Beyond Base-Pairs: Mapping the Functional GenomeRegulatory sequences of mouse genome sequenced for first time
Popularly dubbed “the book of life,” the human genome is extraordinarily difficult to read. But without full knowledge of its grammar and syntax, the genome’s 2.9 billion base-pairs of adenine and thymine, cytosine and guanine provide limited insights into humanity’s underlying genetics.
In a paper published in the July 1, 2012 issue of the journal Nature, researchers at the Ludwig Institute for Cancer Research and the University of California, San Diego School of Medicine open the book further, mapping for the first time a significant portion of the functional sequences of the mouse genome, the most widely used mammalian model organism in biomedical research.
“We’ve known the precise alphabet of the human genome for more than a decade, but not necessarily how those letters make meaningful words, paragraphs or life,” said Bing Ren, PhD, head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research at UC San Diego. “We know, for example, that only one to two percent of the functional genome codes for proteins, but that there are highly conserved regions in the genome outside of protein-coding that affect genes and disease development. It’s clear these regions do something or they would have changed or disappeared.”
Chief among those regions are cis-regulatory elements, key stretches of DNA that appear to regulate the transcription of genes. Misregulation of genes can result in diseases like cancer. Using high-throughput sequencing technologies, Ren and colleagues mapped nearly 300,000 mouse cis-regulatory elements in 19 different types of tissue and cell. The unprecedented work provided a functional annotation of nearly 11 percent of the mouse genome, and more than 70 percent of the conserved, non-coding sequences shared with other mammalian species, including humans.
As expected, the researchers identified different sequences that promote or start gene activity, enhance its activity and define where it occurs in the body during development. More surprising, said Ren, was that the structural organization of the cis-regulatory elements are grouped into discrete clusters corresponding to spatial domains. “It’s a case of form following function,” he said. “It makes sense.”
While the research is fundamentally revealing, Ren noted it is also just a beginning, a partial picture of the functional genome. Additional studies will be needed in other types of cells and at different stages of development.
“We’ve mapped and understand 11 percent of the genome,” said Ren. “There’s still a long way to march.”

Beyond Base-Pairs: Mapping the Functional Genome
Regulatory sequences of mouse genome sequenced for first time

Popularly dubbed “the book of life,” the human genome is extraordinarily difficult to read. But without full knowledge of its grammar and syntax, the genome’s 2.9 billion base-pairs of adenine and thymine, cytosine and guanine provide limited insights into humanity’s underlying genetics.

In a paper published in the July 1, 2012 issue of the journal Nature, researchers at the Ludwig Institute for Cancer Research and the University of California, San Diego School of Medicine open the book further, mapping for the first time a significant portion of the functional sequences of the mouse genome, the most widely used mammalian model organism in biomedical research.

“We’ve known the precise alphabet of the human genome for more than a decade, but not necessarily how those letters make meaningful words, paragraphs or life,” said Bing Ren, PhD, head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research at UC San Diego. “We know, for example, that only one to two percent of the functional genome codes for proteins, but that there are highly conserved regions in the genome outside of protein-coding that affect genes and disease development. It’s clear these regions do something or they would have changed or disappeared.”

Chief among those regions are cis-regulatory elements, key stretches of DNA that appear to regulate the transcription of genes. Misregulation of genes can result in diseases like cancer. Using high-throughput sequencing technologies, Ren and colleagues mapped nearly 300,000 mouse cis-regulatory elements in 19 different types of tissue and cell. The unprecedented work provided a functional annotation of nearly 11 percent of the mouse genome, and more than 70 percent of the conserved, non-coding sequences shared with other mammalian species, including humans.

As expected, the researchers identified different sequences that promote or start gene activity, enhance its activity and define where it occurs in the body during development. More surprising, said Ren, was that the structural organization of the cis-regulatory elements are grouped into discrete clusters corresponding to spatial domains. “It’s a case of form following function,” he said. “It makes sense.”

While the research is fundamentally revealing, Ren noted it is also just a beginning, a partial picture of the functional genome. Additional studies will be needed in other types of cells and at different stages of development.

“We’ve mapped and understand 11 percent of the genome,” said Ren. “There’s still a long way to march.”


Clarity Begins at Exome Sequencing Protein-making Part of Genome Can Change Diagnosis and Patient Care

In the June 13 issue of Science Translational Medicine, an international team led by researchers from the University of California, San Diego School of Medicine reports that the new technology of exome sequencing is not only a promising method for identifying disease-causing genes, but may also improve diagnoses and guide individual patient care.
In exome sequencing, researchers selectively and simultaneously target and map all of the portions of the genome where exons reside. Exons are short, critical sequences of DNA in genes that are translated into proteins – the biological workhorses involved in virtually every cellular function, plus various structural or mechanical duties.
The researchers, headed by principal investigator Joseph G. Gleeson, MD, professor of neurosciences and pediatrics at UC San Diego and Rady Children’s Hospital-San Diego, sequenced the exomes of 118 patients who had been diagnosed with specific neurodevelopmental diseases. In each of the cases, all known genetic causes of their disease had been previously excluded.
Not surprisingly, the scientists found that exome sequencing newly identified numerous disease-causing genes, including the identification of the EXOC8 gene as a cause of Joubert syndrome, a condition affecting the developing cerebellum, and GFM2 as a cause for a condition that results in a small brain combined with pediatric diabetes.
More surprising, the researchers discovered that in approximately 10 percent of cases, exome sequencing led to the identification of a known disease-causing gene, prompting a change in diagnosis and care for some patients.  
More here
Clarity Begins at Exome
Sequencing Protein-making Part of Genome Can Change Diagnosis and Patient Care

In the June 13 issue of Science Translational Medicine, an international team led by researchers from the University of California, San Diego School of Medicine reports that the new technology of exome sequencing is not only a promising method for identifying disease-causing genes, but may also improve diagnoses and guide individual patient care.

In exome sequencing, researchers selectively and simultaneously target and map all of the portions of the genome where exons reside. Exons are short, critical sequences of DNA in genes that are translated into proteins – the biological workhorses involved in virtually every cellular function, plus various structural or mechanical duties.

The researchers, headed by principal investigator Joseph G. Gleeson, MD, professor of neurosciences and pediatrics at UC San Diego and Rady Children’s Hospital-San Diego, sequenced the exomes of 118 patients who had been diagnosed with specific neurodevelopmental diseases. In each of the cases, all known genetic causes of their disease had been previously excluded.

Not surprisingly, the scientists found that exome sequencing newly identified numerous disease-causing genes, including the identification of the EXOC8 gene as a cause of Joubert syndrome, a condition affecting the developing cerebellum, and GFM2 as a cause for a condition that results in a small brain combined with pediatric diabetes.

More surprising, the researchers discovered that in approximately 10 percent of cases, exome sequencing led to the identification of a known disease-causing gene, prompting a change in diagnosis and care for some patients.  

More here

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