts of AT rich motifs. Pursuit of these AT rich motifs identified an AAAG motif that was variable in region immediately upstream of the start site of the Estrogen Related Receptor Gamma gene, a gene that had previously been implicated in breast cancer and tamoxifen resistance. This locus was found to be a promoter for the gene. A long allele was found to be approximately 3 times more prevalent in breast cancer patients (germline) than in cancer-free patients (p<0.01) and thus may be a risk marker.

I conclude

Summary according to how I understood that:

micro-S.(=microsatellite) are 2-5 units repeated 5-50 times .... the cut point of 5 pairs makes the telomere a mini-S. in human but micro-S. in some others.

now the repeat can get variable: (from mini-S. article) this can be via transcriptase slippage in mitosis or crossover in meiosis (here) he added transcriptase slippage in meiosis which make sense cause meiosis have two steps and replication also occur (2nd stage of meiosis continue just like ordinary cell division)

(variation can be in the length of repeat)

---

the repeat can be in non-coding area (help in mapping) , or in the following areas:

1- in the exons (coding) : In mammals, 20% to 40% of proteins contain repeating amino acids, e.g. on length change:

- the Runx2 gene lead to differences in facial length in domesticated dogs

- Length changes in polyalanine tracts within the HoxA13 gene are linked to Hand-Foot-Genital Syndrome

- more than 40 neurological diseases in humans.

- evolutionary change to surface proteins in pathenogenic bacteria (to become resistant)

- triplet expansion diseases such as fragile X syndrome and Huntington's disease.

2- in regulatory region: examples are:

-Length changes affect fimbriae formation in Haemophilus influenza

- in the control regions of the Vasopressin 1a receptor gene in voles influence their social behavior, and level of monogamy.

3- in introns (they are "skipped" part of the gene, but surprisingly also have an effect "mechanism unknown") .... examples are:

- GAA triplet expansion in the first intron of the X25 gene appears to interfere with transcription, and causes Friedreich Ataxia.[26]

- Tandem repeats in the first intron of the Asparagine synthetase gene are linked to acute lymphoblastic leukaemia.[27]

- A repeat polymorphism in the fourth intron of the NOS3 gene is linked to hypertension in a Tunisian population.[28]

- Reduced repeat lengths in the EGFR gene are linked with osteosarcomas.

4- in transposon: regulation of gene expression.

---

PCR make the DNA much enough to be visible by electrophoresis, PCR need a primer

primers matching the repeat used for the "inter-repeat" part PCR, while

primers matching the inter-repeat will be used for repeat PCR

- so one produces primers for the other. -

(we can start make primer for one and use it to produce primers of the other by PCR)

(note he called the part between repeats: inter-simple sequence repeat=issr)

---

making a primer:

- if we are searching in a specific region: look by eye or software (repeat masker) to find repeat, now look at flanking DNA and make a primer.

- random segments:((I think that DNA is huge a lot so that if we don't know where to look then it will be not practical to do sequencing, so our first mission to find small segment where we sequence DNA))

DNA random segments inserted into plasmid or bacteriophage then transferred to E-coli, ((my idea is that: now he should disperse these bacteria largely upon culturing so that each bacteria that make a colony will be one bacteria that received one type of DNA segment))
fluorescently–labelled oligonucleotide used to search these colonies to see which colony harbor the DNA segment that have the desired repeat.

now we sequence this segment and make a primer matching flanking DNA.

alternative method: use oligonucleotide probe to hybridizes with the repeat in the microsatellite, and the probe/microsatellite complex is then pulled out of solution. continue as normal ((sequencing and choosing flanking DNA I guess))

(he discussed a primer that match flanking DNA for "repeat-PCR", by common sense: same principle used for issr primers the only difference is that "after sequencing" choose the repeat areas around the issr)

Diversity of DNA: - the repeat is highest variable: used for individual identification (by few number of repeats) - issr : less variable: used in DNA fingerprinting but for phylogeography analyses or maybe delimiting species; (not individual identification) - gene sequence : least variable.

Limitation: - mutation -> primer not bind -> "null allele" -> false homozygot. solution: use different set of primers.

- if we apply PCR primers across different species the null alleles become likely, they can be indicated by an excessive frequency of homozygotes causing deviations from Hardy-Weinberg equilibrium expectations. ((I don't know what is this equation))

- in tumours: microsatellites may be gained or lost rapidly, so tumour cell line might show a different genetic fingerprint from that of the host tissue. so in cancer research they assess loss of heterozygosity. ((I can understand that not all tumours behave like that, and it should make some importance, otherwise we would be proving the same fact: tumour getting different fingerprint))

---

in forensic:

- identifying an individual made by profiles of 13 core micro-S loci, or 10 plus sex marker(British SGM+ system).

- Y-STRs (microsatellites on the Y chromosome) are often used in genealogical DNA testing. ((I recall anthropology relied a lot on Y chromosome in their conclusions about ancestries & how human populations migrated)) — Preceding unsigned comment added by Yasir muhammed ali (talk • contribs) 16:16, 27 March 2016 (UTC)

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