biology

JADE1

JADE1 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 JADE1 rather than just read about it. In short: JADE1 is a protein that in humans is encoded by the JADE1 gene. Family A small family of proteins named Gene for Apoptosis and Differentiation (JADE) includes three members encoded by individual genes: Plant Homeo-domain-17 (PHF17, JADE1), PHF16 (JADE3), and PHF15 (JADE2).

Key takeaways

JADE1 belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect JADE1 to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of JADE1 from memory before moving on to harder problems.

Reference excerpt

JADE1 is a protein that in humans is encoded by the JADE1 gene.

Family A small family of proteins named Gene for Apoptosis and Differentiation (JADE) includes three members encoded by individual genes: Plant Homeo-domain-17 (PHF17, JADE1), PHF16 (JADE3), and PHF15 (JADE2). All JADE family proteins bear two notable mid molecule domains: the canonical Plant Homeo-domain (PHD) zinc finger and extended PHD-like zinc finger. JADE1 therefore is classified as a member of the PHD protein family. There are two known protein products of the PHF17 gene, the full length JADE1 (JADE1L) and its splice variant missing the C-terminal fragment also called short isoform (JADE1S).

Discovery Nagase et al. cloned and sequenced 100 individual cDNAs from fetal brain cDNA library, including clone KIAA1807 which was designated PHF17. The predicted 702-amino acid protein product of that clone was similar to the human zinc finger protein BR140 (BRPF1). Based on sequence database analysis the study suggested that PHF17 may function in nucleic acid managing pathway. Using yeast two hybrid pull down approach to search for new partners of protein product of the Von Hippel Lindau gene (pVHL) another study identified cDNA which matched to KIAA1807 clone. The protein product of that cDNA was given name JADE1 (Jade-1, PHF17). The deduced 509 amino acid long protein product of JADE1 cDNA was further confirmed as physical partner of pVHL. In a genetic screen study searching for genes involved in embryogenesis, the mouse orthologue of JADE1 was identified. That study, provided first characterization of the JADE1 gene and defined novel JADE family. The study yielded mice with knock out of JADE1 gene. Jade1 transcripts in both humans and mice undergo alternative splicing and polyadenylation producing two major transcripts, the full length 6 kb mRNA and 3.6 kb mRNA. Two resultant protein products of the JADE1 gene were designated JADE1S for the short (which is same as(3)) and JADE1L for the long isoform. Several minor transcripts are also detected. The database analysis revealed two additional JADE1 paralogues and members of JADE family, JADE2, and JADE3. JADE3 is identical to E9 protein identified in an earlier independent study which suggested role in apoptosis for PHF16/JADE3/E9 in breast cancer cells. JADE1 has been mapped to chromosome 4 (4q26-q27). JADE1 is conserved and its orthologues have been found or predicted in most every metazoan. Gene structure and sequences, variants, conservation, orthologues and paralogs, JADE1 phylogenetic tree and large scale screening of JADE1 tissue expression can be found in several extensive databases (https://www.genecards.org; http://useast.ensembl.org).

Structure The full length JADE1 polypeptide bears one canonical and one extended PHD zinc finger domain. Other domains include the N-terminal candidate PEST domain, enhancer of polycomb-like domain and the C-terminal nuclear localization (NLS) signal (prosite.expasy.org). JADE1 protein is a target for post translational modifications, including phosphorylation (Fig 1 Six amino acid residues were identified to be phosphorylated in cell cycle-dependent manner via Aurora A kinase pathway. JADE1 is a target of phosphorylation by Casein kinase 2 (CK2). In addition, multiple phosphorylation sites are found by high throughput screening approaches and in silico analysis. Summary schematic for JADE1L and JADE1S protein phosphorylation sites with references is found in. Proteins bearing tandem canonical and extended PHD fingers form a small subfamily within the large PHD protein family (www.genenames.org). Other proteins bearing tandem of PHD fingers and related to JADE1 include proteins that are components of chromatin binding and modifying complexes BRPF1, BRPF3 and BRD1. The crystal structure of JADE1 PHD domains has not been solved. Canonical PHD finger motif has signature C4HC3, represents relatively small, stable structure, and is distinct from the C3HC4 type RING finger. PHD domains are able to recognize and bind specific methylated lysine of histone H3, which defines these domains as epigenetic histone code readers. Reviews describing structure and properties of PHD fingers in depth are available.

Cellular function JADE1 proteins are multifunctional and interact with several protein partners.

… excerpt ends here. Continue reading the full article.

Illustrations

Worked examples

Example 1 — a first encounter with JADE1

Start with the simplest possible case. Write down what JADE1 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 JADE1 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 JADE1 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 JADE1

In research: JADE1 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 JADE1 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: JADE1 is common in secondary-school and first-year university syllabi. It links to neighbouring topics Genes on human chromosome 4, Transcription factors, Wikipedia articles with corresponding academic peer reviewed articles, so understanding it makes those chapters shorter.
In everyday life: Look for JADE1 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 JADE1 in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what JADE1 means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain JADE1 out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is JADE1 in simple terms?

JADE1 is a protein that in humans is encoded by the JADE1 gene. Family A small family of proteins named Gene for Apoptosis and Differentiation (JADE) includes three members encoded by individual genes: Plant Homeo-domain-17 (PHF17, JADE1), PHF16 (JADE3), and PHF15 (JADE2).

Why does JADE1 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 JADE1?

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 JADE1.