Spotted in the Literature: The First PippinHT Publication!
We began shipping the high-throughput version of our automated Pippin DNA size selection platform last year, and it’s a thrill to see what we believe is the first reference to it in a peer-reviewed publication.
A team of scientists from Huazhong Agricultural University in China recently published “Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation” in Nucleic Acids Research. In the paper, lead author Maojun Wang and colleagues tracked epigenetic modifications during development of the cotton fiber.
Through extensive testing, they found that one type of methylation increased over time, while a second type of methylation decreased, and that the same changes were not seen in nearby tissue. In addition, “integrated multi-omics analyses revealed that dynamic DNA methylation played a role in the regulation of lipid biosynthesis and spatio-temporal modulation of reactive oxygen species during fibre differentiation,” the scientists report.
They used PippinHT during MNase digestion of chromatin, purifying the digested samples and then size-selecting for 100 bp – 200 bp fragments. Those were later run in MNase-seq and ChIP-seq pipelines on an Illumina HiSeq instrument.
Congrats to the authors of this publication for their very cool epigenetic findings, and also to PippinHT for making it into the scientific literature!
Building on a RAD Idea
It’s been a few years since the Hoekstra lab at Harvard first published its double-digest RAD-seq protocol. Since then, the approach has been rapidly adopted by the community for massively parallel genotyping, particularly of non-model organisms, and has been the foundation for lots of new protocol and tool development.
ddRAD-seq was itself an iteration on the original RAD-seq (restriction-site associated DNA sequencing) method from the Cresko lab at the University of Oregon. It introduced an important tool for people interested in using the second digest step, which relied on automated size selection with the Pippin Prep to generate useful results.
In addition to the widespread use of ddRAD-seq for organisms ranging from fish to mosquitos, the community has continued to develop and expand RAD-based protocols. The recently published hyRAD protocol adds a hybridization capture step to make the approach useful with degraded DNA samples, such as those found in museum collections. EpiRADseq swaps in a methylation-sensitive restriction enzyme, enabling scalable and cost-effective quantification of methylation across whole genomes. And SimRAD is a novel software tool designed to improve ddRAD-seq results by accurately estimating the number of loci generated. Meanwhile, scientists have optimized ddRAD-seq methods for Ion Torrent sequencing and reviewed best practices for RAD-based approaches in general. One team compared ddRAD-seq to sequence capture and found that the RAD-based method generated more data for less money, noting that it would be particularly valuable for organisms without existing genome resources. This paper compared sequence data to SNP data from ddRAD-seq projects for phylogenetic inference, yielding advice for making phylogenetic trees from SNP data more accurate.
For a look at some great findings from recent ddRAD-seq studies, check out these papers:
New Publications Ponder the Basics of Life and What Makes Us Human
Two recent papers published in Science are not only landmarks in their fields, but also feature our BluePippin automated DNA size selection platform. We’re honored to be included in these important publications.
The first paper, “Design and synthesis of a minimal bacterial genome,” comes from Clyde Hutchison, Craig Venter, and collaborators. The team built a bacterial genome containing just 473 genes determined to be necessary for life. The achievement followed a robust testing process in which each gene in the Mycoplasma mycoides genome was systematically altered to determine whether it was necessary for the organism’s survival. After stripping out all non-essential DNA, the scientists were left with a 531 Kb genome. Interestingly, the function of nearly a third of all genes included in the final genome has not been determined. The team used BluePippin’s High-Pass protocol with the PacBio RS II for de novo assembly of the artificial genome.
The second paper comes from scientists at the University of Washington, the McDonnell Genome Institute, and other organizations. “Long-read sequence assembly of the gorilla genome” used PacBio sequencing to improve assembly quality by 150x compared to previous drafts of the gorilla genome, closing 93 percent of gaps and adding a significant amount of new sequence. Scientists got the best view yet of structural variation, ancestral evolution, and genetic diversity within our primate cousin, and created a valuable resource that will allow the community to make even more discoveries — especially about the difference between humans and closely related primates. BluePippin helped the scientists maximize read lengths by removing smaller fragments prior to sequencing.
Taken together, these publications get us a few steps closer to understanding life at its most basic level, as well as what makes us human. We’re eager to see how the research community will build on these great advances in the future.
Kick Up Your Heels for DNA Day
It’s that time of year again — the time our kids look at us, shake their heads, and ask, “There’s a day to celebrate DNA? Seriously?”
But for those of us in the industry, DNA Day is a big deal. April 25th was chosen to honor major milestones in our understanding of DNA (Watson and Crick’s publication on the double helix structure and the completion of the Human Genome Project), and for the community it’s a great day to reflect on the remarkable advances in this field. Here, we consider a few areas where progress is particularly impressive.
Diversity of DNA: Never in history have we had such a clear view of the genetics of organisms from extremophiles to extinct species, and everything in between. Cheap sequencing allows scientists to go far beyond model organisms, exploring genomes all across the tree of life. RAD-based sequencing approaches have made it more affordable to do massive-scale genotyping of non-model organisms as well. In addition, we’re engaged in the largest-scale studies the field has ever seen, with multiple efforts aiming to recruit 1 million people in cohorts that were until recently inconceivable.
How DNA functions: At last year’s inaugural Festival of Genomics, we listened with great interest as Harvard’s Ting Wu described compelling work to understand the function of DNA based on its folding patterns. Conventional wisdom had long suggested that unwieldy DNA strands scrunch themselves up however they can, but Wu and other scientists have shown that the folding pattern is instead precisely selected, with a significant impact on the downstream functions of that DNA. Findings like this remind us that we’re still at the beginning of the story of DNA, with many more chapters to go before we can truly say we understand it. In a recent paper we really enjoyed, scientists demonstrated that they could encode, encrypt, and extract short messages inserted into synthetic DNA.
How we treat DNA: Today, we think of treating DNA as a component of the NGS pipeline, with lots of effort to improve sample prep for everything from FFPE DNA samples to museum samples or precious clinical samples. But down the road, we may literally treat our DNA, using tools like CRISPR to edit out genetic problems from living people as a standard clinical treatment.
We hope you’ll be doing something fun to celebrate DNA Day this year. Follow along on Twitter with #DNADay16 to see how the community’s making it a special event.
Scientists Report Method for Secure Communication Using DNA
It’s a study that would make John le Carré proud. DARPA-funded MIT scientists published results of a new method for encrypting messages in synthetic DNA for highly secure communication. It popped up on our radar because our BluePippin automated size selection instrument was used during sequence analysis.
In the PLoS One paper, “Multiplexed Sequence Encoding: A Framework for DNA Communication,” authors Bijan Zakeri, Peter Carr, and Timothy Lu describe new approaches to encoding, encrypting, and fragmenting messages across multiple plasmids. “With synthesis and sequencing speeds rising, and costs rapidly declining, DNA is an intriguing option for the transfer and storage of digital information,” they write.
The team designed QWERTY-style keyboards to easily convert English words into nucleic acids, being careful to assign codons in a way that would minimize homopolymers in the resulting DNA sequence, though they note that users would be able to shuffle codon assignments for their own preference or to increase security of the message.
Next, they created what they call a “secret-sharing system” that encrypts the message and splits it across several DNA molecules, requiring the recipient to use a combination key to reveal the message. “This approach can add an additional layer of protection for a communication and also provide opportunities to explore introducing tiers of complexity within a communication that is afforded by the unique makeup of DNA as a chemical polymer for information storage,” the scientists write. (In a step we really enjoyed, the team also took the opportunity to encode decoy messages into the DNA.)
For the final part of the process, the team came up with a new approach to extract the original message. “We investigated a new method that allows for the multiplexed sequencing of multiple DNA molecules with a common primer, where regions within distinct DNA molecules that have matching information can be identified from a single sequencing reaction via chromatogram patterning,” they report. They validated the whole process by encoding watermarks, messages, and a combination key into six synthetic DNA strands, honoring the cryptography field by using an important World War II communication.
The scientists note that this work demonstrates proof of concept, and that they plan to follow up with additional innovations in future efforts.