Scientists discover dynamics of transcription in living mammalian cells

August 6, 2007

Transcription — the transfer of DNA’s genetic information through the synthesis of complementary molecules of messenger RNA — forms the basis of all cellular activities. Yet little is known about the dynamics of the process — how efficient it is or how long it takes. Now, researchers at the Albert Einstein College of Medicine of Yeshiva University have measured the stages of transcription in real time. Their unexpected and surprising findings have fundamentally changed the way transcription is understood.

The researchers used pioneering microscopy techniques developed by Dr. Robert Singer, co-chair of anatomy & structural biology at Einstein and senior author of the study, which appears in the August issue of Nature Structural & Molecular Biology.

The study focused on RNA polymerase II--the enzyme responsible for transcription. During transcription, growing numbers of RNA polymerase II molecules assemble on DNA and then synthesize RNA by sequentially recruiting complementary RNA nucleotides.

To visualize the transcription process, the researchers used living mammalian cells, each of which contained 200 copies of an artificial gene that they had inserted into one of the cell’s chromosomes. Then, by attaching fluorescent tags to RNA polymerase II, they were able to closely monitor all three phases of the transcription process: binding of the enzyme molecules to DNA, initiation (when the enzyme links the first few RNA nucleotides together) and elongation (construction of the rest of the RNA molecule). As they observed the RNA polymerase II molecules attaching to DNA and making new RNA, they saw many cases where enzyme molecules attached — and then promptly fell off.

“One surprising finding was how inefficient the transcription process really is, particularly during its first two stages,” says Dr. Singer. “It turns out that only one percent of polymerases that bind to the gene actually remain on to help in synthesizing an RNA molecule. Transcription is probably inefficient for a reason. We’re not sure why, but it may be because all the factors needed for transcription have to come together at the right time and the right place, so there’s a lot of falling off and adding on of polymerases until everything is precisely coordinated.”

The researchers observed that the binding phase of transcription lasted six seconds and initiation lasted 54 seconds. By contrast, the final stage of transcription — elongation of the RNA molecule — took a lengthy 517 seconds (about eight minutes). The possible reason: The “lead” polymerase on the growing polymerase II enzyme sometimes “paused” for long periods, retarding transcription in the same way that a Sunday driver on a narrow road slows down all traffic behind him. But in the absence of pausing, elongation proceeded much faster — about 70 nucleotides synthesized per second — than has previously been reported.

These two phenomena — pausing and rapid RNA synthesis during elongation — may be crucial for regulating gene expression. “With this sort of mechanism, you could have everything at the ready in case you suddenly needed to rev up transcription,” says Dr. Singer. “Once the ‘paused’ polymerase starts up again, in a very short time you could synthesize a new batch of messenger RNA molecules that might suddenly be needed for making large amounts of a particular protein.”

Source: Albert Einstein College of Medicine

Explore further: Chemists and applied physicists observe RNA polymerase at work in real time

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not rated yet Apr 05, 2008

New Light On Transcription Mechanics


A. Transcription Of Genes

A gene is a DNA sequence (in my view: an organism, member of the genome's genes collective commune. DH) that is transcribed to produce a functional product.

"Before a cell can begin to divide or differentiate, the genetic information within the cell's DNA must be copied, or "transcribed," onto complementary strands of RNA. RNA polymerase II (pol II) is an enzyme that, by itself, can unwind the DNA double helix, synthesize RNA, and proofread the result. When combined with other molecules that regulate and control the transcription process, pol II is the key to 'successful interpretation of an organism's genetic code'".
(per my view should be: 'successful regeneration and functioning of the genome organism').

B. New Light On Transcription Mechanics

The researchers activated (induced into action. DH) 'heat shock genes', which protect cells from sudden rises in temperature, and watched them in real time as they began to be transcribed. The researchers also tagged Pol II with a fluorescent marker to track its movements within the nucleus.

"You see the genes decondense and fill up with polymerase, but they're not moving anywhere...", the transcription machinery assembles at the called-upon locus, regardless of its position in the nucleus.

Looking at the location of co-regulated heat shock genes, genes that are transcribed (copied for functioning. DH) simultaneously, they found that co-regulated pairs that occupied distinct sites before heat shock were no closer together after heat shock.

And the researchers found that over time Pol II began to recycle itself within newly formed "compartments" around the activated gene.

"At some point you accumulate enough polymerase that it feeds back, so in a sense you've created a factory de novo" said Lis. "This is, to our knowledge, the first demonstration of Pol II recycling at a specific gene in vivo."

C. Beautiful, impressive combination of developed novel research techniques and procedures, and impressive results.

Fwd by Dov Henis

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