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How much do we learn? Natural selection is the best criticism of science

Credit: CC0 Public DomainIn 2003, the Human Genome Project for the World revealed the three billion chemical units in human DNA. Since then, researchers have designed many ways of organizing and assessing this overwhelming amount of information. Now, researchers at Cold Spring Harbor Laboratory (CSHL) have determined that development can help control these efforts. Researchers have already concluded that only one percent of the human genome consists of the genes that make the proteins that our bodies need to grow and function. But they have also learned that about five percent of the human genome has remained the same or preserved, over countless generations of mutation and evolution. "It indicates that an additional four percent of the genome does something that is really important, even though we do not know exactly what it is," explained Adam Siepel, a calculation biologist and professor at CSHL. In order to solve the mystery of the four percent, researchers have spent more than a decade and developed powerful methods to look for different functions among different pieces of the genome. And in order to understand the influences the genome has on an organism, they have been watching evidence from the epigenome. Epigenom is a universe of chemical compounds that attach to DNA, which affects how and when parts of the genome are used by cells. Searching for patterns among epigenomic factors has enabled researchers to guess where important parts of the genome may be and whether they share biological function. However, this is no…



Credit: CC0 Public Domain

In 2003, the Human Genome Project for the World revealed the three billion chemical units in human DNA. Since then, researchers have designed many ways of organizing and assessing this overwhelming amount of information. Now, researchers at Cold Spring Harbor Laboratory (CSHL) have determined that development can help control these efforts.

Researchers have already concluded that only one percent of the human genome consists of the genes that make the proteins that our bodies need to grow and function. But they have also learned that about five percent of the human genome has remained the same or preserved, over countless generations of mutation and evolution.

“It indicates that an additional four percent of the genome does something that is really important, even though we do not know exactly what it is,” explained Adam Siepel, a calculation biologist and professor at CSHL.

In order to solve the mystery of the four percent, researchers have spent more than a decade and developed powerful methods to look for different functions among different pieces of the genome. And in order to understand the influences the genome has on an organism, they have been watching evidence from the epigenome. Epigenom is a universe of chemical compounds that attach to DNA, which affects how and when parts of the genome are used by cells.

Searching for patterns among epigenomic factors has enabled researchers to guess where important parts of the genome may be and whether they share biological function. However, this is no more sure than trying to determine the importance of a scene in a game by just seeing the props and costumes involved.

“This uncertainty about the true biological significance of many epigenomic measurements is a critical barrier not only for the interpretation of available data, but also for potential decisions about how much new data to be collected, of what kind and in what combinations” describes Siepel and his colleague Brad Gulko in the latest publication of Nature Genetics .

Siepellaboratoriet has found a way around this barrier.

“So I and I decided to get this from another angle,” added Siepel. “We asked,” What happens if we let evolution do the job of telling how much of the genome is important? “and,” How much do we learn from each epigenomic dataset? “”

The researchers used data from modern human populations to find evidence of the latest natural selection. Then they compared the genes of humans and chimpanzees to obtain information that goes back five to seven million years to the divergence of people from our big monkey cousins.

“This meant that we could see how much natural selection it was all the time,” Siepel explained.

The result was a way to control future research. Siepel and his colleagues grouped sites within the genome based on epigenomic properties and how the consequences of each site have been for our survival according to evolutionary history. The resulting scores for each function were then aggregated to create “fitness impact maps” or FitCons maps.

If natural selection has been a powerful influence in a place in the genome preserves it for innumerable generations despite mutation and evolution-this part of the genome should be important for survival. In addition, if an epigenomalysis detects several of these preserved sites than not, it will prove to be an informative study.

Siepel hopes that his co-researchers will be able to refer to FitCons to determine which epigenetic markers ell Combinations of markers can prove the most informative for further investigation.

“This is an attempt to see what we can learn by considering evolutionary information along with what we already know,” he said.


Explore further:
Take advantage of data from Nature’s Great Evolutionary Experiment

More information:
Brad Gulko et al., An evolutionary framework for measuring epigenomic information and estimation of cell-type fitness outcomes, Nature Genetics (2018). DOI: 10,1038 / s41588-018-0300-z

Journal Reference:
nature Genetics

Provided by:
Cold Spring Harbor Laboratory

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