Genome complexity: plants control gene expression (Introduction)

by David Turell , Sunday, May 22, 2016, 15:17 (3108 days ago) @ David Turell

Researchers have mapped out regions of non-coding DNA that control gene expression and transcription in plants, another example of 'junk DNA goodbye!':-https://www.sciencedaily.com/releases/2016/05/160519130231.htm-"New findings yield insights into how plants get their traits. Revealing a landscape of protein-binding zones on DNA, collectively dubbed the "cistrome," shows how plants control where and when genes are expressed.-***-"Revealing this landscape of protein-binding zones on DNA, collectively dubbed the "cistrome," shows how plants control where and when genes are expressed. Previous methods for mapping the cistrome in plant cells were difficult and slow, but the new approach, detailed in the May 19, 2016 issue of Cell, overcomes those hurdles to offer a sweeping view of this critical aspect of genetic regulation.-"This is one of the first efforts to globally characterize all the regulatory elements in a plant genome," says senior author Joseph Ecker, professor and director of Salk's Genomic Analysis Laboratory and holder of the Salk International Council Chair in Genetics. "The cistrome has been a missing piece of information for trying to understand how plants function."-***-"To test out the utility of DAP-seq, Ecker, Huang, O'Malley and their colleagues mapped where 529 transcription factors bound to the genome of Arabidopsis thaliana, the plant most studied by scientists. They identified 2.7 million binding sites. They then repeated the experiments using DNA containing or not containing cytosine methylation--a process of marking the genome's surface with chemical methyl tags to further inhibit or activate genes. The binding patterns of about three-quarters of the transcription factors that they tested changed.-"'This allowed us to expose binding sites that we might miss if we didn't remove the methylation. With this approach we can see binding sites that may be active in only a subset of cells or tissues," says O'Malley. The new results show not only how regulatory proteins alter gene expression, but the roles the epigenomic methylation marks may play in this regulation.-***-"Ecker and collaborating groups at Duke University and the University of Western Australia revealed that different types of cells in the Arabidopsis root have different patterns of methylation. Using DAP-seq, they'll now be able to study how those patterns in root cells affect the binding of transcription factors."-Comment: Just another example of the fact that much of the DNA in plants and animals is useful, not junk. DNA is manufacturing proteins for replacement, but it must regulate speed of production, where the proteins go, how the various organ systems are coordinated and regulated, among many obvious duties beyond coding for protein. It is amazing this was not obvious to science years ago, but Darwin dedicated scientists used the concept of 'junk DNA' in a twisted way to support Darwin theory of chance evolution: if it didn't code, it was junk, left over from previous attempts to advance by chance mutations.