The plant Arabidopsis thaliana. Credit: Salk Institute
What determines how a cell’s genome is regulated to make sure correct development and growth? Turns out, the components of the genome which are turned on or off in every cell-type or tissue play a significant position on this course of. Now, a staff at Salk has proven that the CLASSY gene household regulates which components of the genome are turned off in a tissue-specific method. The CLASSYs primarily management the place the genome is marked by DNA methylation—the addition of methyl chemical teams to the DNA that act like tags saying, “flip off.” Because DNA methylation exists throughout various organisms, together with crops and animals, this analysis has broad implications for each agriculture and drugs. The work, printed in Nature Communications on January 11, 2022, identifies the CLSY genes as main components underlying epigenetic range in plant tissues.
“There have been many observations that one cell or tissue kind has a distinct DNA methylation sample than one other, however how the methylation pathways are modulated to finish up with completely different outcomes in several tissues has remained poorly understood,” says senior writer Julie Law, affiliate professor in Salk’s Plant Molecular and Cellular Biology Laboratory. “We discovered that which CLSYs are expressed in a given tissue is the mechanism controlling how the core DNA methylation equipment is directed to completely different genomic places in several tissues.”
The research of DNA methylation falls below the sphere of epigenetics—molecular modifications that change how the DNA capabilities with out altering the DNA sequence itself. It’s each a mandatory course of and a harmful one. For occasion, it helps set up cell identification in a growing embryo however may cause most cancers later in life. In crops, defects in DNA methylation may cause developmental defects and negatively impression crop yields.
DNA methylation is regulated by many components, together with sure sorts of small RNAs. Working with the mannequin plant Arabidopsis thaliana, the Salk staff found that the CLASSY gene household (CLSY 1–4) acts at completely different places relying on the tissue, revealing how various patterns of methylation are generated throughout plant growth.
The present work expands on a earlier research by Law and her staff wherein they discovered that in Arabidopsis, the CLSY genes decide which websites within the genome are methylated, through small RNAs. The present research addresses the bigger query of whether or not this course of may end up in completely different methylation patterns in several Arabidopsis tissues: leaf, flower bud, ovule, and rosette.
The researchers discovered that CLSY genes have been expressed otherwise relying on the plant tissue kind. For instance, all 4 CLSY genes have been expressed in flower buds, whereas CLSY3 was strongly expressed in ovules and CLSY1 was expressed in leaf and rosette tissues.
The researchers then in contrast crops with mutant CLSY genes towards wild-type crops. They discovered that relying on the tissue, completely different combos of CLSY members of the family, and even particular person CLSY proteins, managed small RNA and DNA methylation patterns at hundreds of websites all through the genome. These findings reveal the CLSY genes’ position in shaping the tissues’ epigenetic panorama.
The staff’s findings might open the door to advances in lots of areas, from boosting crop yields in crops to informing precision drugs in people. “Before figuring out how a range of DNA methylation patterns was generated throughout growth, we did not have the power to control that system. Finding that the CLSYs management methylation in a tissue-specific method represents a significant advance because it supplies scientists a strategy to alter DNA methylation patterns with a lot larger precision,” says Law.
Other authors included Ceyda Coruh, Guanghui Xu, Laura M. Martins, Clara Bourbousse and Alice Lambolez of Salk; and Ming Zhou of Zhejiang University in China.
Understanding how DNA is selectively tagged with ‘don’t use’ marks
More info:
The CLASSY household controls tissue-specific DNA methylation patterns in Arabidopsis, Nature Communications (2022). DOI: 10.1038/s41467-021-27690-x
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Salk Institute
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Plants depend on the CLASSY gene household to diversify their epigenomes (2022, January 11)
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