NFAT

Key takeaways

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

Reference excerpt

Nuclear factor of activated T-cells (NFAT) is a family of transcription factors shown to be important in immune response. One or more members of the NFAT family is expressed in most cells of the immune system. NFAT is also involved in the development of immune, cardiac, skeletal muscle, and nervous systems. NFAT was first discovered as an activator for the transcription of IL-2 in T cells (as a regulator of T cell immune response) but has since been found to play an important role in regulating many more body systems. NFAT transcription factors are involved in many normal body processes as well as in development of several diseases, such as inflammatory bowel diseases and several types of cancer. NFAT is also being investigated as a drug target for several different disorders.

Family members The NFAT transcription factor family consists of five members: NFATc1, NFATc2, NFATc3, NFATc4, and NFAT5. NFATc1 through NFATc4 are regulated by calcium signalling, and are known as the classical members of the NFAT family. NFAT5 is a more recently discovered member of the NFAT family that has special characteristics that differentiate it from other NFAT members. Calcium signalling is critical to activation of NFATc1-4 because calmodulin (CaM), a well-known calcium sensor protein, activates the serine/threonine phosphatase calcineurin (CN). Activated CN binds to its binding site located in the N-terminal regulatory domain of NFATc1-4 and rapidly dephosphorylates the serine-rich region (SRR) and SP-repeats which are also present in the N-terminus of the NFAT proteins. This dephosphorylation results in a conformational change that exposes a nuclear localization signal which promotes nuclear translocation. On the other hand, NFAT5 lacks a crucial part of the N-terminal regulatory domain which in the aforementioned group harbours the essential CN binding site. This makes NFAT5 activation completely independent of calcium signalling. It is, however, controlled by MAPK during osmotic stress. When a cell encounters a hypertonic environment NFAT5 is transported into the nucleus where it activates transcription of several osmoprotective genes. Therefore, it is expressed in the kidney medulla, skin and eyes but it can be also found in the thymus and activated lymphocytes.

Structure NFAT transcription factors consist of an intrinsically disordered regulatory N-terminus with the nuclear localization signal, serine-rich region and SP-repeats, a central Rel homology DNA-binding domain with an immunoglobulin-like fold that bind DNA either on its own or in a complex with transcription factor AP-1, and a C-terminal transactivation domain.

Signalling and binding

Canonical signalling Although phosphorylation and dephosphorylation are key for controlling NFAT function by masking and unmasking nuclear localization signals, as shown by the high number of phosphorylation sites in the NFAT regulatory domain, this dephosphorylation cannot occur without an influx of calcium ions. The classical signalling relies on activation of phospholipase C (PLC) through different receptors like the T-cell receptor (TCR) (PLCG1) or B-cell receptor (BCR) (PLCG2). This activation leads to release of inositol-1,4,5-triphosphate (IP3) and diacylglycerol (DAG). The IP3 is especially important for calcium influx because it binds to a IP3 receptor located in the membrane of the endoplasmic reticulum (ER). This causes a short sharp increase in calcium concentration in cytosol as the ions leave the ER through the IP3 receptor. However, this is not enough to activate NFAT signalling. The release of calcium ions from ER is sensed by STIM proteins which are ER transmembrane proteins. Under normal circumstances the STIM proteins bind calcium ions but if most of them are released from ER the bound ions are released from the STIM proteins as well. This causes them to oligomerize and subsequently interact with ORAI1 which is an indispensable protein of CRAC complex. This complex serves as a channel which selectively allows the influx of calcium ions from outside of a cell. This phenomenon is called store-operated calcium entry (SOCE). Only this longer inflow of calcium ions is capable of fully activating NFAT through the CaM/CN mediated dephosphorylation as stated above.

Alternative signalling Although SOCE is the main activation mechanism of most of the proteins of the NFAT family, they can also be activated by an alternative pathway. This pathway was until now proofed only for NFATc2. In this alternative activation SOCE is insignificant as shown by the fact that cyclosporine (CsA), which inhibits CN mediated dephosphorylation, does not abrogate this pathway. The reason for this is that it is activated through IL7R which leads to subsequent phosphorylation of single tyrosine in NFAT mediated by Jnk3 kinase a member of MAPK kinase subfamily.

DNA binding Nuclear import of NFAT and its subsequent export is dependent on the calcium level inside of a cell. If the calcium level drops, the exporting kinases in a nucleus such as PKA, CK1 or GSK-3β rephosphorylate NFAT. This causes that NFAT reverts into its inactive state and is exported back to the cytosol where maintenance kinases finish the rephosphorylation in order to keep it in the inactivated state. NFAT proteins have weak DNA-binding capacity. Therefore, to effectively bind DNA, NFAT proteins must cooperate with other nuclear resident transcription factors generically referred to as NFATn. This important feature of NFAT transcription factors enables integration and coincidence detection of calcium signals with other signalling pathways such as ras-MAPK or PKC. In addition, this signalling integration is involved in tissue-specific gene expression during development. A screen of ncRNA sequences identified in EST sequencing projects discovered a 'ncRNA repressor of the nuclear factor of activated T cells' called NRON. NFAT-dependent promoters and enhancers tend to have 3-5 NFAT binding sites which indicates that higher order synergistic interactions between relevant proteins in a cooperative complex is needed for effective transcription. The best known class of these complexes is composed of NFAT and AP-1 or other bZIP proteins. This NFAT:AP-1 complex binds to the conventional Rel-family proteins DNA binding sites and is involved in gene transcription in immune cells.

NFAT function in different cell types

… excerpt ends here. Continue reading the full article.

Worked examples

Example 1 — a first encounter with NFAT

Start with the simplest possible case. Write down what NFAT claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, 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 NFAT 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 NFAT 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 NFAT

In research: NFAT appears in science 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 NFAT 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: NFAT is common in secondary-school and first-year university syllabi. It links to neighbouring topics Immune system, Transcription factors, so understanding it makes those chapters shorter.
In everyday life: Look for NFAT 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.

How to study NFAT in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what NFAT 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 NFAT out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is NFAT in simple terms?

Nuclear factor of activated T-cells (NFAT) is a family of transcription factors shown to be important in immune response. One or more members of the NFAT family is expressed in most cells of the immune system.

Why does NFAT matter?

Because it connects several science 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 NFAT?

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 NFAT.