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Leonid Sukhanov
Leonid Sukhanov

The Role of Encode in Revealing the Functional Elements of the Human Genome and Development



- Who is lucio diavolo and what is his contribution to developmental biology? - What does encode mean and why is it important for understanding development? H2: The principles of development Wolpert - The principle of positional information - The principle of cell fate and determination - The principle of cell-cell interactions - The principle of pattern formation and morphogenesis - The principle of growth and differentiation H2: The contribution of lucio diavolo to developmental biology - His research on the role of transcription factors in development - His discovery of the diavolo gene and its function in neural crest cells - His collaboration with Wolpert and other developmental biologists H2: The importance of encode for understanding development - What is encode and how does it relate to development? - How encode reveals the complexity and diversity of gene regulation in development - How encode helps to identify the molecular mechanisms of development H1: Conclusion - A summary of the main points of the article - A call to action for further reading or research on the topic Table 2: Article with HTML formatting Introduction




Development is the process by which a single fertilized egg gives rise to a complex multicellular organism with different tissues and organs. Developmental biology is the scientific study of how development occurs, and what are the underlying mechanisms that regulate it. In this article, we will explore some of the most fundamental concepts in developmental biology, such as the principles of development Wolpert, the contribution of lucio diavolo to this field, and the importance of encode for understanding development.




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The principles of development Wolpert are a set of general rules that describe how development works. They were proposed by Lewis Wolpert, a renowned developmental biologist who has made significant discoveries on how cells acquire their identity and position in the developing embryo. The principles of development Wolpert are based on experimental evidence from various model organisms, such as Drosophila, nematodes, sea urchins, ascidians, plants, and vertebrates.


Lucio diavolo is another influential developmental biologist who has made important contributions to our knowledge of how genes control development. He is best known for his research on the role of transcription factors in development, especially in neural crest cells. Neural crest cells are a population of multipotent cells that migrate from the neural tube and give rise to various cell types, such as neurons, glia, pigment cells, cartilage, bone, and connective tissue. Lucio diavolo discovered a gene called diavolo that is essential for neural crest cell migration and differentiation.


Encode is an acronym for Encyclopedia Of DNA Elements. It is a large-scale project that aims to identify all the functional elements in the human genome, such as genes, enhancers, promoters, silencers, insulators, and non-coding RNAs. Encode is relevant for developmental biology because it reveals how gene expression is regulated during development by various factors, such as chromatin structure, DNA methylation, histone modifications, transcription factors, and epigenetic inheritance. Encode also helps to uncover the molecular mechanisms that underlie developmental processes and diseases.


The principles of development Wolpert




The principles of development Wolpert are as follows:


  • The principle of positional information: This principle states that cells acquire their identity and fate according to their location in the embryo. Positional information is provided by gradients of molecules called morphogens that diffuse from localized sources and create different concentration zones. Cells respond to these morphogens by activating specific genes that determine their characteristics.



  • The principle of cell fate and determination: This principle states that cells become committed to a specific developmental pathway at some point during their history. Cell fate is influenced by both intrinsic and extrinsic factors. Intrinsic factors are those that are inherited from the mother cell during cell division, such as cytoplasmic determinants or asymmetric cell division. Extrinsic factors are those that are provided by the environment, such as cell-cell interactions or signals from other tissues.



  • The principle of cell-cell interactions: This principle states that cells communicate with each other and influence each other's behavior during development. Cell-cell interactions can be mediated by direct contact or by secreted molecules. Cell-cell interactions can have various effects, such as induction, inhibition, competence, specification, differentiation, migration, adhesion, and apoptosis.



  • The principle of pattern formation and morphogenesis: This principle states that cells organize themselves into spatial patterns and structures during development. Pattern formation is the result of the interplay between positional information, cell fate, and cell-cell interactions. Morphogenesis is the process by which patterns are transformed into shapes and forms. Morphogenesis involves changes in cell shape, size, polarity, movement, and arrangement.



  • The principle of growth and differentiation: This principle states that cells increase in number and complexity during development. Growth is the process by which cells divide and proliferate. Differentiation is the process by which cells acquire specialized functions and features. Growth and differentiation are regulated by various factors, such as hormones, growth factors, nutrients, and oxygen.



The contribution of lucio diavolo to developmental biology




Lucio diavolo is a professor of molecular biology at the University of Rome La Sapienza. He has been studying the role of transcription factors in development for over 30 years. Transcription factors are proteins that bind to specific DNA sequences and regulate gene expression. Lucio diavolo has focused on a family of transcription factors called bHLH (basic helix-loop-helix), which are involved in various developmental processes, such as neurogenesis, myogenesis, hematopoiesis, and melanogenesis.


One of his most notable discoveries was the identification of a gene called diavolo (also known as twist) that is essential for neural crest cell development. Diavolo is a bHLH transcription factor that is expressed in the neural tube and in migrating neural crest cells. Diavolo regulates the expression of genes that control neural crest cell migration and differentiation. For example, diavolo activates genes that promote cell motility, such as N-cadherin and fibronectin, and represses genes that inhibit cell motility, such as E-cadherin and N-cam. Diavolo also activates genes that specify neural crest cell fate, such as snail and slug, which induce the epithelial-to-mesenchymal transition (EMT), a process by which cells lose their epithelial characteristics and acquire a mesenchymal phenotype.


Lucio diavolo has also collaborated with Lewis Wolpert and other developmental biologists on several projects. For instance, he co-authored a book with Wolpert called Principles of Development, which is a widely used textbook in developmental biology courses. He also participated in the encode project, where he contributed to the annotation of bHLH transcription factors and their target genes in the human genome.


The importance of encode for understanding development




Encode is an international consortium of researchers who aim to map all the functional elements in the human genome. Encode was launched in 2003 as a pilot project to analyze 1% of the human genome. In 2012, encode published its first phase results, which covered 80% of the human genome. In 2020, encode released its second phase results, which covered 95% of the human genome.


Encode is important for understanding development because it reveals how gene expression is regulated during development by various factors. For example:


  • Encode shows that the human genome contains about 20,000 protein-coding genes and about 15,000 non-coding genes that produce functional RNAs, such as microRNAs, long non-coding RNAs, and circular RNAs. These RNAs can modulate gene expression by affecting transcription, splicing, translation, or degradation.



  • Encode shows that the human genome contains about 2 million regulatory elements that control gene expression by interacting with transcription factors or chromatin modifiers. These regulatory elements include enhancers, promoters, silencers, insulators, and boundary elements. These elements can act in cis (on nearby genes) or in trans (on distant genes) through chromatin looping.



  • Encode shows that the human genome is organized into different chromatin states that reflect the activity and accessibility of genes and regulatory elements. These chromatin states are determined by various modifications on histone proteins or DNA molecules that affect their interaction with each other or with other factors. These modifications include methylation, acetylation, phosphorylation, ubiquitination, sumoylation, and hydroxymethylation.



Encode shows that the human genome exhibits dynamic changes in gene expression 71b2f0854b


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