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Nitchakan Chaiprukmalakan

Missing Lincs - Science News - 6 views

    • Nitchakan Chaiprukmalakan
       
      Scientists are finding more information about the importance of the non coding RNAs, lincRNAs.
  • Only now have scientists begun identifying the previously invisible contractors who make sure that materials get where they are supposed to be and in the right order to build a human being or any other creature. Some of these little-known workers belong to a class of molecules called long intergenic noncoding RNAs.
  • And the lincRNAs originate in what scientists used to view as barren wastelands between protein-coding genes. But new research is showing that these formerly underappreciated workers have important roles in projects both large and microscopic.
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  • In the last few years, scientists have learned that lincRNAs, as well as other RNAs that are long and noncoding but not intergenic, perform a variety of jobs. Some serve as guides showing proteins where to go, while others tether proteins to different types of RNA, or to DNA. Some work as decoys, distracting regulatory molecules from their usual assignments. Some may even have multiple roles, all the while chattering away to other RNA within cells. (It is not idle gossip; RNA communication within cells may ward off diseases such as cancer.) And as the ultimate multitaskers, lincRNAs keep proper cellular development ticking along and help define what makes mice mice and people people.
  • That archive contains about 3 billion genetic letters, far more than the genomes of less complex organisms such as roundworms and fruit flies.
  • In 2005, the research revealed that even though genes that code for proteins make up only 1.5 percent of the mouse genome, more than 63 percent of the genome’s DNA is copied into RNA. In humans the number is even higher, with up to 93 percent of the genome made into RNA, even though protein-coding genes make up less than 2 percent of the genome.
  • At first, many scientists didn’t know what to make of the excess RNA. Some thought it was overexuberance on the part of the DNA-copying machinery. But gradually researchers began to realize that many of those extra RNAs had important jobs to do.
  • Some, though, appear to act like general contractors — not hammering in the nails and pouring the foundations of cells themselves, but dictating how the job should be done.
  • One of the most famous long noncoding RNAs, known as XIST, is also one of the most hands-on. XIST is in charge of shutting down one of the X chromosomes in every single cell of women and girls
  • XIST doesn’t have a long commute to work; it coats whichever X chromosome makes it, preventing other genes on the chromosome from being activated
  • One of the most well-studied linc­RNAs, named HOTAIR, wasn’t lucky enough to get a job close to home. It is copied from DNA on chromosome 12 but has to travel to chromosome 2 to shut down several genes in a group known as the HOXD cluster, genes important for proper development of an organism
  • Not only does HOTAIR help direct development, but it is also important throughout life to help cells pinpoint their location in the body.
  • Whether promoting health or mis­directing cells, lincRNAs don’t necessarily act alone.
  • A lincRNA known as HOTTIP also works with a crew of histone modifiers, but instead of shuttering genes, HOTTIP’s crews hang grand-opening signs to attract gene-activating machinery
  • In the recipe for humans, lincRNAs are in the thick of things from the very beginning. At least 26 different lincRNAs need to be on to keep an embryonic stem cell a stem cell
  • Just how lincRNAs choose which genes to turn on and off isn’t yet known. But Pier Paolo Pandolfi, a geneticist at Beth Israel Deaconess and Harvard Medical School, suspects that the lincRNAs are whispering to each other and to other RNAs, keeping tabs on all a cell’s goings-on. Pandolfi laid out his hypothesis for how this chatter might help control protein production and other processes in the Aug. 5 Cell.
  • The Columbia team and Pandolfi’s team independently found that tweaking levels of a few messenger RNAs that distract microRNAs from PTEN messenger RNA can lead to prostate cancer or a type of brain tumor called glioblastoma. Just messing with levels of a messenger RNA from another gene known as ZEB2 throws off PTEN protein levels and can lead to melanoma in mice, Pandolfi’s group reported in another paper in the Oct. 14 Cell.
  • Losing one noncoding RNA may be disastrous for a cell, but for want of noncoding RNAs whole species may never have evolved, argues Queensland’s Mattick. He and others say the real function of lincRNAs is to give evolution a sort of molecular clay from which to mold new designs.
  • Humans have several lincRNAs that are found in no other species. Many of those RNAs are made in the brain, leading scientists to speculate that the molecules may be at least partially responsible for that important organ’s evolution.
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    Is RNA the most important molecule in the cell? There is a lot of evidence leading to new understandings of RNA and it's role in many different mechanisms within a cell.
Mickey Tsai

Parkinson's disease sufferer Sheila Roy can write for the first time in 15 years thanks... - 0 views

  • one of only 15 people worldwide to undergo the radical treatment, which involves inserting corrective genes into the brain
  • The genes provide the coded instructions for proteins needed to make dopamine, a brain chemical essential for proper control of movement.
  • Lack of dopamine leads to the symptoms of tremor, stiffness and poor balance associated with Parkinson’s.
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  • Mrs Roy is taking part in an early-stage study of the ProSavin therapy
  • Following her treatment Sheila Roy has been able to carry out tasks like writing, something she has been unable to do for 15 years
  • Gene therapies hold great promise for people with Parkinson’s in the future, as they could mean an end to the daily regime of drugs that most people with the condition currently face.
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    A woman with Parkinson's was able to write for the first time in 15 years because of gene therapy. Parkinson's includes symptoms such as tremors, loss of balance which makes it impossible to do even simple tasks. Doctors injected a modified virus carrying the genes to the motor centre of her brain which provide coded instructions for proteins needed to make dopamine. Lack of dopamine leads of the symptoms associated with Parkinson's. This is part of the ProSavin therapy developed by Oxford BioMedica. Gene therapies hold a lot of hope for people with Parkinson's that could end the daily routine of drugs that most of them go through.
nidthamsirisup

Mysterious Noncoding DNA: 'Junk' or Genetic Power Player? | PBS NewsHour - 0 views

  • Genes represent only a tiny fraction -- 1 percent -- of our overall genetic material. Then there's the other 99 percent of our DNA -- the stuff that doesn't make protein
  • Researchers have found that some of this noncoding DNA is in fact essential to how our genes function and plays a role in how we look, how we act and the diseases that afflict us.
  • Embedded in this 99 percent is DNA responsible for the mechanics of gene behavior: regulatory DNA. Greg Wray of Duke University's Institute for Genome Sciences and Policy describes the regulatory DNA as the software for our genes, a set of instructions that tells the genome how to use the traditional coding genes.
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  • "It's like a recipe book," Wray said. "It tells you how to make the meal. You need to know the amounts. You need to know the order. The noncoding DNA tells you how much to make, when to make it and under what circumstances."
  • common diseases are probably more influenced by regulatory differences, Harismendy said. These include Type 2 diabetes, Crohn's disease, Alzheimer's Disease and a variety of cancers, including breast, colon, ovarian, prostate and lung.
  • According to Wray, research has shown that diseases like bipolar syndrome and clinical depression may be associated with noncoding mutations that determine whether the brain is producing too much or not enough of a particular neurotransmitter. One noncoding mutation gives a person almost complete protection against the nasty malaria parasite, plasmodium vivax.
  • Another piece of noncoding DNA regulates the enzyme responsible for lactose tolerance, the ability to digest milk. Research by Wray and other scientists has shown that in four populations where dairy consumption is a vital part of the diet, new mutations have appeared that essentially keep the gene that produces the lactase enzyme from switching off.
  • And recent research done by evolutionary biologists suggests that differences in regulatory DNA may represent a major part of what separates us from chimpanzees.
nidthamsirisup

Stem Cell Treatment Spurs Cartilage Growth - Science News - 0 views

  • A small molecule dubbed kartogenin encourages stem cells to take on the characteristics of cells that make cartilage, a new study shows
  • And treatment with kartogenin allowed many mice with arthritis-like cartilage damage in a knee to regain the ability to use the joint without pain.
  • Kartogenin steers the stem cells to wake up and take on cartilage-making duties. This is an essential step in the cartilage repair that falls behind in people with osteoarthritis, the most common kind of arthritis, which develops from injury or long-term joint use.
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  • The molecule turned on genes that make cartilage components called aggrecan and type II collagen. Tests of mice with cartilage damage similar to osteoarthritis showed that kartogenin injections lowered levels of a protein called cartilage oligomeric matrix protein. People with osteoarthritis have an excess of the protein, which is considered a marker of disease severity.
  • kartogenin inhibits a protein called filamin A in the mesenchymal stem cells
Kaoko Miyazaki

The Rinn Lab - 0 views

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    John Rinn (RNA researcher at Harvard Medical School) continues on his ongoing research about Long Intergenic Noncoding RNA's (lincRNAs). lincRNAs used to be overlooked and classified as 'waste' products, but today it is seen as the contractors that create the DNA's coding sequence needed for the organism's structure. In simpler terms, lincRNAs are responsible for putting molecular materials in places they are supposed to be - as though following a rough draft to make a final master piece. Because lincRNAs have so many functions, if step goes wrong, it could cause potential harm to the organism such as creating a tumor. But because of their many functions like guiding the interactions of protein DNA to name one, John Rinn and other current scientists hypothesize that lincRNAs are what differentiates us from other organisms and makes us, us.
Paige Prescott

Old Cancer Drugs Offer New Tricks - Science News - 0 views

  • Drugs that alter some chemical tags on DNA make cancer cells behave more like normal cells
  • And the drugs seem to make cancer cells more susceptible to chemotherapy and attacks from the immune system.
  • drugs called azacitidine and decitabine, when used in low doses, change gene activity in leukemia and breast cancer cells in the lab. If DNA is a cell’s hard drive, then chemical tags attached to the DNA or DNA-packaging proteins called histones serve as software packages to tell the hard drive how to function. This type of chemical programming is called epigenetics.
Mickey Tsai

Autism gender bias clue found - Health - CBC News - 0 views

  • four times more common among males than females.
  • rare family with four generations in which males carrying the glitch were affected but females were not.
  • When male fetuses are missing one copy of the gene, it throws off their developmental process enough to lead to autism but female biology differs enough that it doesn't matter.
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  • now that doctors know that the SHANK 1 gene is involved and it can be tested for, they'll know to follow affected males very closely and offer treatments early on.
  • lved and it can be tested for, they'll know to follow affected males very c
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    Scientists have long wondered why autism is much more common among males than females. When males miss one copy of a gene it messes up the development process enough to cause autism but female biology differs enough to make it not matter. Now that scientists have identified that the SHANK 1 gene is involved they can test for it and could offer treatments early.
Rafael Chen

Scientists develop tools to make more complex biological machines from yeast - 0 views

  • creating a new type of biological "wire," using proteins that interact with DNA and behave like wires in electronic circuitry
  • it can be re-engineered over and over again
  • fundamental DNA components, called "promoters," which are needed for re-programming yeast
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  • Future applications of this work could include tiny yeast-based machines that can be dropped into water supplies to detect contaminants, and yeast that records environmental conditions during the manufacture of biofuels to determine if improvements can be made to the production process.
  • help to improve things such as pollution monitoring and cleaner fuels
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    Scientist uses yeast as the foundations in making more complex biological machines through genetic engineering.
Rafael Chen

New Plant Mutation Produces Tap Root With Large Amounts Of Oil, Proteins, And Starch - 1 views

  • The discovery could lead to genetically engineered plants that store commercially useful substances in an enlarged root
  • The pickle mutation mimics what happens in seeds, which typically are the major structures accumulating and storing proteins and oil
  • In this mutation the cells destined to become primary root cells retain the character of embryonic cells
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  • They fail to make the switch from embryonic to adult
  • The mutation has its greatest effect when gibberellin is not present during the first 24 hours of growth
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    A mutation in plants that makes the tap root accumulate large amounts of oils, proteins, and starch was discovered by scientist, this could lead to genetically engineered plants that store commercially useful substances in an enlarged root.
orasa sukmark

Making a Friendlier Mosquito - Biology Online - 1 views

  • Genetically modified mosquitoes that cannot transmit malaria are one hope for battling the disease that still kills over one million people a year. But that plan faces some serious snags, according to UC Davis researchers who are suggesting an alternative strategy.
  • nsmit malaria are one hope for battling the disease that still kills over one million people a year. But that plan face
  • Genetically modified mosquitoes that cannot transmit malaria are one hope for battling the disease that still kills over one million people a year.
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  • enetically modified mosquitoes that cannot transmit malaria are one hope for battling the disease that still kills over one million people a year. But that plan faces some serious snags, according to UC Davis researchers who are suggesting an alternative strategy
  • releasing into the wild mosquitoes genetically engineered to resist malaria
  • If the resistant mosquitoes breed and spread their genes through the population, malaria transmission should be shut down.
  • the malaria resistance genes available are not very effective
  • , there's no way to reliably push the genes through the population.
  • Transposons are essentially DNA parasites that snip themselves in or out of the genome under the right circumstances. Scientists can add a new gene into a transposon and use it to carry that DNA into the insect genome. But it's in the interest of that transposon to just get rid of the extra DNA,
  • a transposon that gives an advantage to mosquitoes that already carry genes to block malaria, so that those genes spread through the population by natural selection.
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    scientists have found a way to reduce mosquitoes that can transmit malaria. 
wasin kusakabe

Athletic frogs have faster-changing genomes - 0 views

    • wasin kusakabe
       
      Physical activities can change the DNA sequence which can be passed on to later generations. However this has only been tested on frogs and may not apply to mammals like us.
  • athletic frogs tended to have faster-changing genomes.
  • Stretches of DNA accumulate changes over time
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  • Physically fit frogs have faster-changing genomes
  • During exercise, the circulatory system provides blood and oxygen to the tissues that are needed most
  • When physical activity has stopped, the rush of blood and oxygen when circulation is restored to those tissues produces a burst of free radicals that can cause wear and tear on DNA, eventually causing genetic changes that -- if they affect the DNA of cells that make eggs or sperm -- can be passed to future generations.
nidthamsirisup

Epigenetics Seeks Clues to Mental Illness in Genes' Life Story - Science in 2011 - NYTi... - 0 views

  • epigenetics, the study of how people’s experience and environment affect the function of their genes.
  • Studies suggest that such add-on, or epigenetic, markers develop as an animal adapts to its environment, whether in the womb or out in the world — and the markers can profoundly affect behavior.
  • In studies of rats, researchers have shown that affectionate mothering alters the expression of genes, allowing them to dampen their physiological response to stress. These biological buffers are then passed on to the next generation: rodents and nonhuman primates biologically primed to handle stress tend to be more nurturing to their own offspring, and the system is thought to work similarly in humans.
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  • the offspring of parents who experience famine are at heightened risk for developing schizophrenia, some research suggests — perhaps because of the chemical signatures on the genes that parents pass on.
  • in some people with autism, epigenetic markers had silenced the gene which makes the receptor for the hormone oxytocin. Oxytocin oils the brain’s social circuits, and is critical in cementing relationships; a brain short on receptors for it would most likely struggle in social situations.
  • In one large study of people with schizophrenia, researchers at Johns Hopkins are analyzing blood and other data to see whether the degree of epigenetic variation is related to the inherited risk of developing the disorder. In another, researchers at Tufts are studying the genes of animals dependent on opiates to see how epigenetic alterations caused by drug exposure affect the opiate sensitivity of the animals’ offspring.
Nitchakan Chaiprukmalakan

New study: Tracking proteins that repair DNA - 0 views

  • DNA damage could be caused by many things including toxins, radiation, or a failure in molecular chemistry. If it happens in one cell, the damage may do nothing, or at worse cause the cell to die. If damage occurs in a reproductive cell (a zygote) it can be an inherited mutation; the consequences of which can go on for generations
  • The DNA repair workers are (so far as we know) protein molecules.
  • Under microscopic observations it was seen that the UvrA protein randomly jumps from one DNA molecule to the next, staying about 7 seconds before moving on. However, when UvrA formed a complex with two UvrB molecules (UvrAB), the search became more sophisticated and slower. The complex would slide along the DNA strand for as long as 40 seconds before moving to another molecule. Sometimes it was observed that the UvrAB motion would ‘pause,’ apparently checking for structural abnormalities that might indicate DNA damage.
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  • It’s assumed the protein complex is analyzing, but the mechanism of analysis is unknown. It’s also unknown if the UvrAB complex (or similar complex) actually does the repair, or if it signals for some other protein complex(es) to make the repair.
Nickyz P.

GEN | Magazine Articles: Firm Focuses Operations on Gene Silencing - 0 views

  • It is developing therapeutics to prove the validity of ddRNAi in treating cancer, infectious diseases, and disorders of the central nervous system.
  • The ddRNAi platform focuses on the long-term downregulation of genes, making it suitable for targeting chronic life-threatening diseases. “We are silencing genes instead of introducing new genes, which separates us from traditional gene therapy companies,” Dr. French asserts.
  • “This targeted treatment markedly enhanced the benefits of radiation therapy in both cellular and tumor models,” the researchers concluded. Other radiotherapy-resistant tumors may benefit from the shRNAs created for the prostate cancer study.
Oranicha Jumreornvong

EBSCOhost: What Makes Each Brain Unique - 0 views

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    NEUROSCIENCE How can identical twins grow up with different personalities? "Jumping genes" move around in neurons and alter the way they work YOUR BRAIN IS SPECIAL. So is mine. Differences arise at every level of the organ's astonishingly intricate architecture; the human brain contains 100 billion neurons, which come in thousands of types and collectively form an estimate of more than 100 trillion interconnections.
pet-chompoo sa-ngarmangkang

Heart Failure Gene Discovered...In the Kidney - St. Louis News - Daily RFT - 0 views

  • risk for heart failure
  • e high blood pressure
  • t's related to the kidney.
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  • "It also makes hormones involved in maintaining blood volume."
  • So they began sequencing the kidney gene, looking for problems.
  • "The CLCNKA polymorphism decreases the kidney's functionality by about half,"
  • gene remains silent with no effect on the body until there's an injury to the heart
  • the blood flow to the kidney decreases and the kidney secretes the hormones angiotensin and aldosterone which lead to a high risk of heart failure."
  • More blood with less space to move leads to high blood pressure
  • puts more pressure on the heart.
  • presence of the gene drives the risk of heart failure from 20 percent to 27 percent for people with one copy and 54 percent for people with two
Paige Prescott

DNA The Code of Life | The Language of Life | deCODEme - 4 views

  • Genes are especially important segments of DNA that directly influence one or more traits. They are relatively small segments of chromosomes, where the sequence of DNA nucleotides encodes a recipe for making a protein. Small differences in the sequence of DNA nucleotides of a particular gene can lead to differences in the structure and behavior of the proteins they encode. It is these differences, in turn, that account for the variable characteristics of the people around you.
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    deCodeMe is a private company that sells DNA technology
orasa sukmark

Junk DNA Can Revive and Cause Disease, Study Finds - NYTimes.com - 0 views

  • can rise from the dead like zombies
  • dead gene come back to life and cause a disease
  • a dead gene come back to life and cause a disease.
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  • Some of those genes, surprised geneticists reported Thursday, can rise from the dead like zombies, waking up to cause one of the most common forms of muscular dystrophy.
    • adisa narula
       
      Do these genes revive automatically?
  • It is a dominant genetic disease.
  • people who have the disease cannot smile.
  • FSHD affects about 1 in 20,000 people
  • function, if any, is largely unknown.
  • function, if any, is largely unknown
  • FSHD, is one of the most common forms of muscular dystrophy.
  • in a way FSHD was the easy case — it is a disease that affects every single person who inherits the genetic defect. Other diseases are more subtle, affecting some people more than others, causing a range of symptoms.
  • The dead gene was also repeated on chromosome 10, but that area of repeats seemed innocuous, unrelated to the disease. Only chromosome 4 was a problem.
  • chromosome 4 was a problem.
  • No one whose dead gene was repeated more than 10 times ever got FSHD
  • it was not completely inactive. It is always transcribed
  • copied by the cell as a first step to making a protein.
  • But the transcriptions were faulty, disintegrating right away. They were missing a crucial section, called a poly (A) sequence, needed to stabilize them.
  • But the transcriptions were faulty, disintegrating right away. They were missing a crucial section, called a poly (A) sequence, needed to stabilize them.
  • extra copies change the chromosome’s structure, shutting off the whole region so it cannot be used.
Nitchakan Chaiprukmalakan

Biotechdaily - Human Mitochondrial Mutations Repaired by New Technique - 2 views

  • researchers have identified a generic approach to correct mutations in human mitochondrial DNA by targeting corrective RNAs,
  • In adults, many aging disorders have been associated with defects of mitochondrial function, including diabetes, Parkinson’s disease, cancer, heart disease, stroke, and Alzheimer’s disease.
  • The introduction of nucleus-encoded small RNAs into mitochondria is critical for the replication, transcription, and translation of the mitochondrial genome,
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  • The study defined a new role for a protein called polynucleotide phosphorylase (PNPASE) in regulating the import of RNA into mitochondria. Reducing the expression--or output--of PNPASE decreased RNA import, which impaired the processing of mitochondrial genome-encoded RNAs. Reduced RNA processing inhibited the translation of proteins required to maintain the mitochondrial electron transport chain that consumes oxygen during cell respiration to produce energy. With reduced PNPASE, unprocessed mitochondrial-encoded RNAs accumulated, protein translation was inhibited, and energy production was compromised, leading to stalled cell growth.
  • Geng Wang developed a strategy to target and import specific RNA molecules encoded in the nucleus into the mitochondria and, once there, to express proteins needed to repair mitochondrial gene mutations.
  • First, the researchers had to find a way to stabilize the reparative RNA so that it was moved out of the nucleus and then localized to the mitochondrial outer membrane. This was accomplished by modifying an export sequence to direct the RNA to the mitochondrion. Once the RNA was in the area of the transport machinery on the mitochondrial surface, then a second transport sequence was required to direct the RNA into the targeted organelle. With these two modifications, a wide range of RNAs were targeted to and imported into the mitochondria, where they worked to repair defects in mitochondrial respiration and energy production in two different cell line models of human mitochondrial disease.
    • Nitchakan Chaiprukmalakan
       
      This article shows the importance of the RNAs in making proteins for the mitochondria to work efficiently.  The article summarizes a method in repairing the mitochondria that is still being worked on.
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    Mutations in the mitochondrial genome inflicts diseases
Nitchakan Chaiprukmalakan

Plant research reveals new role for gene silencing protein - 0 views

    • wasin kusakabe
       
      Termination is equally as important as other sections of Transcription
  • Termination is the final stage of transcription.
  • Without termination, transcription continues down the chromosome unchecked.
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  • The expression of a gene, when an organism's DNA is transcribed into a useable product, requires activation via a promoter or an external trigger.
  • DCL4 is a back-up to termination processes, helping a gene to be successfully expressed
  • If a gene ends badly, aberrant RNA will trigger silencing pathways
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    this new way to making the mature mRNA is very interesting. gotta love it. 
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