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Evolution is driven by gene regulation
August 10, 2007New Haven, Conn. - It is not just what's in your genes, it's how you turn them on that accounts for the difference between species - at least in yeast - according to a report by Yale researchers in this week's issue of Science.
"We've known for a while that the protein coding genes of humans and chimpanzees are about 99 percent the same," said senior author Michael Snyder, the Cullman Professor of Molecular Cellular and Developmental Biology at Yale. "The challenge for biologists is accounting for what causes the substantial difference between the person and the chimp."
Conventional wisdom has been that if the difference is not the gene content, the difference must be in the way regulation of genes produces their protein products.
Comparing gene regulation across similar organisms has been difficult because the nucleotide sequence of DNA regulatory regions, or promoters, are more variable than the sequences of their corresponding protein-coding regions, making them harder to identify by standard computer comparisons.
"While many molecules that bind DNA regulatory regions have been identified as transcription factors mediating gene regulation, we have now shown that we can functionally map these interactions and identify the specific targeted promoters," said Snyder. "We were startled to find that even the closely related species of yeast had extensively differing patterns of regulation."
In this study, the authors found the DNA binding sites by aiming at their function, rather than their sequence. First, they isolated transcription factors that were specifically bound to DNA at their promoter sites. Then, they analyzed the sequences that were isolated to determine the similarities and differences in regulatory regions between the different species.
"By using a group of closely and more distantly related yeast whose sequences were well documented, we were able to see functional differences that had been invisible to researchers before," said Snyder. "We expect that this approach will get us closer to understanding the balance between gene content and gene regulation in the question of human-chimp diversity."
Yale University
Comparing gene regulation across similar organisms has been difficult because the nucleotide sequence of DNA regulatory regions, or promoters, are more variable than the sequences of their corresponding protein-coding regions, making them harder to identify by standard computer comparisons.
"While many molecules that bind DNA regulatory regions have been identified as transcription factors mediating gene regulation, we have now shown that we can functionally map these interactions and identify the specific targeted promoters," said Snyder. "We were startled to find that even the closely related species of yeast had extensively differing patterns of regulation."
In this study, the authors found the DNA binding sites by aiming at their function, rather than their sequence. First, they isolated transcription factors that were specifically bound to DNA at their promoter sites. Then, they analyzed the sequences that were isolated to determine the similarities and differences in regulatory regions between the different species.
"By using a group of closely and more distantly related yeast whose sequences were well documented, we were able to see functional differences that had been invisible to researchers before," said Snyder. "We expect that this approach will get us closer to understanding the balance between gene content and gene regulation in the question of human-chimp diversity."
Yale University
Gene Regulation Current Events and Gene Regulation News RSS'Junk' DNA proves functional
In a paper published in Genome Research on Nov. 4, scientists at the Genome Institute of Singapore (GIS) report that what was previously believed to be "junk" DNA is one of the important ingredients distinguishing humans from other species.
A new relationship between brain derived neurotrophic factor and inflammatory signaling
In the October 14th edition of Science Signaling researchers at Boston University School of Medicine (BUSM), The Children's Hospital of Philadelphia/University of Pennsylvania School of Medicine and The University of Colorado Denver School of Medicine have shown that the development of epilepsy in adult rats is linked to functional changes in the expression of alpha 1 containing GABA-A receptors, the main inhibitory neurotransmitter receptor in the brain, that may be dependent upon BDNF-induced activation of the Janus kinase (JAK)/signal transducers and activators of transcription (STAT) pathway.
Study finds value in 'junk' DNA
For about 15 years, scientists have known that certain "junk" DNA -- repetitive DNA segments previously thought to have no function -- could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants.
Caltech scientists find cells coordinate gene activity with FM bursts
How a cell achieves the coordinated control of a number of genes at the same time, a process that's necessary for it to regulate its own behavior and development, has long puzzled scientists.
Conaway Lab Identifies Novel Mechanism for Regulation of Gene Expression
The Stowers Institute's Conaway Lab has demonstrated that an enzyme called Uch37 is kept in check when it is part of a human chromatin remodeling complex, INO80. The results were published in today's issue of Molecular Cell.
Cancer-causing gut bacteria exposed
Normal gut bacteria are thought to be involved in colon cancer but the exact mechanisms have remained unknown. Now, scientists from the USA have discovered that a molecule produced by a common gut bacterium activates signalling pathways that are associated with cancer cells.
Trichoplax genome sequenced -- 'rosetta stone' for understanding evolution
Yale molecular and evolutionary biologists in collaboration with Department of Energy scientists produced the full genome sequence of Trichoplax, one of nature's most primitive multicellular organisms, providing a new insight into the evolution of all higher animals.
Genome of saltwater creature could aid understanding of gene grouping
The genetic code of a simple saltwater creature could help researchers learn more about how groups of genes function in humans and other species.
Deep sequencing study reveals new insights into human transcriptome
In a collaborative project scientists from the Max-Planck-Institute for Molecular Genetics in Berlin (MPI MolGen), Germany and Genomatix with a business in Munich, Germany and Ann Arbor, MI, USA, applied next generation sequencing and analysis methods to generate an unprecedented view at the human transcriptome.
UT Southwestern researchers identify new targets for RNAs that regulate genes
Tiny strands of genetic material called RNA - a chemical cousin of DNA - are emerging as major players in gene regulation, the process inside cells that drives all biology and that scientists seek to control in order to fight disease.
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