Welcome to TransposonBank!  This site is intended to help you learn about transposable elements (TEs) and their effects on our everyday lives.  We will look at examples from the worlds of garden peas, the critically important food crop rice, and the interrelationships between a commercial crop, cotton, its pest, and current management strategies.  

What We Know Today

Scientists today know relatively little about transposable elements except that they are fragments of DNA that can move around on their own in the genomes of higher organisms. However, we do know that TEs can affect the phenotypic expression of genes and thus the appearance and behavior of the organisms.  While we do not really understand how transposable elements originated, they represent the single largest component of the genetic material for most eukaryotic organisms. There are many different types of transposable elements and they are grouped together into families based on both structural and functional similarities.

Because TEs are fragments of DNA, they are often recognized by their nucleotide sequence. Sequence information is interpreted by scientists in the same way that letters and words are interpreted by anyone who knows how to read. In fact, scientists use their eyes as much as they do computers when they are studying sequence information from a genome.  Specific patterns of A’s and G’s and C’s and T’s represent a kind of molecular signature and help identify members of different families, thus providing clues to how they move around.  

Transposable elements can be very large, comprised of tens of thousands of base pairs, or quite small (as small as 300 bp). TEs move around within the genome by duplicating copies of themselves (Group Elements) and inserting the new copies in different locations or they simply jump in and out of the genome, leaving small footprints in their wake. Scientists recognize them as repeated sequences (copies and footprints). Overall, TEs comprise what is known as the repetitive fraction of eukaryotic genomes. Even though they are common, each family of TEs has different characteristics and TEs are very variable in size and sequence identity. Locating them has not been an easy task.

Transposable Elements in Crops

Transposable elements were first discovered in corn. Recently, researchers have learned that they are responsible for Mendel’s wrinkled peas and that they play a role in the appearance of pesticide-resistant cotton pests. We also believe that they play a role in the diversity of rice, a food crop that supports ? % of the world’s human population. This site focuses on the knowledge that rice genomicists and breeders are gathering about specific characteristics that distinguish the transposable element families found in rice and introduces you to the methods that the scientist use for discovery and analysis. 

Bioinformatics

Although few eukaryotic genomes have yet been fully sequenced, the information from those that have is already overwhelming our ability to make sense of it.  DNA sequence information is being assembled, organized and interpreted by researchers working in government, academia, and the private sector in an effort to understand how the genomes of living things are structured, how they function and how they evolved.  Transposable elements represent one of the most intriguing components of these genomes because of their abundance, their ability to move autonomously in and out of the chromosomes and their associations with genes that lead to phenotypic change.

Bioinformatics may be broadly defined as the interface between biological sciences, computational sciences, and mathematics by applying multiple database techniques and mathematical algorithms to gene and protein sequence information.  The database technology consists of storing the complex biological data while also being able to search and retrieve relevant information to aid in the analysis of biological problems.  IT tools automate many of the processes, some of which take large amounts of computing power.  

How To Use This Site

We recommend that you go through this website in order - Introduction, Everyday Effects, Discovery, TE Families, Blast Off, and References - to become familiar with the subject matter.  All sections are available at any time if you would like to refer to an earlier section. After reading about the effects of transposable elements on the function of genes, learn how researchers have used genome databases to discover and characterize transposable elements, and how they are creating specialized information resources that catalogue information about TEs, where they come from, what relationships exist between different families, how TEs move within a genome and what phenotypic consequences they may have. 

           Scientists believe that Transposable Elements play a vital role in evolution, but they are still discovering what that means.  The Everyday Effects section talks about how researchers propose that the folding of the outer skin of Mendel’s wrinkled peas is caused by TEs . It also provides an example how TEs play a role in the development of resistance to BT toxin in moths.

            Our Discovery section provides an in-depth tutorial on how to use BLAST, one of the most popular software system for gene sequence searches that is available online to all users of the National Center for Bioinformatics (NCBI). We explain how interface works and how to interpret the results.  When you run your own explorations of the rice genome, you will be running BLAST on a server at the Cornell Theory Center (CTC), Cornell University’s high-performance computing and interdisciplinary research center.

Before you actually use our BLAST interface, the TE families section will provide you with information about a few TE families that are common in the rice genome.  Look carefully at the different families to become familiar with their unique characteristics.  The differences that distinguish one family from another provide the basis for how scientists recognize different families and interpret their different lifestyles.  Once we understand these families, the importance of searching for transposons is to help learn more about TEs.  Previously scientists would spend years trying to determine the importance of a small number of TEs.  Learning how to search for families of TEs allows scientists to identify TEs on a larger scale therefore increasing the amount of  information that can be gathered on how these elements function, their importance in the genome, and how they effect gene expression.

At that point you should be ready to BLAST OFF!!! When you do, you will be searching for new transposable elements within one of the previously established transposon families.  You will be able to Blast against the latest version of the rice genome released by NCBI as of 5/20/2002. If you think you have found any novel transposable elements, send us an email at McCouch’s lab?