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Pregnancy Timeline by SemestersFetal liver is producing blood cellsHead may position into pelvisBrain convolutions beginFull TermWhite fat begins to be madeWhite fat begins to be madeHead may position into pelvisImmune system beginningImmune system beginningPeriod of rapid brain growthBrain convolutions beginLungs begin to produce surfactantSensory brain waves begin to activateSensory brain waves begin to activateInner Ear Bones HardenBone marrow starts making blood cellsBone marrow starts making blood cellsBrown fat surrounds lymphatic systemFetal sexual organs visibleFinger and toe prints appearFinger and toe prints appearHeartbeat can be detectedHeartbeat can be detectedBasic Brain Structure in PlaceThe Appearance of SomitesFirst Detectable Brain WavesA Four Chambered HeartBeginning Cerebral HemispheresFemale Reproductive SystemEnd of Embryonic PeriodEnd of Embryonic PeriodFirst Thin Layer of Skin AppearsThird TrimesterSecond TrimesterFirst TrimesterFertilizationDevelopmental Timeline
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Home | Pregnancy Timeline | News Alerts |News Archive Aug 14, 2013

 

Dorsal-ventral patterning (gene alignment shown in RED) is one of a few genes active before and after the midblastula transition. Segmentation genes (GREEN) are turned on during the midblastula transition. Cell nuclei are shown in blue.

The midblastula transition is a stage during blastula formation in embryonic development in which genes now represent the zygote, a unique organism. Transcription refers to a particular segment of DNA being copied into RNA by the enzyme, RNA polymerase, in order to contribute to the developing organism. Dorsal  refers to a position towards the developing organism's back. Ventral is the position located towards the developing organism's front.


Image Credit: Kai Chen






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How genes tell cell 'Read me now!'

Stowers research shows that DNA sequences at the beginning of genes contain more information than previously thought.

When egg and sperm combine, the new embryo bustles with activity. Cells multiply so rapidly, they largely ignore their DNA, other than to copy and read just a few essential genes. Embryonic cells mainly rely on molecular instructions placed in the egg from the mother in the form of RNA.

The cells translate these RNA molecules into proteins that manage almost everything in the first minutes or hours of the embryo's life. Then, during the "midblastula transition," cells start transcribing (reading) massive amounts of their own DNA. How embryonic cells flag a small set of genes for transcription before the midblastula transition, holds important information about normal development and disease in animals and in humans.

A new study by researchers at the Stowers Institute for Medical Research, led by associate investigator Julia Zeitlinger, Ph.D., sheds light on these questions. It appears in the Aug. 13 issue of eLife Sciences.


In the fruit fly Drosophila melanogaster, genes active in the first two hours of fertilization are read quickly due to a region aptly named the "promoter." Within each promoter region, short control elements— or "boxes"—instruct crews of RNA polymerases, where and when to begin transcribing (reading and interpreting) a gene.


Researchers have long thought that once an RNA polymerase appears at the worksite it quickly finishes the job of trascription. "Our most important result is that promoters are different," Zeitlinger says. "The general paradigm for a long time has been a promoter is a promoter. But really, what we see is that they have different functions."


While a postdoctoral fellow at MIT, Zeitlinger unexpectedly discovered RNA polymerase II will pause at the beginning of a gene, as if taking a lunch break. More often than not, pausing occurred at genes specific to development. A thought ocurred, pausing may signal molecular construction workers on site that a huge work order is coming.


"We wondered whether pausing was prepartion for global gene activation during the midblastula transition," says Kai Chen, PhD, a former graduate student in Zeitlinger's lab and the study's first author. "We expected to see widespread pausing before that transition."

The fruit fly Drosophila melanogaster is a perfect test subject for this experiment as the fly embryo takes two hours to reach the midblastula transition. This provides scientists plenty of time to analyze this early embryonic phase. Chen used a method called ChIP-seq to locate RNA polymerase II molecules on a gene.


Paused polymerases showed up only at the beginning of genes. Working polymerases, however, could be found throughout the gene body.


These results took the Stowers team by surprise. Before the midblastula transition, RNA Polymerase II appeared to rarely pause as it transcribed roughly 100 early genes. No construction crews sat idle on inactive genes in preparation for the midblastula transition. Pausing only became widespread during the midblastula transition.

"What we found was not what we expected at all," Zeitlinger says. Before the midblastula transition, instead of preparing for a huge workload the construction crews were busy completing rush jobs. "The polymerase has to come to the promoter and immediately transcribe because there's so little time to do the job. That's one way of making transcription faster. "

When Chen and colleagues computationally compared the DNA sequences of promoters—where pausing occurred compared with where it didn't—a pattern emerged. They found that three different types of promoters correlated with the construction crew's pausing behavior.

The genes that RNA Polymerase II reads before the midblastula transition were often preceded by a promoter that seemed to yell, "Urgent! Don't even think about pausing."


Promoter genes contain what's known as a TATA-box, a conserved arrangement of nucleotides, commonly TATAA.

Midblastula genes are regulated by promoters containing elements found within paused RNA polymerase as well: GAGA, Downstream Promoter Element (DPE), Motif Two Element (MTF) and Pause Button (PB).

But a third type of promoter was also found, containing both the TATA-box and pausing sequences. This third type of promote does not pause immediately - but begins to pause during the midblastula transition.


Zeitlinger hopes learning more about promoters will give clues to the functions of unknown genes, as promoter sequences are not specific to flies. Differences among promoter types may be conserved in other animals as well.

Zeitlinger adds: "My lab is interested in understanding how development or even diseases are encoded in the genome. If we understand transcription, then we can predict a lot of what genomes encode, in terms of disease or differences between individuals. Promoters had been seen by some scientists as sort of boring, but now, they are starting to get really interesting."

Abstract
Massive zygotic transcription begins in many organisms during the midblastula transition when the cell cycle of the dividing egg slows down. A few genes are transcribed before this stage but how this differential activation is accomplished is still an open question. We have performed ChIP-seq experiments on tightly staged Drosophila embryos and show that massive recruitment of RNA polymerase II (Pol II) with widespread pausing occurs de novo during the midblastula transition. However, ∼100 genes are strongly occupied by Pol II before this timepoint and most of them do not show Pol II pausing, consistent with a requirement for rapid transcription during the fast nuclear cycles. This global change in Pol II pausing correlates with distinct core promoter elements and associates a TATA-enriched promoter with the rapid early transcription. This suggests that promoters are differentially used during the zygotic genome activation, presumably because they have distinct dynamic properties.

DOI: http://dx.doi.org/10.7554/eLife.00861.001

Other contributors include Jeff Johnston, Wanqing Shao, Samuel Meier and Cynthia Staber, all from the Stowers Institute.

The study was funded by the Stowers Institute for Medical Research, the Pew Charitable Trust and an NIH New Innovator Award.

About the Stowers Institute for Medical Research

The Stowers Institute for Medical Research is a non-profit, basic biomedical research organization dedicated to improving human health by studying the fundamental processes of life. Jim Stowers, founder of American Century Investments, and his wife Virginia opened the Institute in 2000. Since then, the Institute has spent over 900 million dollars in pursuit of its mission.

Currently the Institute is home to nearly 550 researchers and support personnel; over 20 independent research programs; and more than a dozen technology development and core facilities. Learn more about the Institute at http://www.stowers.org.

Original press release: http://www.eurekalert.org/pub_releases/2013-08/sifm-uhg081313.php