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PRDM9

PRDM9 is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand PRDM9 rather than just read about it. In short: PR domain zinc finger protein 9 is a protein that in humans is encoded by the PRDM9 gene. PRDM9 is responsible for positioning recombination hotspots during meiosis by binding a DNA sequence motif encoded in its zinc finger domain.

PRDM9 — main illustration
PRDM9 — illustration

Key takeaways

  • PRDM9 belongs to biology; place it in that map before memorising details.
  • Learn the definition first, then one example that makes the definition concrete.
  • Connect PRDM9 to a quantity you can measure, compute or draw — that is where exam questions come from.
  • Reproduce the core statement of PRDM9 from memory before moving on to harder problems.

Reference excerpt

PR domain zinc finger protein 9 is a protein that in humans is encoded by the PRDM9 gene. PRDM9 is responsible for positioning recombination hotspots during meiosis by binding a DNA sequence motif encoded in its zinc finger domain. PRDM9 is the only speciation gene found so far in mammals, and is one of the fastest evolving genes in the genome.

Domain Architecture

PRDM9 has multiple domains including KRAB domain, SSXRD, PR/SET domain (H3K4 & H3K36 trimethyltransferase), and an array of C2H2 Zinc Finger domains (DNA binding).

History In 1974 Jiri Forejt and P. Ivanyi identified a locus which they named Hst1 which controlled hybrid sterility. In 1982 a haplotype was identified controlling recombination rate wm7, which would later be identified as PRDM9. In 1991 a protein binding to the minisatelite consensus sequence 5′-CCACCTGCCCACCTCT-3′ was detected and partially purified (named Msbp3 - minisatelite binding protein 3). This would later turn out to be the same PRDM9 protein independently identified later. In 2005 a gene was identified (named Meisetz) that is required for progression through meiotic prophase and has H3K4 methyltransferase activity. In 2009 Jiri Forejt and colleagues identified Hst1 as Meisetz/PRDM9 - the first and so far only speciation gene in mammals. Later in 2009 PRDM9 was identified as one of the fastest evolving genes in the genome. In 2010 three groups independently identified PRDM9 as controlling the positioning of recombination hotspots in humans and mice. in 2012 it was shown that almost all hotspots are positioned by PRDM9 and that in its absence hotspots form near promoters. In 2014 it was reported that the PRDM9 SET domain could also trimethylate H3K36 in vitro, which was confirmed in vivo in 2016. In 2016 it was shown that the hybrid sterility caused by PRDM9 can be reversed and that the sterility is caused by asymmetric double strand breaks.

Function in Recombination PRDM9 mediates the process of meiosis by directing the sites of homologous recombination. In humans and mice, recombination does not occur evenly throughout the genome but at particular sites along the chromosomes called recombination hotspots. Hotspots are regions of DNA about 1–2kb in length. There are approximately 30,000 to 50,000 hotspots within the human genome corresponding to one for every 50–100kb DNA on average. In humans, the average number of crossover recombination events per hotspot is one per 1,300 meioses, and the most extreme hotspot has a crossover frequency of one per 110 meioses. These hotspots are binding sites for the PRDM9 Zinc Finger array. Upon binding to DNA, PRDM9 catalyzes trimethylation of Histone 3 at lysine 4 and lysine 36. As a result, local nucleosomes are reorganized and through an unknown mechanism the recombination machinery is recruited to form double strand breaks.

Notes

References

Further reading

External links PRDM9+protein,+human at the U.S. National Library of Medicine Medical Subject Headings (MeSH) UCSC GenomeWiki - PRDM9: Meiosis and Recombination This article incorporates text from the United States National Library of Medicine, which is in the public domain.

Illustrations

PRDM9 illustration
PRDM9 illustration
PRDM9 illustration
PRDM9 illustration

Worked examples

Example 1 — a first encounter with PRDM9

Start with the simplest possible case. Write down what PRDM9 claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to PRDM9 before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about PRDM9 ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of PRDM9

In research
PRDM9 appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry
Engineering practice reuses PRDM9 in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom
PRDM9 is common in secondary-school and first-year university syllabi. It links to neighbouring topics Genes on human chromosome 5, Transcription factors, so understanding it makes those chapters shorter.
In everyday life
Look for PRDM9 outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.
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How to study PRDM9 in 20 minutes

  1. Read the reference excerpt below once, without taking notes.
  2. Close the page and write down what PRDM9 means in your own words.
  3. Compare your version with the excerpt and mark what you missed.
  4. Work through the three examples above with pen and paper.
  5. Explain PRDM9 out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is PRDM9 in simple terms?

PR domain zinc finger protein 9 is a protein that in humans is encoded by the PRDM9 gene. PRDM9 is responsible for positioning recombination hotspots during meiosis by binding a DNA sequence motif encoded in its zinc finger domain.

Why does PRDM9 matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study PRDM9?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on PRDM9.

Tags

  • Genes on human chromosome 5
  • Transcription factors

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