Hematology researchers at The Children's Hospital of Philadelphia have manipulated key biological events in adult blood cells to produce a form of hemoglobin normally absent after the newborn period. Because this fetal hemoglobin is unaffected by the genetic defect in sickle cell disease (SCD), the cell culture findings may open the door to a new therapy for the debilitating blood disorder.
"Our study shows the power of a technique called forced chromatin looping in reprogramming gene expression in blood-forming cells," said hematology researcher Jeremy W. Rupon, M.D., Ph.D., of The Children's Hospital of Philadelphia. "If we can translate this approach to humans, we may enable new treatment options for patients."
Rupon presented the team's findings today at a press conference during the annual meeting of the American Society of Hematology (ASH) in New Orleans. Rupon worked in collaboration with a former postdoctoral fellow, Wulan Deng, Ph.D., in the laboratory of Gerd Blobel, M.D., Ph.D.
Hematologists have long sought to reactivate fetal hemoglobin as a treatment for children and adults with SCD, the painful, sometimes life-threatening genetic disorder that deforms red blood cells and disrupts normal circulation.
In the normal course of development, a biological switch flips during the production of hemoglobin, the oxygen-carrying component of red blood cells. Regulatory elements in DNA shift the body from producing the fetal form of hemoglobin to producing the adult form instead. This transition occurs shortly after birth. When patients with SCD undergo this transition, their inherited gene mutation distorts adult hemoglobin, forcing red blood cells to assume a sickled shape.
In the current study, Rupon and Blobel reprogrammed gene expression to reverse the biological switch, causing cells to resume producing fetal hemoglobin, which is not affected by the SCD mutation, and produces normally shaped red blood cells.
The scientists built on previous work by Blobel's team showing that chromatin looping, a tightly regulated interaction between widely separated DNA sequences, drives gene transcription -- the conversion of DNA code into RNA messages to carry out biological processes.
In the current study, the researchers used a specialized tool, a genetically engineered zinc finger (ZF) protein, which they custom-designed to latch onto a specific DNA site carrying the code for fetal hemoglobin. They attached the ZF to another protein that forced a chromatin loop to form. The loop then activated gene expression that produced embryonic hemoglobin in blood-forming cells from adult mice. The team obtained similar results in human adult red blood cells, forcing the cells to produce fetal hemoglobin.
Rupon and Blobel will continue investigations aimed at moving their research toward clinical application. Rupon added that the approach may also prove useful in treating other diseases of hemoglobin, such as thalassemia.

A molecular technique that will help the scientific community to analyze-on a scale previously impossible-molecules that play a critical role in regulating gene expression has been developed by a research team led by a chemist and a plant biologist at Penn State University. The scientists developed a method that enables more-accurate prediction of how ribonucleic acid molecules (RNAs) fold within living cells, thus shedding new light on how plants-as well as other living organisms-respond to environmental conditions. A paper by the research team-led by Sarah M. Assmann, Waller Professor of Biology, and Philip Bevilacqua, professor of chemistry-is scheduled for early online publication in the journal Nature on 24 November 2013.
"Scientists have studied a few individual RNA molecules, but now we have data on almost all the RNA molecules in a cell-more than 10,000 different RNAs," Assmann said. "We are the first to determine, on a genome-wide basis, the structures of the RNA molecules in a plant, or in any living organism."

Temperature and drought are among the environmental stress factors that affect the structure of RNA molecules, thereby influencing how genes are "expressed"-how their functions are turned on or turned off. "Climate change is predicted to cause increasingly extreme and unpredictable heat waves and droughts, which would impact our food crops, in part by affecting the structures of their RNA molecules and so influencing their translation into proteins," Bevilacqua said. "The more we understand about how environmental factors affect RNA structure and thereby influence gene expression, the more we may be able to breed-or develop with biotechnological methods-crops that are more resistant to those stresses. Such crops, which could perform better under more-marginal conditions, could help feed the world's growing population."
The scientific achievement of the Penn State research team-postdoctoral scholar Yiliang Ding, graduate students Yin Tang and Chun Kit Kwok, and Professor of Statistics Yu Zhang, along with Assmann and Bevilacqua-involved determining the structures of the varieties of RNA molecules in a plant named Arabidopsis thaliana. This plant is used worldwide as a model species for scientific research.
Arabidopsis thaliana, commonly known as mouse-ear cress, is an ideal organism for RNA studies, the researchers say, because it is the first plant species to have its full genome sequenced and has the greatest number of genetic tools available.
RNA is the intermediate molecule between DNA and proteins in all living things. It is a critical component in the pathway of gene expression, which controls an organism's function. Unlike the double-stranded DNA molecule, which is compressed into cells by twisting and wrapping around proteins, RNA is single stranded, and folds back on itself. The researchers set out to answer the question, How exactly does RNA fold in a cell and how does that folding regulate gene function?
"We needed a tool to answer that question," says Bevilacqua. "That tool involves introducing a chemical into the plant that can modify some segments of the RNA but not others, which then gives a readout of the structure of the RNA. Using this technique we can figure out which classes of genes are associated with certain RNA structural traits. And we can try to understand how these RNA structural changes relate to certain biological functions."
"Previously, researchers would query the structures of individual RNAs in a cell one by one, and it was a tedious process," says Assmann. "You can't abstract rules or generalities about how RNAs are behaving just from knowing the structures of one or a few RNAs-you can't get a pattern. Now that we have genome-wide information for a particular organism, we can start to abstract patterns of how RNA structure influences gene expression and ultimately plant function. Other scientists can query their organisms of interest and ask what rules they can abstract. Are there universal rules that will be true for all organisms for how RNA structure influences gene expression?"
Bevilacqua adds, "Because RNA is so central in its role in gene regulation, the tools we've developed can be transferred to scientists who are working with essentially any biological system."
Long-term potential implications of the methodology include human health-for example, how an infection-induced fever could affect the RNA structures of both humans and pathogens.

Pioneering new research from a team of Indiana University Bloomington biologists has shown for the first time that a protein which has been long known to be critical for the initiation of protein synthesis in all organisms can also play a role in the regulation of gene expression in some bacteria, and probably land plants as well.
The protein, called translation initiation factor 3, or IF3, is one of three proteins that make up the core structure of the machinery needed to guide the joining of messenger RNAs and ribosomes as protein translation commences. These three proteins have been widely considered to simply operate in a constitutive manner and play little, if any, role in regulating the expression of genes.
The new findings, from the laboratory of David M. Kehoe, professor of biology in the Indiana University Bloomington College of Arts and Sciences, reveals that IF3, in addition to its well-accepted function during translation initiation, also regulates the expression of genes that encode components of the photosynthetic machinery in response to changes in the color of light in the surrounding environment, a process known as "chromatic acclimation."
These photosynthesis genes produce red-pigmented proteins called phycoerythrin in cyanobacteria when the cells are grown in green light and allow these organisms to efficiently absorb the predominant ambient light color for photosynthesis. The team uncovered the novel function of IF3 while searching for mutants that incorrectly regulated phycoerythrin. The discovery of this mutant was at first surprising, because in all other bacteria that have been examined, mutations in infC (the gene that encodes IF3) are lethal.
The team solved this puzzle by uncovering a second infC gene in Fremyella diplosiphon, the model organism for the study of light color responsiveness in cyanobacteria. While both IF3s, which have been named IF3a and IF3b, can act in the traditional role of translation initiation, only IF3a was found to also regulate photosynthetic gene expression.
By exploring the genomes of hundreds of prokaryotes and eukaryotes in collaboration with members of the laboratory of Indiana University Distinguished Professor and Class of 1955 Professor Jeffrey Palmer, the group identified a wide range of species whose genomes appear to have the potential to encode multiple IF3s, with one organism apparently encoding five distinct IF3 family members. And since almost none of these species are capable of chromatic acclimation, Kehoe believes that multiple IF3s must be used to regulate a wide range of environmental and perhaps developmental responses in both prokaryotes and eukaryotes.
"Particularly interesting was our finding that IF3 families exist in a number of plant species, including commercially important crops," Kehoe said. "This means that new approaches to the modification of traits in agriculturally significant plant species may be possible by manipulating the expression patterns of different IF3 family members."
The discovery has generated excitement for an additional reason. Historically, scientists have had a difficult time studying IF3 because it is so essential for translation initiation that it can not be altered without causing death. In fact, it remains one of the few proteins involved in translation for which no effective antibiotic has been developed. But the ability of the Kehoe team to delete either of the two infC genes in F. diplosiphon without causing lethality will allow the group to modify both IF3a and IF3b at will.
"Now that we know that F. diplosiphon contains two functionally different IF3s, and that each is nonessential, we have a unique opportunity to enhance our understanding of how the structural features of IF3 are related to its function," Kehoe said. "Advancing our understanding of the role of IF3 in translation is likely to provide opportunities to develop new antibiotics that are targeted to this class of proteins."
"A unique role for translation initiation factor 3 in the light color regulation of photosynthetic gene expression" is now available in early online editions of the Proceedings of the National Academy of Sciences. Co-authors with Kehoe and Palmer were Andrian Gutu, a former Ph.D. student in the Kehoe lab who is now a Howard Hughes Medical Institute Postdoctoral Fellow at Harvard University; April Nesbit, a former postdoctoral researcher in the Kehoe lab who is now a lecturer at Purdue Northwest; and Andrew Alverson, a former postdoctoral fellow in the Palmer lab who is now a faculty member at the University of Arkansas. Primary funding for the work was provided by the National Science Foundation, with support provided to Nesbit by the National Institutes of Health.