New ENCODE Paper Reveals Remarkable Chromatin Diversity at Regulatory Elements

 

Today marks a major milestone for the ENCODE consortium! More than 30 papers will be published today in Nature, Genome Biology, and Genome Research from teams of scientists working on various facets of the project.

 

One of those, a publication in Genome Research, reports on a surprising level of heterogeneity among patterns of chromatin modifications as well as nucleosome positioning around regulatory elements such as transcription factor binding sites in the human genome. In the past, these genomic elements have been studied primarily by averaging patterns of chromatin marks across populations of sites, leading to the perception that patterns were much more uniform. The nucleosome positioning sequence data mapping and analysis was performed on the DNAnexus platform.

 

Lead author Anshul Kundaje was a postdoc for Serafim Batzoglou and Arend Sidow at Stanford University during the project reported in the paper. Now a research scientist at MIT, Kundaje says the work was an integral part of the ENCODE consortium’s efforts to elucidate functional elements in the human genome. The scientists looked at 119 human transcription factors and regulatory proteins to better understand how nucleosomes are positioned and how histone modifications are made around binding sites. In the paper, the authors report that asymmetry of nucleosome positioning and histone modifications is the rule, rather than the exception.

 

Kundaje and his colleagues relied on ChIP-seq data for the 119 transcription factors in a variety of cell types, with corresponding data for histone modifications. They also generated similar data for nucleosome positioning. To improve accuracy, the team sequenced extremely deeply, ultimately generating some 5 billion reads on the SOLiD sequencing platform. “The data sets were incredibly massive,” Kundaje says. “Processing these data sets locally was quite a challenge.” The group turned to DNAnexus, uploading their sequence files to the cloud and preprocessing the data with the company’s probabilistic mapping tool. “DNAnexus made that process incredibly simple,” he adds.

 

Figure 1:The mapping of the 5 billion reads was performed using the DNAnexus mapper.

Using a new tool they developed — the Clustered AGgregation Tool (CAGT) for pattern discovery — the scientists found that nucleosome positioning and histone modification at transcription factor binding sites is far more diverse than was previously thought. Rather than averaging across the regions as most studies have done, the new clustering tool was able to analyze the differences in magnitude, shapes, and orientation of the many patterns identified.

 

“What we found is that the results you get from the clustering approach are dramatically different from what you get by simply averaging across all types,” Kundaje says. “We found a large diversity of patterns of histone modifications as well as nucleosome positioning around almost every transcription factor binding site.”

 

Even the well-known and remarkably well studied transcription factor CTCF, long established as an insulator, was found to have surrounding chromatin patterns pointing to other functions throughout the genome.

 

Figure 2: Analysis using CAGT reveals the surprising diversity of patterns of an active chromatin mark H3K27ac around the binding sites of the CTCF protein that is well-known for its repressive insulator role.

 

The authors used their clustering tool to group the patterns into some 25 distinct signatures “that completely capture the diversity of all the modifications across all binding sites in a variety of cell types,” Kundaje says. The method uses ‘metapatterns’ to explain that diversity, and that information can reveal the function of these elements in context. “By accounting for combinatorial relationships between various binding events and how they affect chromatin, this gives you a more complete biological sense of what a transcription factor is doing in a cell type,” he adds.

 

Kundaje is already following up on this study by looking at other species to see whether the heterogeneity of modification patterns holds true in other organisms. He continues to use DNAnexus for analysis of sequencing data, especially in read mapping, quality control, and genome browsing, he says.

 

Using DNAnexus for the team’s ENCODE study “made the process significantly easier,” Kundaje adds, noting that the cloud provider’s direct integration of the genome browser was particularly helpful. DNAnexus allowed Kundaje and his colleagues to go from data to visualization with minimal processing steps in between, he says. “It frees up your time to focus on the more interesting work.”

 

For a glimpse of some of Kundaje’s data, DNAnexus has made the 20 samples available on DNAnexus in the Public Data folder, called Encode. Click here to sign up for a free account.

 

Check out the Kundaje et al. paper “Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.”

 

Scientific Collaborators in New York and Jerusalem Uncover New Mutation Underlying Rare Sensory Disease

The study described below was published in the April 2012 edition of the Annals of Neurology, the journal for the American Neurological Association and the Child Neurological Society.

At a time when many people are asking when DNA sequence information will have a real application in healthcare, a nonprofit organization based in Brooklyn, New York, is proving that linkage mapping and exome sequencing are already making a major difference in people’s lives.

Bonei Olam is charged with helping families with genetic or undiagnosed diseases, many of them dealing with infertility challenges, to conceive healthy babies using tools such as pre-implantation genetic diagnosis. In 2008, Bonei Olam opened its Center for Rare Jewish Genetic Disorders to find the underlying molecular causes of some of these conditions. They responded to hundreds of families who had been unable to find a diagnosis through traditional medical routes, and established key collaborations with universities, including Hadassah Medical Center in Israel, to help perform the studies. Over the years, the center has funded SNP arrays, Sanger sequencing, variant validation, and the sequencing of more than 100 exomes for family after family.

It was through one of those studies that collaborators from Hadassah Medical Center, New York University, and Bonei Olam discovered a novel mutation that leads to a previously uncharacterized disease linked to hereditary sensory autonomic neuropathy, a group of disorders with the common theme of loss of function in peripheral sensory nerves. This new version is far more severe than its familial dysautonomia cousin and is caused by a mutation in the DST gene, which destabilizes the Dystonin protein. The study, called “Hereditary sensory autonomic neuropathy caused by a mutation in dystonin” was published by Dr. Simon Edvardson, Prof. Orly Elpeleg, and the rest of their team in the Department of Genetic and Metabolic Diseases at Hadassah in the April 2012 issue of Annals of Neurology.

Chaim Jalas, Director of Genetic Resources and Services at the Center for Rare Jewish Genetic Disorders and a co-author on the paper, says that this particular project began when two related families approached Bonei Olam, each having lost at least one child to this uncharacterized disease. The disorder was lethal: all of the affected children, three in total, died by the age of 2.

The team started off with SNP arrays to perform linkage analysis in both families, and later performed exome sequencing on one of the affected children to find the causative mutation. Much of the clinical and functional work in the eight-month project — including identifying the mutated gene and studying its effect in cell lines — was led by Prof. Orly Elpeleg at Hadassah Medical Center in Jerusalem.

Since Bonei Olam doesn’t have an in-house bioinformatics team, Jalas relies for interpretation on various software tools as well as the cloud-based storage and analysis platform from DNAnexus. For this project, he uploaded the raw sequence reads to DNAnexus and ran the Exome analysis tool followed by the Variant analysis tool, which located the mutation — the DST variant that results in an unstable transcript in Dystonin, a protein used in the cytoskeleton. “What DNAnexus does for us is all the bioinformatics, starting from uploading raw reads to performing the alignment, the variant calling, the annotation, and graphical display of the reads on the reference genome,” Jalas says. In the past, the DNAnexus Variant analysis tool has been able to find a variant that other software packages have missed, he says — but he’s most confident when two different software packages call the same variant so it’s more likely to be real.

Once DNAnexus returned the answer, Jalas shared the data with his collaborators, who could log in with their own accounts to review the information. Finally, the research team confirmed the mutation by Sanger sequencing.

Since Bonei Olam isn’t your typical research institute, the real triumph was not the research finding or the publication of this mutation; it’s that “one of the two families is currently pregnant with a healthy baby,” Jalas says.

Ultimately, the success of these studies may prompt Bonei Olam to move toward whole genome sequencing. “I think at some point we will do whole genomes,” Jalas says. “We’re looking into a pilot study of families for whom exome sequencing did not find a causative genetic mutation where we know for sure it’s a genetic condition.”

Paper information:
Hereditary sensory autonomic neuropathy caused by a mutation in dystonin
Simon Edvardson, MD; Yuval Cinnamon, PhD; Avraham Shaag, PhD; Orly Elpeleg, MD, from Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center
Chaim Jalas, from Bonei Olam, Center for Rare Jewish Genetic Disorders
Channa Maayan, MD, from Department of Pediatrics, Hadassah, Hebrew University Medical Center
Felicia B. Axelrod, MD, from Department of Pediatrics, New York University School of Medicine
DOI: 10.1002/ana.23524
http://onlinelibrary.wiley.com/doi/10.1002/ana.23524/abstract