Transcription Runs Like Clockwork
It’s not just a few key genes and proteins that cycle on and off in humans in a 24-hour circadian pattern as the sun rises and falls - but thousands
Howard Hughes Medical Institute researchers have discovered that thousands of genes in organs throughout the body show predictable daily fluctuations, and their cycles of activity are controlled in a complex variety of ways.
At the core of the new discovery is the finding the function of the enzyme that transcribes genes to be made into proteins -- RNA polymerase -- varies according to the circadian cycle. The study was published online August 30, 2012, by the journal Science.
“This finding gives us a new picture of the
temporal dynamics of transcription.”
Joseph S. Takahashi
Understanding how genes are cycled on and off throughout the day is key to understanding a number of biological functions, including human sleep and metabolism, says HHMI investigator Joseph S. Takahashi of the University of Texas Southwestern Medical Center. “If you look at the targets of these circadian genes, the top category is metabolic pathways. The clock is intimately involved in controlling metabolism on a daily basis.”
“This finding gives us a new picture of the temporal dynamics of transcription,” he says. “It gives us a new and interesting way to look at circadian cycles as well as polymerases and transcription in general.”
Takahashi has been studying the circadian gene
Clock and its protein product since discovering it
in the 1990s. He and others established that CLOCK
and two other proteins, BMAL1 and NPAS2,
bind to genes during the day to activate them,
whereas four other circadian regulators,
the proteins PER1, PER2, CRY1, and CRY2,
repress genes during the night.
All of the researchers wanted a global view of how activators and repressors work together to maintain the body’s 24-hour rhythms. So they undertook an in-depth study of where in the genome these regulatory proteins bound to target genes. Beginning with the liver cells of mice.
The team was surprised to find that one or more of the proteins bound to more than 20,000 sites. At more than 1,000 of those sites, all seven proteins could bind, however, many of the sites were targets for either circadian activators or repressors, but not both.
That was a surprise too, Takahashi:“We naively had thought that they would all just bind to the same locations.”
To determine how binding of the circadian proteins affected gene activity, the scientists went on to test the daily patterns of expression for all genes active in the liver.
To begin producing a protein from an active gene, cells first transcribe the information in that gene into RNA (thus, the amount of RNA corresponding to a particular gene can be used to measure gene activity).
Before an RNA molecule is used to produce a protein, however, it must undergo processing, which can influence how much protein will be produced. Interrupting portions of the code, known as introns, are cut-out. This leaves segments known as exons, which contain the essential information for building the protein specified by the gene.
Takahashi’s team then measured the presence of exon RNA and intron RNA in the liver cells separately. If the gene expression cycles were being controlled entirely at the level of transcription, exon and intron RNA would always increase and decrease at the same time.
But they found something entirely different. More than 2,000 genes showed circadian patterns of expression at the exon level, but fewer than 1,400 genes showed circadian patterns at the intron level. Moreover, of the intron RNA transcripts that cycled - all peaked at the same time, whereas the exon RNA transcript peaks were scattered throughout different times of day.
Takahashi: “When we compared the intron- and exon-cycling gene sets, we found very little overlap. Only about 22 percent of the exon-cycling genes are being regulated at the level of transcription.”
Increases and decreases happened at a later level of regulation for 78 percent of exon-cycling genes - rather than at the initial transcription of DNA to RNA, evidenced by the intron and exon RNA transcripts not matching up.
Delving further into how regulation occurs in genes that do have cycling at the transcription level, in order to figure out why they all peak at the same time, Takahashi and colleagues tested the timing of the first step in transcription, the binding of RNA polymerase II to the genes.
He discovered that binding of RNA polymerase II was occurring much earlier in the day than gene transcription.
CLOCK and BMAL1, the activators of transcription, recruit RNA polymerase II at the beginning of the cycle, but are repressed by the presence of the inhibitor, CRY1. As a consequence, RNA polymerase is paused for a few hours before it can begin transcription. Thus, the circadian-rhythm-dependent steps involve both RNA polymerase recruitment and release from this poised state.
“What we ended up discovering was that
RNA polymerase II initiation is circadian
on a genome-wide level.
Along with the global regulation of RNA polymerase II
and transcription, we also found a global regulation
of chromatin state by the circadian clock.
Histone proteins that are critical for maintaining
the integrity of DNA were also modified extensively
on a circadian basis across the genome.”
Joseph S. Takahashi
Accordingly, this suggests that virtually every gene has the potential to be modulated along with the circadian cycle.
The next step, Takahashi believes, is to figure out how RNA polymerase is controlled on a daily basis and what makes the polymerase pause in some genes at certain times of the day. And, of course, there is the question of how other RNA molecules are being regulated after transcription - that still remains.
Original article: http://www.hhmi.org/news/takahashi20120830.html