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Epigenetic Biotimer Revealed in Flowers

Photo credit: Ⓒ David Coppedge.

Biology should never be considered ordinary. Take almost any biological process, and the details are likely to overwhelm the reader. That is certainly the case with a new paper about flowering in plants. Even in the well-studied lab plant Arabidopsis thaliana, researchers described dozens of genes, proteins, and accessory molecules working together to ensure the proper moment for flowering.

The paper in Plant Cell is difficult to read for laymen, because geneticists have given very odd names to genes and proteins. Then, according to custom, some genes for A. thaliana are written in italics, but other genes and their protein products are italicized in ALL CAPS. One must wade through a jungle of names like KNUCKLESGIANT KILLER, SPOROCYTLESS, DEFECTIVE ANTHER DEHISCIENCE1, and AT HOOK MOTIF NUCLEAR LOCALIZED PROTEIN18. After first mention in a paper, fortunately, these are usually abbreviated to KNU, GKI, SPL, and so forth, but then it is hard to remember what they do, especially when they all interact in complex ways. 

Complexifying the situation further, the nomenclature rules have changed over time and are not consistent between publications. Some letters are not capitalized, and some have a suffix consisting of letters and numbers to identify a particular allele. There are also rules for mutant forms and wild type forms. The rules may seem like a mess to non-specialists (read about them at, but I suppose the strange mnemonic names are more helpful than hard-to-memorize strings like g2934ab0x or worse (although rules for epigenetic marks are less mnemonic, like H3K27me3 (“histone 3, lysine 27, methyl group 3”). For this reason, I will try to refrain from referring to the labels and focus instead on processes and functions that go on, which are truly amazing.

The Basics

In a nutshell, scientists at the Nara Institute of Science and Technology (NAIST) in Japan identified key genes, proteins, and epigenetic factors that switch on flowering with precision timing. So accurate was the “biotimer” they found, they could predict when flowering would occur, even if they altered some of the components. They created mutants of some components, and with a mathematical model they designed, they could calculate to the day when an apical meristem (i.e., the tip of a growing stem) would switch its stem cells from proliferation mode to differentiation mode and start to grow the parts of the flower. The precision astonished them. says,

The intricate process of flower development has long fascinated scientists seeking to unravel the mysteries behind nature’s precision timing. In a study published in the journal The Plant Cell, a research team led by Nara Institute of Science and Technology (NAIST), Japan has shed light on the inner workings of floral meristem termination and stamen development, uncovering a unique mechanism driven by the interplay of genetic and epigenetic factors. [Emphasis added.]

In Southern California where I live, everyone is thrilled when the poppies bloom. Vast acres of the plants bloom together in late March or early April, as if on cue, painting whole valleys and hillsides in golden orange. The flowers can also close up if the temperature drops or the wind blows and then reopen when the sun shines warmly again. How do they do it? In every part of the world, plants show remarkable timing in their flowering: cherry blossoms in Washington DC, tulips in Holland, daylilies in Taiwan. Their secrets remain mysterious. In California, everyone thought the heavy winter rains would yield a poppy superbloom, but it was only modest compared to those of past years during the drought. Somehow, plants sense just the right combination of external cues to put on their best show.

To unlock the secrets of this remarkable system, the researchers devised a mathematical model capable of predicting gene expression timing with astonishing accuracy. By modifying the length of H3K27me3-marked regions within the genes, they successfully demonstrated that gene activation could be delayed or reduced, confirming the influence of this epigenetic timer. The team’s findings offer a novel perspective on how nature controls the gene expression during flower development.

The Histone Code

The story revolves around epigenetic markers on the genes of the A. thaliana stem cells. Over twenty years ago, David Allis (1951-2023) introduced a bold concept: there was another code at work in the genome: a combinatorial regulatory system. In its obituary, Nature Genetics says,

Perhaps Allis’s most famous conceptual contribution to the field of chromatin research was the elaboration of the ‘histone code’ hypothesis more than 20 years ago. This framework suggested that histone post-translational modifications (PTMs), in different combinations, along with the proteins that can ‘write’, ‘read’ or ‘erase’ them, constitute the basis for a gene regulatory code. In other words, certain histone PTMs could label particular chromatin regions and potentially influence their transcriptional activity. Many of these histone PTMs have been used extensively to characterize or infer a cell state, identity and behavior. For example, methylation marks at H3K27 and H3K9 are mostly associated with gene repression, whereas others, such as H3K4 methylation and H3K27 acetylation, are associated with active regulatory regions.

And so it is in A. thaliana, the authors of the current paper show. The genetic code has the blueprint to make the parts; the epigenetic “histone code” has the switch and the timer.

How It Works

The biotimer described in the paper works by a process of “passive dilution” that is cell cycle dependent. The normal condition for the AGAMOUS transcription factor is to repress flowering. This factor, abbreviated AG, is studded with histone markers (H3K27me3) which repress multiple genes required for “floral meristem termination,” the term for the switch to flowering. Stem cells will proliferate (divide) endlessly by mitosis until the switch is thrown to stop making clones of themselves and start differentiating into stamens, pistils, and petals. It reminds me of Paul Nelson’s comment about chicken egg development in the documentary Flight, where he describes how certain cells in the embryo “are committing themselves, in most cases irreversibly, to particular functional roles.”

For flowers to form, the floral meristem (floral stem cells) must irreversibly commit to becoming cells making up the various floral organs (sepals, petals, stamens, and carpels), a process known as floral meristem termination. Proper timing of floral meristem termination involves temporal activation of the transcription factor gene KNUCKLES (KNU) by its upstream regulator AGAMOUS (AG) via cell cycle-dependent dilution of the repressive histone modification at lysine 27 of histone H3 (H3K27me3) along the KNU coding sequence. This intrinsic ‘biotimer’ will activate KNU at precisely the right time to ensure proper flower development.

Passive dilution involves the washing out of the histone markers at each cell division. AG evicts PRC2, a histone methylator, and prevents histone H3 marks on nucleosomes. If a cell has six of these repressive markers at the beginning, the daughter cells will have three after the next cell division. At some point, there will not be enough markers to repress differentiation, and the cell will commit irreversibly to floral meristem termination. By inserting values into their mathematical model of this passive dilution mechanism, they were able to accurately predict when a plant in the lab would commence flowering. They validated the model with mutant forms of the genes, either speeding up or slowing down this mechanistic “countdown timer” operated by the epigenetic code. When one protein was activated too early, it produced short stamens that were sterile. This shows that attention to timing between parts of the system is crucial to successful flower development.

Interestingly, the biotimer was also temperature dependent. The team grew some of the plants at 18°C (64° F) instead of the usual 22° C (72° F) and observed that flowering was delayed. The explanation is that lower temperature slows down mitosis, which slows down the passive dilution mechanism. 

We also observed a delay in KNU activation by growing plants at 18°C, likely due to slower growth kinetics. This observation emphasizes the dynamic regulation of H3K27me3 in response to extracellular and intracellular cues and suggests a role for the cell cycle–dependent biotimer in coordinating the balance between cell proliferation and differentiation.

It’s a wise strategy to ensure that flowers will have good weather conditions for blooming. Temperature is only one external cue that probably affects the timer. “Additional experiments will be necessary,” they say, to clarify the effect of lower temperatures and other external cues. These may include water and nutrient availability, day length, risk of herbivores, presence of fungal partners, or other factors.

Appropriately the paper avoids Darwin. How flowering plants exploded into appearance was an abominable mystery to him. The evolution-free paper and news release used a term alien to unguided natural processes but familiar to engineers and designers of complex systems with multiple cooperating parts: 

Through meticulous investigations in the model plant Arabidopsis thaliana, the team discovered that AG serves as a master conductor, orchestrating gene expression through a process known as cell cycle-coupled H3K27me3 dilution. This remarkable phenomenon involves the dilution of a histone modification called H3K27me3 along specific gene sequences, effectively kickstarting gene activation. The scientists identified several key genes directly regulated by AG at various time points of this cycle.

The study revealed a genetic network tightly controlled by AG, with genes such as KNUCKLES (KNU), AT HOOK MOTIF NUCLEAR LOCALIZED PROTEIN18 (AHL18), and PLATZ10 emerging as critical players. “By unraveling the inner workings of this regulatory circuit, we gained unprecedented insight into the intricate timing mechanisms that drive proper floral meristem termination and stamen development,” says first author Margaret Anne Pelayo.

Orchestration: aside from its well-known meaning in music — getting all the skilled instrumentalists to play their own designed parts at the right time in harmony — it also means “the plans or planning necessary to arrange something or cause something to happen.” To see an automatic mechanism in a humble herb working to achieve orchestration of multiple parts within a stem cell in a meristem as it switches to flower preparation is quite remarkable. Yet even that is just the start of an entire concert of orchestrated masterpieces as the organs develop, the petals take on their shapes and colors, and the completed flower opens for business. Below, watch as a musical orchestra celebrates this biological orchestration. Bravo!