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Thursday, June 8, 2017

Widespread Methylation in Earliest Fungi Offers Clue to Expression of Essential Genes

The Joint Genome Institute recently announced results from a project that used SMRT Sequencing to generate high-quality genome assemblies and detect epigenetic modifications for fungal species that represent the earliest branches of that kingdom’s phylogeny. The work was done as part of the 1000 Fungal Genomes Project, which aims to better characterize a diverse range of fungal species. Published in Nature Genetics, “Widespread adenine N6-methylation of active genes in fungi” comes from lead author Stephen Mondo, senior author Igor Grigoriev, and collaborators at JGI and other institutions. The major finding is that N6-methyldeoxyadenine (6mA) is seen at the earliest stages…

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Thursday, March 3, 2016

Prevalent Methylation in Prokaryotic Genomes Suggests Regulatory Functions

A new publication from scientists at Lawrence Berkeley National Laboratory, the Joint Genome Institute, and other organizations reports a landmark study of genome-wide methylation in prokaryotes. The analyses of 230 bacteria and archaea species revealed both more methylation than expected and novel epigenetic mechanisms. “­­­The Epigenomic­­­ Landscape of Prokaryotes” from lead author Matthew Blow, senior author Richard Roberts, and collaborators was recently published in PLoS Genetics. The team used SMRT Sequencing to detect 6-methyladenosine (m6A), 4-methylcytosine (m4C), and 5-methylcytosine (5mC) across the 230 genomes. “Bisulfite sequencing has enabled genome-wide surveys of 5mC methylation, but a historic absence of tools for…

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Wednesday, October 21, 2015

Guest Blog: Rich Roberts Urges Scientists to ‘Think Methylation’ in Microbial Sequencing

Richard Roberts, Nobel Laureate and Chief Scientific Officer of New England Biolabs, offers his thoughts on the utility of methylation data for understanding prokaryotes. In his words: “Please run SMRT Analysis to detect methylation in your prokaryotic PacBio data. Most bacteria and archaea encode DNA methylases, many of which are known components of restriction-modification systems. Usually, these are quite specific in terms of the sequences they recognize; the restriction component becomes a key defense mechanism preventing phages, plasmids, and other DNA elements from infecting the cell. Until recently, it was quite difficult to determine the recognition sequences of these methylases.…

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Wednesday, August 26, 2015

In Bacterial Study, Scientists Link Epigenetic Switch to Virulence, Antibiotic Resistance, and More

Scientists from Griffith University, Ohio State University College of Medicine, and other institutions recently published a detailed study of phase-variable expression of a DNA methyltransferase in non-typeable Haemophilus influenzae, the predominant cause of pediatric middle ear infections. The team found that the bacterium’s epigenetic switch regulates proteins used in current vaccine candidates and influences important traits including antibiotic resistance, ability to evade the host immune system, and biofilm formation, which significantly contributes to chronic infection. The paper, “A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae,” was published in Nature Communications last month by lead…

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Tuesday, July 14, 2015

SMRT Sequencing Contributes to Detection of DNA Methylation in C. elegans

A recent paper in the journal Cell presents novel findings of DNA methylation in C. elegans, an organism previously believed not to have such epigenetic marks. Scientists used several approaches to analyze the adenine N6-methylation (6mA) found in C. elegans, including SMRT® Sequencing to directly observe base modifications across the genome. From lead authors Eric Greer and Mario Blanco with senior author Yang Shi at Harvard Medical School, “DNA Methylation on N6-Adenine in C. elegans” describes a range of technological methods deployed to assess methylation across the worm’s genome. The team queried the nematode with specific antibodies for 6mA; immunofluorescence;…

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Monday, June 15, 2015

Scientists Publish New Methylation Analysis Protocols Using SMRT Sequencing

Scientists from the Icahn School of Medicine at Mount Sinai and the University of Saskatchewan teamed up to develop an innovative approach to methylation analysis using Single Molecule, Real-Time (SMRT®) Sequencing. The resulting method was just published in BMC Genomics. Lead author Yao Yang and colleagues note in the paper [“Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS)”] that existing methods for methylation analysis are limited by cost and throughput in the case of Sanger sequencing, or short read lengths with NGS technologies. Their goal was to develop a method combining long reads, high accuracy,…

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Tuesday, September 30, 2014

New Papers Detail Complexity of Methylome-Related Virulence in Human Pathogens

In two new publications, one published today, scientists from Australia, Italy, the UK, and the US report critical and surprising new findings about DNA methylation-related complexity of bacteria. Adding to the list of advances from genome-wide epigenetic analysis, these projects enhance our understanding of how methylation systems work in human pathogens — and offer important clues for future investigations into how to treat them. Today’s paper, “A random six-phase switch regulates pneumococcal virulence via global epigenetic changes,” was published in Nature Communications by scientists at the University of Leicester, University of Siena, University of Adelaide, and Griffith University. Senior authors…

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Monday, August 18, 2014

Genome-Wide Methylation in Human Microbiome Samples

Scientists in Florida and Finland recently published a report of their work studying methylation patterns in two human microbiome samples. While microbiome studies have become quite popular, the authors note there have been no prior papers detailing genome-wide methylation of bacteria found in those studies. Their goal was to ascertain how much added functional variation might occur based on methylation patterns. “The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei,” published in Frontiers in Microbiology, comes from lead author Michael Leonard and senior author Eric Triplett at the University of Florida plus a team of…

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Tuesday, July 29, 2014

Novel Study of Genome-wide PT Modifications in Bacteria Performed with SMRT Sequencing

A recent paper from scientists in China and the United States demonstrates a novel view of phosphorothioate (PT) DNA modifications in two bacterial genomes. Scientists from Shanghai Jiao Tong University, Massachusetts Institute of Technology, Wuhan University, and Pacific Biosciences teamed up to deploy Single Molecule, Real-Time (SMRT®) Sequencing to generate the first genome-wide view of PT modifications and to better understand their function. “Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences” by Cao et al. was published in Nature Communications. The authors note that PT modifications, which replace a non-bridging phosphate oxygen with sulphur, were only recently…

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Monday, June 23, 2014

Unprecedented Read Length at the Icahn Institute:
Precise Sizing + SMRT Sequencing

At the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai in New York City, technology development expert Robert Sebra, Ph.D., sees tremendous need for long-read, high-accuracy sequencing for use in microbial surveillance, detection of repeat expansions, and other research applications. To meet that demand, he relies on Single Molecule, Real-Time (SMRT®) Sequencing from Pacific Biosciences with BluePippin™ automated DNA size selection from Sage Science. Together, these tools offer a powerful solution and industry-leading read lengths that allow Sebra and other researchers to resolve repeat elements and structural variants, rapidly close microbial genomes, and measure epigenetic marks. Sebra, an…

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Thursday, May 22, 2014

At ASM, Pioneering Scientists Presented Bacterial Methylome Highlights

This week’s annual meeting of the American Society for Microbiology was every bit as interesting, data-rich, and jam-packed as promised. We’re grateful to everyone who stopped by our booth and got to know more about Single Molecule, Real-Time (SMRT®) Sequencing. Our favorite session, “Bacterial Methylomes,” took place on the last day of the conference and was organized by Rich Roberts, Nobel laureate and Chief Scientific Officer at New England Biolabs. The session highlighted several projects analyzing genome-wide methylation states of bacteria, a task which has been all but impossible due to the technical inability to detect such base modifications. As…

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Thursday, January 16, 2014

Looking Ahead: The 2014 PacBio Technology Roadmap

By Jonas Korlach, Chief Scientific Officer 2013 was an eventful and exciting year for PacBio. As I described in the 2013 roadmap post a year ago, we have applied numerous improvements to SMRT® Sequencing, resulting in longer read lengths, greater sequencing throughput, new and improved data-analysis methods, and more efficient workflows. We are very pleased that these advances resulted in so many publications, conference presentations, and social media contributions, with the number of peer-reviewed scientific publications from the scientific community now exceeding 100. On behalf of all of us at Pacific Biosciences, I would like to express my heartfelt gratitude…

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Thursday, September 5, 2013

Next Week’s ICG Meeting to Include Several SMRT Sequencing Talks

The International Conference on Genomics in the Americas (ICG), organized by BGI and UC Davis, is taking place on Sept 12-13 in Sacramento, CA. One of the keynote presentations in the opening session comes from Nobel Laureate Richard Roberts, Chief Scientific Officer of New England Biolabs. Entitled “Bacterial Methylomes,” the talk will cover some recent work Roberts has done using SMRT® Sequencing to characterize the full, genome-wide methylation marks in various strains of microbes. This kind of work “has yielded a plethora of new and interesting results,” Roberts told BioMed Central recently. Later that day, Ken Dewar from McGill University…

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Tuesday, July 30, 2013

Single-Molecule Sequencing Technology Q&A with Nobel Laureate Rich Roberts

BioMed Central has published an interesting Q&A session on its Biome blog with Nobel Laureate Richard Roberts about why he believes in SMRT Sequencing and thinks non-users should take another look at it, too. He also discusses the critical need for funding to support the functional annotation of the genomes being sequenced, including for new bioinformatics tools. “We should be greatly increasing our efforts to gain functional insights into the millions of genes we are discovering by sequencing and for which we either have no idea of what they do, or many of our predictions are simply wrong,” he says.…

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Monday, July 22, 2013

Whole-Genome Microbial Epigenetics: ASM Workshop videos highlight emerging application of SMRT Sequencing

We recently participated in a workshop on whole-genome microbial epigenetics at the American Society for Microbiology annual meeting in Denver. Using SMRT® Sequencing, the three most common types of bacterial methylation can be studied at base resolution across an entire genome. An exceptional lineup of speakers shared their latest research and we’re pleased to be able to share video of the presentations. Our CSO Jonas Korlach opened the workshop with a brief introduction describing how SMRT Sequencing generates epigenetic information. His presentation was followed by Brian Anton, from New England BioLabs, who presented data on restriction-modification systems and orphan methylases…

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