Model organisms are animals (or plants, or fungi, or bacteria) that scientists have found convenient to use in the lab. Animals that are:

• easy and inexpensive to keep,
• eat cheap food,
• are small and hardy,
• have well-characterized mutations (for example, mutations that lead to certain disease symptoms) for genetic studies, and
• breed easily, with short generation times

In this module, we explore two model organisms that were used for modENCODE studies -- the fruit fly Drosophila melanogaster and the worm Caenorhabditis elegans. Both organisms have contributed to fundamental discoveries on how animals develop from a single cell, how that cell knows which genes it should express, how the different cells in the body communicate with each other, and how the animal behaves in different situations. This knowledge has been vital to improving our understanding of human biology in health and disease.

All of the instructions for a living organism are recorded in its DNA. All cells need some of that information -- for example, information on how to maintain an energy balance, how to generate RNA and proteins, how to replicate when appropriate, and other "housekeeping" functions. But many genes provide information that's needed by only a subset of cell types or at specific stages. This information needs to be made available only to the right cells at the right time. Genes are transcribed (expressed) by a protein called a RNA polymerase to produce an RNA molecule. One mechanism for regulating which genes are transcribed in different cell types is via other proteins, called transcription factors. These proteins bind near a gene and activate the RNA polymerase to transcribe RNA copies of the gene. If the gene codes for a protein, this transcript will be processed to produce mRNA, which in turn is translated into protein. We explore the different steps in this process, and how recent work with the fly and worm has shed light on it, in this module.

Our genomes are very large -- and all of the DNA within a cell must be packaged into chromatin to fit inside a very small nucleus. This packaging can also function in regulating gene expression, and plays a key role in determining which DNA sequences are accessible to the transcription apparatus. The same DNA can be packaged in different ways in different cell types, and the form of packaging can be passed on. The "memory" of the distinctive chromatin packaging, which is superimposed on DNA, is one form of what is termed "epigenetics." Chromatin packing can be altered in response to environmental factors, such as diet; as a consequence, epigenetics is sometimes described as "where the environment meets the genome"! You'll learn more about this kind of gene expression regulation in this module.

When scienctists first began to study our genes at a molecular level, we were limited to looking at one gene at a time. But humans have ~22,000 genes, and changes in the expression of one gene (for example, by a mutation), or a change in the environment of a cell, can cause changes in the expression of thousands of genes! Thus, we need to look at what is happening to all of the genes at the same time. To do this, scientists have developed "high-throughput" and "next-generation" genomic technologies that allow analysis of most or all of the genome at the same time. To deal with the multitude of genes and their complex interactions and the volumes of data required to track them, a whole new discipline of computational biology, or bioinformatics, has developed and grown dramatically in recent years. This module looks at the modENCODE project as an example of the impact of new technologies and the computational methods that have been developed.

Fly: André Karwath/Wikimedia Commons

Worm: WormClassroom

Transcription: European Bioinformatics Institute/Wikimedia Commons

Chromatin: P. J. Horn and C. L. Peterson, Science 297, 1824-1827 (2002)

Genomics: modENCODE Consortium et al., Science 330, 1787-1797 (2010)

Bioinformatics: Fort Collins Museum & Discovery Science Center