Category Archives: Genome

Devangshu Datta: What's in a genome The results of the Encode project may not be sensational but will clearly accelerate research in several key areas Devangshu Datta / New Delhi Sep 21, 2012, 00:55 IST

In early September, several teams working on the human genome published a flood of papers detailing their findings. The Encyclopaedia of DNA Elements Projects (Encode) has made great progress in detailing human genome functions.

This is the biggest set of breakthroughs since the human genome project (HGP) mapped the DNA sequence between 2000 and 2003. However, Encodes results have caused some controversy within the scientific community. The results are not being disputed. But several scientists have stated the press releases were misleading or misinterpreted.

Unusually, for a collaborative project of this scale, the papers were embargoed to ensure coordinated release. The raw data were made available for use, however. All data and papers are now freely available with a special search application on the portal, http://nature. com/encode/.

DNA (deoxyribonucleic acid) carries the information that offers inheritable characteristics. The HGP identified 20,000-plus DNA genes that carried protein-coded information unique to individuals. The coded sequences are responsible for most cell functions. If that set of protein-coded genes is replicated, it produces a clone, or identical twin.

But the coded DNA sequences are a very small proportion roughly 1 to 1.5 per cent of the entire genome. The genome contains many more DNA sequences that possess no protein-coding. It also has RNA (ribonucleic acid) sequences. RNA is required to copy and replicate DNA. RNA passes through the nuclear membrane of cells carrying selective DNA information to be replicated.

It was known that non-coded DNA sequences included switches that controlled and regulated the activity of coded sequences. However, many non-coded sequences also seem redundant. Some are broken bits of discarded genes and disabled viruses. Even some coded DNA is redundant. One hypothesis is that these bits of useless DNA are leftovers from evolutionary history.

Since functions of specific bits of non-coded DNA werent known and since some bits were apparently useless, these sections were misleadingly labelled junk. They are also referred to as dark matter.

Encode has figured out the biochemical activity in much of the junk and also confirms that there are many switches controlling the coded sections. The switches tell coded genes when to switch on and off and determine, for example, which cells become muscles, and which pancreas cells, or neurons.

Encode claims that at least 80 per cent of the junk is biochemically active. This is where confusion has arisen. It was reported that 80 per cent of junk was useful. But biochemically active doesnt necessarily translate to useful. Carrying a useless, disabled gene doesnt hurt the organism and most such sequences are biochemically active.

Visit link:
Devangshu Datta: What's in a genome

20 September 2012 Last updated at 04:13 ET By Helen Briggs BBC News

A detailed map of the Pacific oyster genome has been unveiled by scientists.

The research, published in the journal Nature, shows how oysters manage to survive the harsh environment of the estuary and sea shore.

The mollusc has scores of genes that protect it from extremes of temperature and saltiness, where the land meets the sea.

Oyster farming is a multi-million dollar industry, centred around China, Japan, Korea and the US.

There's clearly been adaptations over millions of years to allow these animals to cope with an incredibly harsh environment

The genome map gives an insight into how the oyster became adapted to marine life, and how it formed its complex shell.

It also reveals secrets that may help scientists breed faster-growing oysters with a better survival rate.

A team of international scientists, from China, the US, and Europe, carried out the genome sequencing work.

Peter Holland, professor of zoology at the University of Oxford, and a co-author of the research, says the oyster has more than 80 genes that protect the oyster from stress.

Read more from the original source:
Oyster genome mystery unravelled

CAMBRIDGE, Mass.--(BUSINESS WIRE)--

GnuBIO http://www.gnubio.com announced today that it has been awarded a $4.5 million Phase II SBIR grant over the next three years through the National Human Genome Research Institutes (NHGRI) Advanced DNA Sequencing Technology Program. After a rigorous process, the grant committee at the NIH chose six projects to fund for this competitive awards program aimed at further advancing DNA sequencing technologies. Out of the total of $19 million, the NHGRI awarded GnuBIO the largest annual amount.

The purpose of the NHGRI grant program is to significantly reduce the cost of genome sequencing while improving both accuracy and speed, while significantly reducing the cost of sequencing a genome. GnuBIO, whose platform is based on Microfluidic DNA Sequencing, will use this funding to further develop its core technology towards rapid and accurate whole genome sequencing for less than $1000.

GnuBIO is commercializing a platform technology that integrates target enrichment, PCR, sequencing and informatics into a single system. The instrument has demonstrated sequencing of genomic DNA amplicons with read lengths up to 1000bp and accuracy higher than 99.9% per base. Unlike other currently available commercial systems, the GnuBIO http://www.gnubio.com platform encompasses all of the steps required for DNA sequencing into a single cartridge, thereby obviating any sample preparation that is required for all other commercial sequencing platforms.

Sequencing reactions on the GnuBIO http://www.gnubio.com platform take place inside droplets using minute reagent volumes. The NHGRI grant will be used to further reduce the size of these droplets and increase parallel processing of sequencing reactions to enable extremely low cost and rapid sequencing of large targets such as exomes and genomes, said Tal Raz, Vice President of Molecular Biology at GnuBIO. Currently, GnuBIO is in the process of preparing for the launch of its beta system, a platform that is capable of inline selection of sequencing targets, inline PCR, inline sequencing, and real-time informatics. The commercial system has a targeted price of $50K USD.

The grant award comes at an ideal time for us as it complements our strategy to launch an affordable sequencing platform that is practical for everyday patient care, said John Boyce, President and CEO of GnuBIO. This grant will enable us to expand our R&D capacity and enhance our core technology by increasing the throughput capability and enabling whole-genome sequencing.

About GnuBIO: GnuBIO is a privately-held company developing next-generation desktop DNA sequencing technology that will compartmentalize the entire DNA sequencing process, combining all of the steps required for sequencing in a single system, and providing the only fully integrated next-generation sequencing workflow.The GnuBIO sequencingtechnology is based on an emulsion based microfluidic technology which also provides a scalable sequencing solution that allows for interrogation of single genes, gene panels or whole genomes. The user of his GnuBIO system simply injects the patient sample into the GnuBIO http://www.gnubio.com cartridge, the appropriate panel is run inclusive of gene capture, PCR, sequencing, and informatics analysis and the results are ready within hours. Unlike any other DNA sequencing system, the entire process is all on the chip, simplifying the complex sample preparation process and breaking the barrier of an obstacle that has prevented the widespread adoption of DNA sequencing.

See the original post:
GnuBIO Awarded $4.5 Million in Funding from the National Human Genome Research Institute to Develop Lower Cost Genome ...

Public release date: 19-Sep-2012 [ | E-mail | Share ]

Contact: Ellen de Graffenreid edegraff@med.unc.edu 919-962-3405 University of North Carolina Health Care

Researchers have long known that individual diseases are associated with genes in specific locations of the genome. Genetics researchers at the University of North Carolina at Chapel Hill now have shown definitively that a small number of places in the human genome are associated with a large number and variety of diseases. In particular, several diseases of aging are associated with a locus which is more famous for its role in preventing cancer.

For this analysis, researchers at UNC Lineberger Comprehensive Cancer Center catalogued results from several hundred human Genome-Wide Association Studies (GWAS) from the National Human Genome Research Institute. These results provided an unbiased means to determine if varied different diseases mapped to common 'hotspot' regions of the human genome. This analysis showed that two different genomic locations are associated with two major subcategories of human disease.

"Our team is interested in understanding genetic susceptibility to diseases associated with aging, including cancer," said PhD student William Jeck, who was first author on the study, published in the journal Aging Cell.

The team examined the large NHGRI dataset and first eliminated hereditable traits such as eye or hair color and other non-disease traits like drug metabolism. The group then focused on variants identified from GWAS that contributed to actual diseases. Combining results from all of these studies, there was enough data to arrive at statistically valid conclusions. The team then mapped the disease associations to the appropriate locations of the genome, counting the number of unique diseases mapping to specific genomic regions, in order to see if disparate diseases mapped randomly throughout the genome, or clustered in hotspots.

"What we ended up with is a very interesting distribution of disease risk across the genome. More than 90 percent of the genome lacked any disease loci. Surprisingly, however, lots of diseases mapped to two specific loci, which soared above all of the others in terms of multi-disease risk. The first locus at chromosome 6p21, is where the major histocompatibility (MHC) locus resides. The MHC is critical for tissue typing for organ and bone marrow transplantation, and was known to be an important disease risk locus before genome-wide studies were available. Genes at this locus determine susceptibility to a wide variety of autoimmune diseases such as arthritis, celiac disease, Type I diabetes, asthma, psoriasis, and lupus," said Jeck.

"The second place where disease associations clustered is the INK4/ARF (or CDKN2a) tumor suppressor locus. This area, in particular, was the location for diseases associated with aging: atherosclerosis, heart attacks, stroke, Type II diabetes, glaucoma and various cancers." he added.

"The finding that INK4/ARF is associated with lots of cancer, and MHC is associated with lots of diseases of immunity is not surprisingthese associations were known. What is surprising is the diversity of diseases mapping to just two small places: 30 percent of all tested human diseases mapped to one of these two places. This means that genotypes at these loci determine a substantial fraction of a person's resistance or susceptibility to multiple independent diseases," said Ned Sharpless, MD, Wellcome Distinguished Professor of Cancer Research and Associate Director of Translational Research at UNC Lineberger.

Another interesting finding was the apparent role of two biological processes in multi-disease association. In addition to the MHC and INK4/ARF loci, five less significant hotspot loci were also identified. Of the seven total hotspot loci, however, all contained genes associated with either immunity or cellular senescence. Cellular senescence is a permanent form of cellular growth arrest, and it is an important means whereby normal cells are prevented from becoming cancerous. It has been long known that senescent cells accumulate with aging, and may cause aspects of aging. This new analysis provides evidence that genetic differences in an individual's ability to regulate the immune response and activate cellular senescence determine their susceptibility to many seemingly disparate diseases.

Read the original post:
Diseases of aging map to a few 'hotspots' on the human genome

Comparison with seven other sequenced genomes identified 8,654 oyster-specific genes (Supplementary Text E3.1) that are probably important in the evolution and adaptation of oysters and other molluscs. With oysters being the only representative, these genes could be shared by other molluscs. Among these genes, gene ontology terms related to protein binding, apoptosis, cytokine activity and inflammatory response are highly enriched (P<0.0001; Supplementary Text E2 and Supplementary Table 17), indicating over-representation of some host-defence genes against biotic and abiotic stress. Manual examination shows that several gene families related to defence pathways, including protein folding, oxidation and anti-oxidation, apoptosis and immune responses, are expanded in C. gigas (Fig. 3a and Supplementary Table 18). The oyster genome contains 88 heat shock protein 70 (HSP70) genes, which have crucial roles in protecting cells against heat and other stresses, compared with ~17 in humans and 39 in sea urchins. Phylogenetic analysis finds clustering of 71 oyster HSP70 genes to themselves, suggesting that the expansion is specific to the oyster (Supplementary Fig. 19). Also expanded are cytochrome P450 (Supplementary Fig. 20) and multi-copper oxidase gene families, which are important in the biotransformation of endobiotic and xenobiotic chemicals26, and extracellular superoxide dismutases, which are important in defence against oxidative stress. The oyster genome has 48 genes coding for inhibitor of apoptosis proteins (IAPs), compared with 8 in humans and 7 in sea urchins, indicating a powerful anti-apoptosis system in oysters. Genes encoding lectin-like proteins, including C-type lectin, fibrinogen-related proteins and C1q domain-containing proteins (C1QDCs), are highly over-represented in the oyster genome (P<0.0001; Supplementary Table 18); these genes have important roles in the innate immune response in invertebrates27, 28, 29. Interestingly, many immune-related genes, including genes coding for Gram-negative bacteria-binding proteins, peptidoglycan-recognition proteins, defensin, C-type-lectin-domain-containing proteins and C1QDCs, are highly expressed in the digestive gland (Supplementary Fig. 21), indicating that the digestive system of this filter feeder is an important first-line defence organ against pathogens.

a, Expansion and expression of key genes in major stress-response pathways in C. gigas. Genes include HSPs and HSF in the heat-shock response; GRP78, CRT, CNX, GRP94, PERK, IRE1 and EIF2a in the endoplasmic reticulum unfolded-protein response (UPRER); IAPs, BCL2 like, BAG, BI1, caspases, FADD and TNFR in apoptotic pathways; CYP450 and MO in oxidation; and SOD, GPX, PRX and CAT in anti-oxidation. Boxes with bold black borders indicate gene families (HSPs, IAPs and SODs) expanded in C. gigas, and the filled colours correspond to their degree of upregulation in RPKMtreatment/RPKMcontrol by stress, found in 61 transcriptomes from oysters challenged with 9 types of stressors (Supplementary Text G2 and Supplementary Table 23). b, Venn diagram of common and unique genes expressed in response to temperature, salinity, air exposure and heavy-metal stress (zinc, cadmium, copper, lead and mercury), showing overlap of responses. c, Number of genes with and without detectable paralogues differentially expressed under stress and normal conditions, showing that genes responding to stress are more likely to have paralogues (P<11010; 2 test). Green sections of the pie chart represent 1,442, 809, 358, 550 and 7,938 paralogues for air exposure, metal, temperature, salinity and normal conditions, respectively.

To investigate genome-wide responses to stress, we sequenced 61 transcriptomes from C. gigas subjected to nine stressors, including temperature, salinity, air exposure and heavy metals (Supplementary Text G1 and Supplementary Tables 19 and 20). We found that 5,844 genes were differentially expressed under at least one stressor, and genes responding to different stressors showed significant overlap (Fig. 3b and Supplementary Fig. 23a). Air exposure induced a response from the largest number of genes (4,420), indicating that air exposure is a major stressor and that oysters have evolved an extensive gene set in defence. Genes differentially expressed in response to stress are more likely to have paralogues (Fig. 3c), suggesting that expansion and selective retention of duplicated defence-related genes are probably important to oyster adaptation. Under most stressors, genes coding for HSPs, histones, IAPs and protein biogenesis were upregulated, and those for protein degradation downregulated, pointing to concerted responses to maintain cellular homeostasis30 (Supplementary Text G3 and Supplementary Table 21). Genes involved in the unfolded protein response to cellular stress in the endoplasmic reticulum (coding for calreticulin, calnexin, 78- and 94-kDa glucose-regulated proteins) were upregulated, indicating that protein quality control is critical in cellular homeostasis under stress.

Air exposure induced up to 67-fold upregulation of five highly expressed IAPs (Supplementary Fig. 24a). Other inhibitors of apoptosis were also upregulated: BCL2 up to fourfold and BAG up to 12-fold (Supplementary Fig. 24b). These apoptosis inhibitors were also highly upregulated under heat and low salinity stress. These findings, along with the expansion of IAPs, suggest that a powerful anti-apoptosis system exists and may be critical for the amazing endurance of oysters to air exposure and other stresses. The existence of an intrinsic apoptosis pathway in invertebrates has been controversial, and parts of the pathways have only recently been demonstrated for two lophotrochozoans31, 32. The finding of key genes belonging to both intrinsic (BAX, BAK, BAG, BCL2, BI1 and procaspase) and extrinsic (TNFR and caspase 8) apoptosis pathways indicates that oysters have advanced apoptosis systems. Powerful inhibition of apoptosis as shown by genomic and transcriptomic analyses may be central to the ability of oysters to tolerate prolonged air exposure and other stresses.

Heat stress induced a ~2,000-fold increase in expression of five highly inducible HSP70 genes or a 13.9-fold increase in average expression of all HSP70 genes, amounting to 4.2% of all transcripts (Supplementary Figs 24c and 25). The genomic expansion and massive upregulation of HSP genes help to explain why C. gigas can tolerate temperatures as high as 49C when exposed to summer sun at low tide33. HSP genes were also upregulated under other stressors and may be central to the oyster defence against all stresses (Supplementary Fig. 25). HSP genes may also inhibit apoptosis by binding to effector caspases34.

Genes involved in signal transduction, including genes coding for G-protein-coupled receptors and Ras GTPase, were also activated by stressors (Supplementary Fig. 24f) and over-represented in the oyster genome (Supplementary Table 11). These regulators may have a role in orchestrating stress responses, which seem to be well coordinated (Fig. 3a and Supplementary Fig. 25). The expansion of key defence genes and the strong, complex transcriptomic response to stress highlight the sophisticated genomic adaptations of the oyster to sessile life in a highly stressful environment.

View post:
The oyster genome reveals stress adaptation and complexity of shell formation

Public release date: 19-Sep-2012 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

September 19, Shenzhen, China An international research team, led by Institute of Oceanology of Chinese Academy of Sciences and BGI, has completed the sequencing, assembly and analysis of Pacific oyster (Crassostrea gigas) genomethe first mollusk genome to be sequencedthat will help to fill a void in our understanding of the species-rich but poorly explored mollusc family. The study, published online today in Nature, reveals the unique adaptations of oysters to highly stressful environment and the complexity mechanism of shell formation.

"The accomplishment is a major breakthrough in the international Conchological research, with great advancement in the fields of Conchology and Marine Biology." said, Professor Fusui Zhang, Academician of Chinese Academy of Sciences, and a well-known Chinese Scientist of Conchology, "The study will provide valuable resources for studying the biology and genetic improvement of molluscs and other marine species. "

Oysters are a soft-bodied invertebrate with a double-hinged shell, which make up an essential part of many aquatic ecosystems. They have a global distribution and for many years they have much higher annual production than any other freshwater or marine organisms. In addition to its economic and ecological importance, the unique biological characteristics of oyster make it an important model for studying marine adaptations, inducing a great deal of biological and genomics research. The completed sequencing of oyster genome will provide a new horizon into understanding its natural mechanisms such as the adaptations to environmental stresses and shell formation, better exploration of marine gene resource, , among others.

Unlike many mammals and social insects, oyster as well as many other marine invertebrates is known to be highly polymorphism, which is a challenge for de novo assembling based on current strategies. In this study, researchers sequenced and assembled the Pacific oyster genome using a combination of short reads and a "Divide and Conquer" fosmid-pooling strategy. This is a novel approach developed by BGI, which can be used to study the genomes with high level of heterozygosity and/or repetitive sequences. After data process, the assembled oyster genome size is about 559 Mb, with a total of ~28,000 genes.

Based on the genomic and transcriptomic analysis results, researchers uncovered an extensive set of genes that allow oysters to adapt and cope with environmental stresses, such as temperature variation and changes in salinity, air exposure and heavy metals. For example, the expansion of heat shock protein 70 (HSP 70) may help explain why Pacific oyster can tolerate high temperatures as HSP family is expanded and highly expressed when in high temperature. The expansion of inhibitors of apoptosis proteins (IAPs), along with other findings, suggested that a powerful anti-apoptosis system exists and may be critical for oyster's amazing endurance to air exposure and other stresses. One notable finding on development is that the oyster Hox gene cluster was broken, and there are unusual gene losses and expansions of the TALE and PRD classes. Hox genes are essential and play critical important role in body plan, the Hox clusters are found to be more conserved in many organisms.

Researchers found paralogs might have the function to change the gene expression for better coping with the stresses. This result suggested that expansion and selective retention of duplicated defense-related genes are probably important to oyster's adaptation. Moreover, many immune-related genes were highly expressed in the digestive gland of the oyster, which indicated its digestive system was an important first-line defense organ against pathogens for the filter-feeder. The shell provides a strong protection against predation and desiccation in sessile marine animals such as oysters. At present, two models have been proposed for molluscan shell formation, but neither of them is accurate enough. In this study, by sequencing the peptides in the shell, researchers identified 259 shell proteins, and further analysis revealed that shell formation was a far more complex process than previously thought. They found many diverse proteins may play important roles in matrix construction and modification. The typical ECM proteins such as Laminin and some collagens were highly expressed in shells, suggesting that shell matrix has similarities to the ECM of animal connective tissues and basal lamina. Hemocytes may mediate fibronectin (FN)-like fibril formation in the shell matrix as they do in ECM. Furthermore, the functional diversity of proteins showed that the cells and exosome may participate in the shell formation.

Xiaodong Fang, Primary Investigator of this project at BGI, said, "The assembly approach of Oyster genome opens a new way for researchers to better crack the genomes with high-heterozygosity and high-polymorphism. The Oyster genome sheds insights into the comprehensive understanding of mollusc genomes or even lophotrochozoa genomes at the whole genome-wide level, with focuses on the studies of diversity, evolutionary adaptive mechanisms, developmental biology as well as genomics-assisted breeding. "

###

View original post here:
Oyster genome uncover the stress adaptation and complexity of shell formation

A Bangladeshi scientist has decoded the genome of a most deadly fungus that causes havoc to global jute and soybean production.

The fungus -- macrophomina phaseolina -- also causes seedling blight, root rot and charcoal rot of more than 500 crop and non-crop species.

The gene sequencing of macrophomina phaseolina would particularly help Bangladeshi scientists to develop jute varieties capable of fighting the fungus that causes an annual yield loss of around 40 billion taka (US$489.45 million) damaging 30 per cent of the country's precious natural fibre, experts said.

Jute is the second largest fibre crop next to cotton. And Bangladesh is the world's second-biggest producer of jute, next to India, and the biggest exporter of the natural fibre.

Bangladesh's globally famed geneticist Dr Maqsudul Alam led a 17-member team since early last year to decode the deadly fungus. The decoding has been done at a recently set up laboratory at Bangladesh Jute Research Institute (BJRI).

Prime Minister Sheikh Hasina announced the scientific achievement of Bangladesh in the Jatiya Sangsad yesterday amid cheers and desk thumping by lawmakers.

Dr Alam and his team's success in decoding fungus genome came just two years after he had decoded jute genome. Maqsudul Alam earlier sequenced the genome of papaya in the United States and rubber plant in Malaysia.

"Macrophomina phaseolina damages jute stems and is responsible for 30 per cent of jute yield loss. Besides, it also causes multiple damage to 500 crop and non-crop species. The US alone suffers 15 billion taka production loss a year due to "charcoal rot" in soybean caused by macrophomina phaseolina," explained biotechnologist Dr Shahidul Islam, a senior member of Dr Alam's team.

Reached over the phone last night, Dr Islam said they had completed the sequencing earlier this year but it has been internationally recognised with its publication in acclaimed UK journal BMC Genomics on September 17.

Genome sequencing helps scientists find genes much more easily and quickly. It allows scientists identify and understand how genes work together on a plant's various features like growth, development and maintenance as an entire organism. This allows them to manipulate the genes and enhance, reduce or add certain features of the plant.

See original here:
Bangladeshi scientist decodes genome of deadly fungus

Image of fresh Pacific oyster courtesy of Guofan Zhang, photo by Tao Liu

The world of the mollusk genome is now our oyster, as researchers have now sequenced the genetic code of this hearty (and delicious) shellfish, revealing it to be even more complex and adaptable than previously imagined.

The new genome provides insights how oysters manage to cope with a dynamic habitat and how they build their shells. The genome of the Pacific oyster (Crassostrea gigas) contains approximately 28,000 genes (compared with the 20,000 or so genes of humans), some 8,654 of which are thought to be specific to oystersor at least to mollusks.

One of the big mysteries surrounding oysters and many other mollusks is how they manage to thrive in such variable marine environments. As sessile creatures that largely stay put, they endure extreme temperature changes, swings in salinity, and prolonged exposure to open air in the intertidal zone. The researchers found 88 different genes that code for so-called heat shock protein 70, which guards cells and tissue against hot temperatures. This extra buffering might explain why oysters can survive in the sun in temperatures up to about 49 degrees Celsius (120 degrees Fahrenheit). By contrast, humans have about 17 genes that make this protein, and even relatively immobile sea urchins have just 39.

Oysters are known for being excellent water filterers, and some environmental groups have even proposed reintroducing these shellfish to New York City waterways to clean up the harbor. How can these oysters stay healthy with so many chemicals and heavy metals flowing through them? The genome reveals one of the oysters secrets: a highly active immune systemespecially in its gut. The researchers found that many of the genes that make immune-related proteins are expressed in the oysters so-called digestive gland, indicating that the digestive system of this filter feeder is an important first-line defense organ against pathogens, the authors noted in their paper published online September 19 in Nature (Scientific American is part of Nature Publishing Group).

Perhaps the key to the survival of this soft-bodied organism is its flexible genome. The researchers sequenced 61 transcriptomes (RNA in the cell or tissue) and then exposed them to familiar oyster stressors. When exposed to air, for example, 4,420 different genes altered their expression. And some exposures produced impressive results. Exposing the transcriptomes to heat invoked a roughly 2,000 times higher expression of five of the heat shock protein 70-coding genes.

The genome of the oyster, the first mollusk to be sequenced, also cracked open some evolutionary clues about the shell of these tenacious bivalves. Once thought to be a fairly simple, self-assembling matrix of calcium carbonate, it now looks to be a complex creation that has undergone eons of evolutionary tweaking. And it shares some surprising signatures with the cell walls of other animals, suggesting that shell formation is an active and elaborate process that involves hundreds of proteins.

The oyster genome had thwarted standard sequencing techniques because it repeats itself in many placesand in others has different codes in the same places in a single individual. So the researchers tried a fosmid-pooling strategy, which allowed them to divide the genome up and compare multiple sequencings of each area. To help the process along further, they also created a more genetically homogenous oyster, using one from four generations of direct sibling inbreeding. They then compared this to a wild-caught oyster, just to make sure their results were not too altered by the chosen individual.

The success with the oyster genome will help open the door to sequencing more of the highly diverse mollusks, including snails, scallops and, perhaps even the master RNA editors themselves, the octopuses. Information from the oyster genome and other sequences in this group could help researchers better understand these organisms role in the oceans, their evolution and how they respond to climate change and ocean acidification as well as better strategies for raising them.

See more here:
Oyster Genome Pries Open Mollusk Evolutionary Shell

Veronica Godoy-Carters research focuses on the genetic mechanisms guiding specialized DNA polymerases, a type of cellular machine important in DNA replication when cells are under stress. Credit: iStockphoto.

Last week, Nature Magazine, Genome Research and Genome Biology published 30 papers on breakthrough research that will change the face of genetics. After nearly a decade of searching, the Encyclopedia of DNA Elements (ENCODE) Consortium has assigned biochemical functions to 80 percent of the genome. Previously considered "junk," the development adds significant insight into the importance of the noncoding regions of DNA. We asked Veronica Godoy-Carter, assistant professor of biology, toexplain.

What is noncoding DNA and why has it been called "junk"?

The genetic material present in all living organisms is DNA. It is understood that "coding" DNA can be "read" by the cellular machinery, as we read a page in a book, mostly as proteins (e.g., your hair and nails are made up of proteins). However, there are sections of the DNA in metazoans (e.g., humans) and in some unicellular organisms known to have no readable code, that is, noncoding DNA.The word "junk" was used in the 14th century to denote an old or inferior rope. Today it is used to characterize useless articles or those of little value. Thus, when researchers started to decipher the linearsequenceof the DNA, it became obvious that a large fraction of it is noncoding. Therefore, the word "junk" was used to describe such noncodingregions.

We've known for a while that noncoding DNA actually has very important physiological functions. How does this new research change or add to that understanding?

ENCODE has shown that, contrary to previous views, most of the sequences of the human genome are not useless. Though it was previously known than noncoding regions were important for regulation, this project has demonstrated that noncoding sequences serve as a roadmap for regulatory DNA binding proteins that effect expression of coding regions. Previous to this large-scale analysis, no one knew about the extent of regulatory regions that existed in "junk" DNA, now referred to as "dark matter." For example, there are many sites that are specifically chemically modified, permitting inhibition or induction of the DNA coding regions. Remarkably, the regulation of expression does not only occur in coding regions that are adjacent to regulatory elements, as previously thought. In some cases, regulation is long range and seems to occur only when the regulatory elements are near coding regions in the three-dimensional space!

How will this new understanding of noncoding DNA change the face of genetic research?

The long-range regulation of coding regions in the DNA is such an exciting finding because it will permit us to start understanding the effect of known changes in the DNA sequence (i.e., mutations) between, say, healthy and cancer tissues. As it turns out, many mutations associated with disease are in noncoding regions, whichpreviously made little sense. Nowit will be possible to map mutations on this roadmap andimportantlyit will be possible to understand how mutations far away in the linear DNA change the regulatory landscape ofcells.

Journal reference: Nature Genome Research Genome Biology

Provided by Northeastern University

The rest is here:
3Qs: New clues to unlocking the genome

DUBLIN--(BUSINESS WIRE)--

Research and Markets (http://www.researchandmarkets.com/research/5ckx7v/us_personalized) has announced the addition of the "US Personalized Cancer Genome Sequencing Market" report to their offering.

The US personalized cancer Whole-Genome Sequencing market is primarily classified into targeted genome sequencing and Whole-Genome Sequencing. Our report entitled US Personalized Cancer Genome Sequencing Market takes into account the Whole-Genome Sequencing services, i.e. one of the most attractive sectors due to its inherent capability of high revenue generation and efficiency in terms of personalized treatment. The US, which is the frontrunner in the provision of such high-end service, is on the focus by market players because of favorable demographics and rising awareness among the industry participants.

In order to properly analyze the virtues and significance of the US personalized cancer Whole-Genome Sequencing market, our report has effectively studied the current and future status of cancer in the whole country as well as states. In view of the fact that cancer affects some age groups in a significant manner, we have also investigated the age wise statistics of the disease. To get proper insight into the market, an in-depth analysis into the high-income group population is provided so that players can have a clear picture about their potential customer base and market to be tapped.

An in-depth study of the regulatory environment governing the US personalized cancer Whole-Genome Sequencing market has also been provided. It has been found that regulations related to personalized cancer sequencing are primarily governed with the accreditation of the laboratories performing the sequencing services and analysis and also the usage of FDA approved tests for conducting these tests. Further we have also discussed the various constraints faced by the industry players with suitable suggestions for overcoming them.

Companies Mentioned:

- Illumina

- Complete Genomics

- Beckman Coulter Genomics

- Expression Analysis

Continue reading here:
Research and Markets: US Personalized Cancer Genome Sequencing Market