Cell: RNA Pathway for Plant Gene Silencing

Biologists at Washington University in St. Louis have made major breakthroughs in understanding the ways in which plant cells use short fragments of RNA to silence unnecessary or extra genes. Basically, as the old saying says, seeing is true, they have been able to see where and how this pathway takes place inside the cell.

Dr. Craig Pikaard, Ph.D., professor of biology at Washington University, and his collaborators have described the role of eight proteins in Arabidopsis in the DNA methylation pathway. This DNA methylation is an outgrowth. , including the chemical modification of cytosine, one of the four bases of DNA. In the case of improper methylation of DNA, higher organisms from plants to humans will encounter many developmental problems: from dwarfism in plants to human tumors and the death of rats. One of the functions of DNA methylation is to turn off some duplicate genes, for example, some transposons that can block or block genes in other places that can be transferred or extended to the genome without suppression. People’s interest in DNA methylation research is of great significance because it helps us understand how some genes are selectively silenced and how silent alleles are reopened in the future. For example, tumor suppressor genes normally help cells maintain normal division, but are often silenced by DNA methylation and histone modifications in cancer cells, resulting in tumor growth. And some disorders of the blood disorder are caused by the loss of expression of genes that are expressed early in human development and silenced in adults. Therefore, the symptoms of these diseases can be alleviated by reopening the expression of these genes in adults.

"The path we are studying is part of an interesting phenomenon of plant development that has been reported in humans, called RNA-mediated DNA methylation," Pikaard explained. "This pathway takes place in the nucleus, Include a short piece of RNA called small interfering RNAs (siRNAs)."

These siRNAs, which are only 24 nucleotides in length, are responsible for methylating the DNA sequence that is paired with its own sequence. This process is performed with the help of other "friends." These "friends" are a group of eight proteins known to be RNA-mediated DNA methylation.

Pikaard and his collaborators used a skilled technique not only to describe the positions of the eight proteins in the pathway but also to obtain the sequences that led to methylation. This is a twist, but in the end it is a cyclical approach. Pikaard and his collaborators were the first to describe the researchers on these pathways and provided a clearer understanding of the steps leading to methylation and gene silencing.

Original English text:

Pathway toward gene silencing described in plants

Biologists at Washington University in St. Louis have made an important breakthrough in understanding a pathway plant cells take to silence unwanted or extra genes using short bits of RNA. Basically, they have made it possible to see where, and how, the events in the Pathway unfold within the cell, and seeing is believing, as the old saying goes.

Craig Pikaard, Ph.D., Washington University professor of biology in Arts & Sciences and his collaborators have described the roles that eight proteins in Arabidopsis plants play in a pathway that brings about DNA methylation, an epigenetic function that involves a chemical modification of cytosine , one of the four chemical subunits of DNA. without proper DNA methylation, higher organisms from plants to humans have a host of developmental problems, from dwarfing in plants to certain tumors in humans, and death in mice. One role of DNA methylation is to Turn off repetitive genes, such as transposable elements that can move or spread throughout a genome and disrupt other gene functions if left unchecked. There is also interest in DNA methylation because understanding how some genes are selected silenced and how silenced alleles can be turned on again May someday have practical benefits. For instance, tumor suppressor genes that normally help keep cells from dividing uncontrollably Often silenced by DNA methylation and histone (proteins that wrap DNA) modifications in cancer cells, contributing to tumor growth. And certain blood disorders resulting from failed genes expressed in adults might be stimulated if versions of those same genes that are only identified very early in Development, but are then silenced in adults, could only be turned on again.

"The pathway we are studying is part of an interesting phenomenon that occurs in plants, and reportedly in humans, too, called RNA-directed DNA methylation," Pikaard explained. "This pathway takes place in the nucleus, and it involves short RNAs, Called small interfering RNAs -- siRNAs."

Those little tykes, just 24 nucleotides long, are somehow responsible for methylation of DNA sequences that match the sequence of the siRNAs, but not without a lot of help from their friends. The friends in this case are the team of eight known proteins of the RNA-directed DNA methylation pathway.

Pilloned by a prominent toolkit of sophisticated techniques, Pikaard and his collaborators not only has the locations of the eight proteins in the pathway but also have provided the sequence of events that leads to methylation. It is a twisted, and contains circular paths, but Pikaard And his colleagues are the first researchers to literally see the pathway and opened provide a clearer understanding of the steps leading to methylation and gene silencing.

The results were published in the July 14, 2006 issue of Cell. The study was funded by the National Institutes of Health, Howard Hughes Medical Institute (HHMI) and Monsanto Company. Pikaards collaborators include Olga Pontes, the first author of the study, other Group members from his Washington University laboratory and the group of Steven E. Jacobsen, Ph.D., an HHMI investigator and professor of biology at the University of California, Los Angeles.

Using mutants, antibodies, and fluorescence microscopy techniques known as RNA fluorescence in situ hybridization (RNA-FISH) and DNA-FISH, Washington University postdoctoral researcher Olga Pontes, Ph.D., was able to unravel where the eight team players are located and In what order events in the RNA-directed DNA methylation pathway transpire. Using antibodies to detect the proteins, together with DNA-FISH to detect the DNA sites that give rise to the siRNAs, Pontes found that half of the team is located with the genes That match the siRNAs.

"The combination of DNA FISH and protein localization allowed us to say which proteins are sitting on the DNA that give rise to the siRNAs and also the loci that are modified by the siRNAs," Pikaard said.

Pontes found the other half of the team located within a special nuclear compartment known as the nucleolus, long known to be the production center for ribosomes. "She got a brilliant signal in the nucleolus, a brilliant dot in the same place for each of the Proteins," said Pikaard. Using RNA-FISH, Pontes also found that the siRNAs were in that same dot within the nucleolus.

Pontes and Pikaard was able to deduce the order of events by studying mutations of all eight genes that give rise to the proteins, finding out what happens to the different proteins as the different genes are mutated, one by one. For instance, the representatives The importance of RNA Polymerase IVa (Pol IVa) by looking at a Pol IVa mutant and noting that the rest of the proteins didnt localize properly. In the RNA-dependent RNA polymerase 2 (RDR2) mutant, Pol IVa is unaffected, but the function The all the other proteins downstream is lost, inferring that it came into the act second. The picture that emerged from this logical approach is that Pol IVa gets things started, churning out RNA that then goes to the nucleolus where it is acted on by RDR2 , Which turns the single-stranded RNA into double-stranded RNA. The Dicer-like 3 protein, DCL3 then chops the RNA into small interfering RNAs (siRNAs). With comes ARGONAUTE4 (AGO4), which grabs hold of the siRNAs while also binding To NRPD 1b, the largest subunit of an alternative form of RNA Polymerase IV, Pol IVb. The AGO4-siRNA-NRPD1b complex is then thought to leave the nucleolus, acquire the second-largest Pol IV subunit, NRPD2, which represent both Pol IVa and Pol IVb, and then seek out the DNA sequences that match the siRNAs. At these sites, the chromatin remodeler DRD1 presumably bulldozes histones and other proteins out of the way to make the DNA accessible for methylation by the de novo cytosine methyltransferase, DRM2.

A paradoxical aspect of the pathway is that siRNAs direct DNA methylation but DNA methylation is also required for the production siRNAs. "Its a circular pathway. You have to produce the siRNA in order to have them come back and methylate the loci, which somehow induces More siRNA production involving Pol IVa". Pikaard said.

"A combination of genetic mutants, transgenes, antibodies, RNA-FISH and DNA-FISH were key to the study. "This toolkit is really powerful," Pikaard said.

"It enabled us to look at a complex pathway and figure out not only the order of events but also the spatial organization of the pathway in the nucleus. Our hope for the future is to develop tools that will enable us to watch the pathway function in Live cells using fluorescent proteins and time-lapsed microscopy, to learn even more."

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