Research Area: Cellular & Molecular Neuroscience

​synapses, vesicles, electrophysiology, protein complexes, signaling, small molecules, disease-linked genes, dendrites, cell death, brain disorders, neurodevelopment

Controlling genes with light

Anne Trafton |

Although human cells have an estimated 20,000 genes, only a fraction of those are turned on at any given time, depending on the cell’s needs — which can change by the minute or hour. To find out what those genes are doing, researchers need tools that can manipulate their status on similarly short timescales.

That is now possible, thanks to a new technology developed at MIT and the Broad Institute that can rapidly start or halt the expression of any gene of interest simply by shining light on the cells.

The work is based on a technique known as optogenetics, which uses proteins that change their function in response to light. In this case, the researchers adapted the light-sensitive proteins to either stimulate or suppress the expression of a specific target gene almost immediately after the light comes on.

“Cells have very dynamic gene expression happening on a fairly short timescale, but so far the methods that are used to perturb gene expression don’t even get close to those dynamics. To understand the functional impact of those gene-expression changes better, we have to be able to match the naturally occurring dynamics as closely as possible,” says Silvana Konermann, an MIT graduate student in brain and cognitive sciences.

The ability to precisely control the timing and duration of gene expression should make it much easier to figure out the roles of particular genes, especially those involved in learning and memory. The new system can also be used to study epigenetic modifications — chemical alterations of the proteins that surround DNA — which are also believed to play an important role in learning and memory.

Konermann and Mark Brigham, a graduate student at Harvard University, are the lead authors of a paper describing the technique in the July 22 online edition of Nature. The paper’s senior author is Feng Zhang, the W. M. Keck Career Development Professor in Biomedical Engineering at MIT and a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research.

Shining light on genes

The new system consists of several components that interact with each other to control the copying of DNA into messenger RNA (mRNA), which carries genetic instructions to the rest of the cell. The first is a DNA-binding protein known as a transcription activator-like effector (TALE). TALEs are modular proteins that can be strung together in a customized way to bind any DNA sequence.

Fused to the TALE protein is a light-sensitive protein called CRY2 that is naturally found in Arabidopsis thaliana, a small flowering plant. When light hits CRY2, it changes shape and binds to its natural partner protein, known as CIB1. To take advantage of this, the researchers engineered a form of CIB1 that is fused to another protein that can either activate or suppress gene copying.

After the genes for these components are delivered to a cell, the TALE protein finds its target DNA and wraps around it. When light shines on the cells, the CRY2 protein binds to CIB1, which is floating in the cell. CIB1 brings along a gene activator, which initiates transcription, or the copying of DNA into mRNA. Alternatively, CIB1 could carry a repressor, which shuts off the process.

A single pulse of light is enough to stimulate the protein binding and initiate DNA copying.

The researchers found that pulses of light delivered every minute or so are the most effective way to achieve continuous transcription for the desired period of time. Within 30 minutes of light delivery, the researchers detected an uptick in the amount of mRNA being produced from the target gene. Once the pulses stop, the mRNA starts to degrade within about 30 minutes.

In this study, the researchers tried targeting nearly 30 different genes, both in neurons grown in the lab and in living animals. Depending on the gene targeted and how much it is normally expressed, the researchers were able to boost transcription by a factor of two to 200.




Epigenetic modifications



An important element of gene-expression control is epigenetic modification. One major class of epigenetic effectors is chemical modification of the proteins, known as histones, that anchor chromosomal DNA and control access to the underlying genes. The researchers showed that they can also alter these epigenetic modifications by fusing TALE proteins with histone modifiers.

Epigenetic modifications are thought to play a key role in learning and forming memories, but this has not been very well explored because there are no good ways to disrupt the modifications, short of blocking histone modification of the entire genome. The new technique offers a much more precise way to interfere with modifications of individual genes.

“We want to allow people to prove the causal role of specific epigenetic modifications in the genome,” Zhang says.

So far, the researchers have demonstrated that some of the histone effector domains can be tethered to light-sensitive proteins; they are now trying to expand the types of histone modifiers they can incorporate into the system.

“It would be really useful to expand the number of epigenetic marks that we can control. At the moment we have a successful set of histone modifications, but there are a good deal more of them that we and others are going to want to be able to use this technology for,” Brigham says.

The research was funded by a Hubert Schoemaker Fellowship; a National Institutes of Health Transformative R01 Award; an NIH Director’s Pioneer Award; the Keck, McKnight, Vallee, Damon Runyon, Searle Scholars, Klingenstein and Simons foundations; and Bob Metcalfe and Jane Pauley.

Optogenetics: A Light Switch for Neurons

by Julie Pryor |

This animation illustrates optogenetics — a radical new technology for controlling brain activity with light. Ed Boyden, the co-inventor of this technology, continues to develop new technologies for controlling brain activity.

Re-creating autism, in mice

Anne Trafton |

By mutating a single gene, researchers at MIT and Duke have produced mice with two of the most common traits of autism — compulsive, repetitive behavior and avoidance of social interaction.

They further showed that this gene, which is also implicated in many cases of human autism, appears to produce autistic behavior by interfering with communication between brain cells. The finding, reported in the March 20 online edition of Nature, could help researchers find new pathways for developing drugs to treat autism, says senior author Guoping Feng, professor of brain and cognitive sciences and member of the McGovern Institute for Brain Research at MIT.

About one in 110 children in the United States has an autism spectrum disorder, which can range in severity and symptoms but usually includes difficulties with language in addition to social avoidance and repetitive behavior. There are currently no effective drugs to treat autism, but the new finding could help uncover new drug targets, Feng says.

“We now have a very robust model with a known cause for autistic-like behaviors. We can figure out the neural circuits responsible for these behaviors, which could lead to novel targets for treatment,” he says.

The new mouse model also gives researchers a new way to test potential autism drugs before trying them in human patients.

A genetic disorder

In the past 10 years, large-scale genetic studies have identified hundreds of gene mutations that occur more frequently in autistic patients than in the general population. However, each patient has only one or a handful of those mutations, making it difficult to develop drugs against the disease.

In this study, the researchers focused on one of the most common of those genes, known as Shank3. The protein encoded by Shank3 is found in synapses — the junctions between brain cells that allow them to communicate with each other. Feng, who joined MIT and the McGovern Institute last year, began studying Shank3 a few years ago because he thought that synaptic proteins might contribute to autism and similar brain disorders, such as obsessive compulsive disorder.

At a synapse, one cell sends messages by releasing chemicals called neurotransmitters, which interact with the cell receiving the signal (known as the postsynaptic cell). This signal provokes the postsynaptic cell to alter its activity in some way — for example, turning a gene on or off. Shank3 is a “scaffold” protein, meaning that it helps to organize the hundreds of other proteins clustered on the postsynaptic cell membrane, which are necessary to coordinate the cell’s response to synaptic signals.

Feng targeted Shank3 because it is found primarily in a part of the brain called the striatum, which is involved in motor activity, decision-making and the emotional aspects of behavior. Malfunctions in the striatum are associated with several brain disorders, including autism and OCD. Feng theorized that those disorders might be caused by faulty synapses.

In a 2007 study, Feng showed that another postsynaptic protein found in the striatum, Sapap3, can cause OCD-like behavior in mice when mutated.

Communication problems

In the new Nature study, Feng and his colleagues found that Shank3 mutant mice showed compulsive behavior (specifically, excessive grooming) and avoidance of social interaction. “They’re just not interested in interacting with other mice,” he says.

The study, funded in part by the Simons Foundation Autism Research Initiative, offers the first direct evidence that mutations in Shank3 produce autistic-like behavior.

Guy Rouleau, professor of medicine at the University of Montreal, says the mouse model should give autism researchers a chance to understand the disease better and potentially develop new treatments. “It looks like this is going to be a good model that will be used to explore, more deeply, the physiology of the disorder,” says Rouleau, who was not involved in this research.

Even though only a small percentage of autistic patients have mutations in Shank3, Feng believes that many other cases may be caused by disruptions of other synaptic proteins. He is now doing a study, with researchers from the Broad Institute, to determine whether mutations in a group of other synaptic genes are associated with autism in human patients.

If that turns out to be the case, it should be possible to develop treatments that restore synaptic function, regardless of which particular synaptic protein is defective in the individual patient, Feng says.

Feng performed some of the research while at Duke, and several of his former Duke colleagues are authors on the Nature paper, including lead author Joao Peca and Professor Christopher Lascola.

Researchers find new actions of neurochemicals

by Catherine Delude |

Although the tiny roundworm Caenorhabditis elegans has only 302 neurons in its entire nervous system, studies of this simple animal have significantly advanced our understanding of human brain function because it shares many genes and neurochemical signaling molecules with humans. Now MIT researchers have found novel C. elegans neurochemical receptors, the discovery of which could lead to new therapeutic targets for psychiatric disorders if similar receptors are found in humans.

Dopamine and serotonin are members of a class of neurochemicals called biogenic amines, which function in neuronal circuitry throughout the brain. Many drugs used to treat psychiatric disorders, including depression and schizophrenia, target these signaling systems, as do cocaine and other drugs of abuse. Scientists have long known of a class of biogenic-amine receptors that are G protein-coupled receptors (GPCRs) and that, when activated, trigger a slow but long-lasting cascade of intracellular events that modulate nervous system activity.

A study in the July 3 issue of Science has found that in C. elegans these chemicals also act on receptors of a fundamentally different type. These receptors are chloride channels that open and close quickly in response to the binding of a neurochemical messenger. By allowing the passage of negatively charged chloride ions across the cell membrane, chloride channels can rapidly inactivate nerve cells.

“These results underscore the importance of determining whether, as in the C. elegans nervous system, a diversity of biogenic amine-gated chloride channels function in the human brain,” said H. Robert Horvitz of the McGovern Institute for Brain Research at MIT and senior author of the study. “If so, such channels might define novel therapeutic targets for neuropsychiatric disorders, such as depression and schizophrenia.”

In 2000, Horvitz’s group discovered that serotonin activates a chloride channel they called MOD-1, which inhibits neuronal activity in C. elegans.

In the current study, Niels Ringstad and Namiko Abe, a postdoctoral researcher and an undergraduate in Horvitz’s laboratory, respectively, looked for other ion channels that could be receptors for biogenic amines. Using both in vitro and in vivo methods, they surveyed the functions of 26 ion channels similar to MOD-1 and found three additional ion channels with an affinity for biogenic amines: dopamine activates one, serotonin another, and tyramine (the role of which in the human brain is unknown) a third. All three were chloride channels, like MOD-1.

“We now have four members of a family of chloride channels that can act as receptors for biogenic amines in the worm,” Ringstad said. “That these neurochemicals activate both GPCRs and ion channels means that they can have very complex actions in the nervous system, both as slow-acting neuromodulators and as fast-acting inhibitory neurotransmitters.”

It is unknown as yet whether an equivalent to this new class of worm receptor exists in the human brain, but Horvitz points out that worms have proved remarkably informative for providing insights into human biology. In 2002, Horvitz shared the Nobel Prize in Physiology or Medicine for the discovery based on studies of C. elegans of the mechanism of programmed cell death, a central feature of some neurodegenerative diseases and many other disorders in humans.

“Historically, studies of C. elegans have delineated mechanisms of neurotransmission that subsequently proved to be conserved in humans,” says Horvitz, the David H. Koch Professor of Biology at MIT and a Howard Hughes Medical Institute Investigator. “The next step is to look for chloride channels controlled by biogenic amines in mammalian neurons.”

This study was supported by the NIH, the Howard Hughes Medical Institute, the Life Sciences Research Foundation, and The Medical Foundation.

McGovern Institute to present inaugural Edward M. Scolnick Prize in Neuroscience Research

Anne Trafton |

The Edward M. Scolnick Prize in Neuroscience Research will be awarded on Friday April 23rd at the McGovern Institute at MIT, a leading research and teaching institute committed to advancing understanding of the human mind and communications. According to Dr. Phillip A. Sharp, Director of the Institute, this annual research prize will recognize outstanding discoveries or significant advances in the field of neuroscience.

The inaugural prize will be presented to Dr. Masakazu Konishi, Bing Professor of Behavioral Biology at the California Institute of Technology. As part of the day’s events, Dr. Konishi will present a free public lecture, “Non-linear steps to high stimulus selectivity in different sensory systems” at 1:30 PM on Friday, April 23rd at MIT (building E25, room 111.) Following the lecture, The McGovern Institute is hosting an invitation-only reception and dinner honoring Dr. Konishi at the MIT Faculty Club. Speakers for the evening award presentation include: Dr. Sharp; Patrick J. McGovern, Founder and Chairman of International Data Group (IDG) and trustee of MIT and the Institute; Edward Scolnick, former President of Merck Research Laboratories; and Torsten Wiesel, President Emeritus of Rockefeller University.

“I am pleased, on behalf of the McGovern Institute, to recognize the important work that Dr. Mark Konishi is doing,” said Dr. Sharp. “Dr. Konishi is being recognized for his fundamental discoveries concerning mechanisms in the brain for sound location such as a neural topographic map of auditory space. Through a combination of his discoveries, the positive influence of his rigorous approach, and the cadre of young scientists he has mentored and trained, Dr. Konishi has improved our knowledge of how the brain works, and the future of neuroscience research. Mark is truly a leader, and well-deserving of this prestigious honor.”

Dr. Konishi received his B.S and M.S degrees from Hokkaido University in Sapporo, Japan and his Doctorate from the University of California, Berkeley in 1963. After holding positions at the University of Tubingen and the Max-Planck Institute in Germany, Dr. Konishi returned to the United States, where he worked at the University of Wisconsin and Princeton University before coming to the California Institute of Technology in 1975 as Professor of Biology. He has been the Bing Professor of Behavioral Biology at Caltech since 1980. With scores of publications dating back to 1971, and as the recipient of fourteen previous awards, Dr. Konishi has forged a deserved reputation as an outstanding investigator.

Among his many findings, Dr. Konishi is known for his fundamental discoveries concerning sound location by the barn owl and the song system in the bird. He discovered that in the inferior colliculus of the brain of the barn owl there is a map of auditory space and he identified the computational principles and the neural mechanisms that underlie the workings of the map.

The creation of the Edward M. Scolnick Prize was announced last year, with the first presentation scheduled for 2004. The annual prize consists of an award equal to $50,000 and will be given each year to an outstanding leader in the international neuroscience research community. The McGovern Institute will host a public lecture by Dr. Konishi in the spring of 2004, followed by an award presentation ceremony.

The award is named in honor of Dr. Edward M. Scolnick, who stepped down as President of Merck Research Laboratories in December 2002, after holding Merck & Co., Inc.’s top research post for 17 years. During his tenure, Dr. Scolnick led the discovery, development and introduction of 29 new medicines and vaccines. While many of the medicines and vaccines have contributed to improving patient health, some have revolutionized the ways in which certain diseases are treated.

About the McGovern Institute at MIT

The McGovern Institute at MIT is a research and teaching institute committed to advancing human understanding and communications. The goal of the McGovern Institute is to investigate and ultimately understand the biological basis of all higher brain function in humans. The McGovern Institute conducts integrated research in neuroscience, genetic and cellular neurobiology, cognitive science, computation, and related areas.

By determining how the brain works, from the level of gene expression in individual neurons to the interrelationships between complex neural networks, the McGovern Institute’s efforts work to improve human health, discover the basis of learning and recognition, and enhance education and communication. The McGovern Institute contributes to the most basic knowledge of the fundamental mysteries of human awareness, decisions, and actions.