ENCODE

<img src="/7e18bf14-3e65-5ff6-a3e2-37b2518b1939.png"/>        The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The project started with two components - a pilot phase and a technology development phase.

The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

The range of experiments is expanding, too. One quickly developing area of study involves looking at interactions between parts of the genome in three-dimensional space. If the intervening DNA loops out of the way, enhancer elements can regulate genes hundreds of thousands of base pairs away, so proteins bound to the enhancer can end up interacting with those attached near the gene. Dekker and his collaborators have been developing a technique to map these interactions. First, they use chemicals that fuse DNA-binding proteins together. Then they cut out the intervening loops and sequence the bound DNA, revealing the distant relationships between regulatory elements. They are now scaling up these efforts to explore the interactions across the genome. “This is beyond the simple annotation of the genome. It’s the next phase,” Dekker says.

More DNA Elements

While somewhat confusing, these are part of the new language of the cell and therefore are being mentioned.

Transcription Factors – Switches Made of Proteins

Proteins, called transcription factors, act as switches.  They bind to DNA and determine whether RNA is made or not. These can be promoters, which activate DNA, or repressors, which block action. Other proteins that act on DNA include co-activators, chromatin remodelers, histone enzymes, kinases that transfer energy phosphate molecules, and methylases that add a methyl group.

ENCODE found 4 million DNA sites, 8% of the DNA, where these factors operate. But, there were 45 million different events where transcription factors occupied DNA. This real number is probably much greater since only certain cells and places within cells have been studied. It is not clear how many of these are active or evolutionarily old switches that are not used now.

These individual switches almost all interact with many genes, and most genes have multiple switches acting upon it at the same time

DNA methylation

These markings on DNA are an important part of epigenetics, that is actions other than DNA that affect heredity. Attaching methyl groups to DNA sections blocks DNA making proteins. Methylation of specific genes is crucial in determining long-range effects of many experiences in life including starvation, stress, and abuse.

Open Chromatin

DNA is tightly bound, wound and looped by multiple large proteins, which in total are called chromatin. Histones are one important large molecule involved in winding and unwinding DNA. Only when DNA is open can it be acted upon. Mechanisms that open the tightly bound DNA allow the DNA to be influenced by the regulatory particles. Somehow, the cell knows exactly where it wants to unfold these loops to find the perfect DNA for the occasion.

Modified histones

There are many modifications that can alter histones, which then change the ability to use DNA. Sixty different modifications have now been identified, and 13 of these have been described in the ENCODE research.

RNA Binding

This is a place where regulatory proteins attach to RNA. ENCODE identified 8 million distinct particles.

DHS (DNase Hypersensitivity Sites)

Hypersensitivity sites are those areas on the DNA where there is no interference from histone molecules. ENCODE identified 200,000 sites per cell type. It also identified three million places where transcription factors bind to these 200,000 open sites. This means that 42% of the DNA that codes for protein is accessible to switching. These sites are very different in different types of cells. ENCODE has found 500,000 enhancers to go with these sites out of 3 million identified but not yet detailed.

Most of these sites are very highly regulated. Each site has dozens to hundreds of co activators. 88% of DHS are active during development of the fetus, and respond with variations based upon exposures.

Additional ENCODE factors

There are additional confounding complications that ENCODE identified:

 There are many very distant regulators. It is important to realize that most of the study of DNA is in two dimensions and yet in reality it is looped and perhaps some regions that seem distant are closer in three dimensions.
 RNA pieces are spliced together while they are being transcribed. Surprisingly, microRNA, which are important regulators, are also spliced together. Splicing creates an entirely different level of complexity. Where is the direction and regulation of this splicing? It is especially perplexing why small RNAs would be spliced together since these seem to be critical regulatory factors to begin with. What is regulating the regulators?
Another confounding development is that transcription factors are now shown to bind at different levels. Therefore, it is not a simple “on” and “off” switch but a dimmer switch at different levels of intensity. Also, they operate in different ways in different circumstances with multiple levels of feedback loops determining their actions in the circuits they influence.
 It is not at all clear how the vast number of small RNAs know how to get to the specific addresses in the cell where they operate.
The same regulatory region can play very different roles in different types of cells, and at different times

ENCODE

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