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A morphogen is a substance governing the pattern of tissue development in the process of morphogenesis, and the positions of the various specialized cell types within a tissue. More precisely, a morphogen is a signaling molecule that acts directly on cells to produce specific cellular responses depending on its local concentration.
Since morphogens diffuse through the tissues of an embryo during early development, concentration gradients are set up. These gradients drive the process of differentiation of unspecialised (stem) cells into different cell types, ultimately forming all the tissues and organs of the body.
Alan Turing, better known for his work in wartime cryptography and the theory of computing, wrote a famous paper, The chemical basis of morphogenesis, correctly predicting a chemical mechanism for pattern formation.
The concept of the morphogen has a long history in developmental biology, dating back to the work of the pioneering Drosophila geneticist, Thomas Hunt Morgan, in the early 20th century. Lewis Wolpert refined the morphogen concept in the 1960s with his famous French flag model, which described how morphogen could subdivide a tissue into domains of different target gene expression (corresponding to the colours of the French flag). This model was championed by the leading Drosophila biologist, Peter Lawrence. Christiane Nusslein-Volhard was the first to identify a morphogen, Bicoid, one of the transcription factors present in a gradient in the Drosophila syncitial embryo. She was awarded the 1995 Nobel Prize in Physiology and Medicine for her work explaining the morphogenic embryology of the common fruit fly. Research groups led by Gary Struhl and Stephen Cohen then demonstrated that a secreted signalling protein, Decapentaplegic (the Drosophila homologue of transforming growth factor beta), acted as a morphogen during the later stages of Drosophila development.
During early development, morphogen gradients result in the differentiation of specific cell types in a distinct spatial order. The morphogen provides spatial information by forming a concentration gradient that subdivides a field of cells by inducing or maintaining the expression of different target genes at distinct concentration thresholds. Thus, cells far from the source of the morphogen will receive low levels of morphogen and express only low-threshold target genes. In contrast, cells close to the source of morphogen will receive high levels of morphogen and will express both low- and high-threshold target genes. Distinct cell types emerge as a consequence of the different combination of target gene expression. In this way, the field of cells is subdivided into different types according to their position relative to the source of the morphogen. This is a general mechanism by which cell type diversity can be generated in animal development.
Some of the earliest and best-studied morphogens are transcription factors that diffuse within early Drosophila melanogaster (fruit fly) embryos. However, most morphogens are secreted proteins that signal between cells.
Genes and signals 
A morphogen spreads from a localized source and forms a concentration gradient across a developing tissue. In developmental biology, 'morphogen' is rigorously used to mean a signaling molecule that acts directly on cells (not through serial induction) to produce specific cellular responses dependent on morphogen concentration.
Well-known morphogens include: Decapentaplegic / Transforming growth factor beta, Hedgehog / Sonic Hedgehog, Wingless / Wnt, Epidermal growth factor, Fibroblast growth factor, and retinoic acid. Morphogens are defined conceptually, not chemically, so simple compounds such as retinoic acid (the active metabolite of retinol or vitamin A) may also act as morphogens.
Fruit fly 
Drosophila melanogaster has an unusual developmental system, in which the first thirteen cell divisions of the embryo occur within a syncytium prior to cellularization. Essentially the embryo remains a single cell with over 8000 nuclei evenly spaced near the membrane until the fourteenth cell division, when independent membranes furrow between the nuclei, separating them into independent cells. As a result, in fly embryos transcription factors such as Bicoid or Hunchback can act as morphogens because they can freely diffuse between nuclei to produce smooth gradients of concentration without relying on specialized intercellular signalling mechanisms. Although there is some evidence that homeobox transcription factors similar to these can pass directly through cell membranes, this mechanism is not believed to contribute greatly to morphogenesis in cellularized[clarification needed] systems.
In most developmental systems, such as human embryos or later Drosophila development, syncytia occur only rarely (such as in skeletal muscle), and morphogens are generally secreted signalling proteins. These proteins bind to the extracellular domains of transmembrane receptor proteins, which use an elaborate process of signal transduction to communicate the level of morphogen to the nucleus. The nuclear targets of signal transduction pathways are usually transcription factors, whose activity is regulated in a manner that reflects the level of morphogen received at the cell surface. Thus, secreted morphogens act to generate gradients of transcription factor activity just like those that are generated in the syncitial Drosophila embryo.
Discrete target genes respond to different thresholds of morphogen activity. The expression of target genes is controlled by segments of DNA called 'enhancers' to which transcription factors bind directly. Once bound, the transcription factor then stimulates or inhibits the transcription of the gene and thus controls the level of expression of the gene product (usually a protein). 'Low-threshold' target genes require only low levels of morphogen activity to be regulated and feature enhancers that contain many high-affinity binding sites for the transcription factor. 'High-threshold' target genes have relatively fewer binding sites or low-affinity binding sites that require much greater levels of transcription factor activity to be regulated.
Thus, the general mechanism by which morphogens subdivide tissues into patterns of distinct cell types is well understood. However, morphogens often have additional activities such as controlling the growth of the tissue or orienting the polarity of cells within it (for example, the hairs on your forearm point in one direction) which are much less understood.
- Turing, A. M. (1952). "The chemical basis of morphogenesis". Philosophicals Transactions of the Royal Society of London B 237 (641): 37–72.
- Russell, Peter (2010). iGenetics : a molecular approach. San Francisco, CA: Pearson Benjamin Cummings. p. 566. ISBN 0-321-56976-8 / 978-0-321-56976-9 Check
- Kam, RK; Deng, Y; Chen, Y; Zhao, H (2012 Mar 22). "Retinoic acid synthesis and functions in early embryonic development.". Cell & bioscience 2 (1): 11. PMID 22439772.
- Derossi D, Joliot AH, Chassaing G, Prochiantz A (April 1994). "The third helix of the Antennapedia homeodomain translocates through biological membranes". J. Biol. Chem. 269 (14): 10444–50. PMID 8144628.
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