Disease and treatment

Researchers discover a basic mechanism determining plant growth

Only about 3% of the DNA in higher organisms represents genes. Scientists are currently seeking to understand how the remaining 97% affects the development of organisms. Now a team at University of Copenhagen have moved closer to capturing the complex evolution of life. By analysing the product of the transcription of genes that occur in the cell, plant researchers have found that many of the transcriptions are greatly abbreviated and that these abbreviated versions appear to help to regulate the transcription itself. This new knowledge is fundamental to understanding plant growth and crucial to learning how to regulate plant growth artificially.

Most people know the importance of a potted plant on a windowsill getting too much water or standing in direct sunlight. Few people, however, probably think about the cascade of complex reactions initiated within the plant when someone empties a glass of water into the saucer under the plant pot. A new research project once again reveals that knowing the genetics of an organism is not nearly sufficient to understand how it develops.

“We studied the transcription of the genetic code in plants and found that each gene is transcribed not into only one but on average four versions. About one seventh of the transcripts are greatly abbreviated versions relative to the full-length genes, and the abbreviated gene transcripts play a crucial role in helping to upregulate and downregulate how many times each gene is transcribed. Understanding this new regulatory mechanism is crucial to learning to understand and potentially regulate plant growth in the future,” explains Sebastian Marquardt, Associate Professor, Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen.

Missing address label

The new study focused on RNA polymerase II – an enzyme present in most organisms – whose role is to transcribe the DNA code in the genes into the sister molecule RNA. DNA stores and transmits genetic information, and the RNA transcriptions transport the genetic information by travelling between the chromosomes, where the genetic code is stored and the ribosomes, where the genetic code is converted into proteins.

“We used a new method, transcript isoform sequencing, to read the start and end of all the RNA molecules in cells. We could thus determine whether the transcripts made from a single DNA unit to RNA differed. The experiments showed that, on average, each DNA molecule in plants was converted into four versions, or isoforms. Naturally, the big question was: why are several versions of the same gene being made?” says Sebastian Marquardt.

The experiments were performed in Arabidopsis thaliana, which has been shown to be an excellent model plant for studying plants in general. The scientists examined the different types of transcriptions and could see some general trends in how they were constructed.

“Naturally, the whole gene was transcribed in some versions, but some of the transcriptions were versions that were either slightly abbreviated, for example, at the end, where the polyadenylation sites were deleted. Polyadenylation is like an address label that tells the cell that the molecules must be transported out of the nucleus so that they can be transcribed into proteins,” explains Sebastian Marquardt.

Replicated in flies and humans

However, many of the RNA molecules lacked these address labels, and 14% were relatively unstable short promoter-proximal RNAs.

“We examined these short promoter-proximal RNAs more closely and found that their function is to help regulate the transcription of DNA to RNA. So we found a feedback mechanism in which some of the transcribed products help influence how many transcriptions are produced,” explains Sebastian Marquardt.

The short promoter-proximal RNA likely both binds to and blocks the RNA polymerase II transcription, thereby slowing down the production of RNA. Thus, the cell’s RNA controls not only where the DNA transcriptions are sent but also how many of them are produced.

“We suspect that equivalents of short promoter-proximal RNA are present in both fruit flies and humans, since we know that some of the same mechanisms exist, so this turns out to be a very exciting discovery that likely illustrates a new principle of gene expression control in nature,” says Sebastian Marquardt.

This also represents a significant discovery for plant biotechnology, perhaps explaining some of the challenges that have been encountered in gene expression in plants.

“The new knowledge clearly shows that we cannot necessarily expect a gene to be expressed in a new plant solely by splicing it into the genome. The regulatory mechanisms are far more complex, and these mechanisms have to be considered in efforts to manipulate plant genomes to address future challenges such as increasing yield in future climates,” says Sebastian Marquardt.

Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis” has been published in Nature Communications. In 2015, the Novo Nordisk Foundation awarded a grant to Sebastian Marquardt for the project Functional Dissection of Long Non-coding RNA (lncRNA) Transcription.

Sebastian Marquardt
Associate Professor
Only a small proportion of the DNA in higher organisms represents genes. Curiously most of what we know about genomic information is derived from studying this minority (e.g. 3% of the human genome comprises genes). The number of genes does not scale with organismal complexity; it is for example similar in humans and worms. We are interested in elucidating functional contributions of the majority of DNA sequences that do not code for proteins (non-coding DNA). We know far less about non-coding DNA sequences than genes. Identifying the biological roles of non-coding DNA represents a pressing question in current genomics research. Interestingly, most non-coding sequences are actively transcribed by RNA polymerase II (Pol II) to yield long non-coding RNA (lncRNA). Gene promoters represent a conserved source of lncRNA through divergent non-coding transcription. However, the generated lncRNA molecules are not usually conserved, whereas genome-wide non-coding Pol II transcription is found in wide range of organisms. Our lab is thus interested in the functional consequences of non-coding transcription independent of the lncRNA molecules. We study how the mechanism of Pol II transcription of non-coding regions affects nearby gene expression through changes in chromatin packaging and modification. Non-coding transcription is sensitive to the cellular environment and responds dynamically. Currently, we are pursuing how this dynamic non-coding transcription may be part of plant environmental sensing mechanisms by studying transcription kinetics in environmental interactions.