Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

The Polycomb repressive complexes PRC1 and PRC2 maintain embryonic stem cell (ESC) pluripotency by silencing lineage-specifying developmental regulator genes. Emerging evidence suggests that Polycomb complexes act through controlling spatial genome organization. We show that PRC1 functions as a master regulator of mouse ESC genome architecture by organizing genes in three-dimensional interaction networks. The strongest spatial network is composed of the four Hox gene clusters and early developmental transcription factor genes, the majority of which contact poised enhancers. Removal of Polycomb repression leads to disruption of promoter-promoter contacts in the Hox gene network. In contrast, promoter-enhancer contacts are maintained in the absence of Polycomb repression, with accompanying widespread acquisition of active chromatin signatures at network enhancers and pronounced transcriptional upregulation of network genes. Thus, PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network. We propose that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

Transcriptional control in large genomes often requires looping interactions between distal DNA elements, such as enhancers and target promoters. Current chromosome conformation capture techniques do not offer sufficiently high resolution to interrogate these regulatory interactions on a genomic scale. Here we use Capture Hi-C (CHi-C), an adapted genome conformation assay, to examine the long-range interactions of almost 22,000 promoters in 2 human blood cell types. We identify over 1.6 million shared and cell type-restricted interactions spanning hundreds of kilobases between promoters and distal loci. Transcriptionally active genes contact enhancer-like elements, whereas transcriptionally inactive genes interact with previously uncharacterized elements marked by repressive features that may act as long-range silencers. Finally, we show that interacting loci are enriched for disease-associated SNPs, suggesting how distal mutations may disrupt the regulation of relevant genes. This study provides new insights and accessible tools to dissect the regulatory interactions that underlie normal and aberrant gene regulation.

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

The mammalian genome harbors up to one million regulatory elements often located at great distances from their target genes. Long-range elements control genes through physical contact with promoters and can be recognized by the presence of specific histone modifications and transcription factor binding. Linking regulatory elements to specific promoters genome-wide is currently impeded by the limited resolution of high-throughput chromatin interaction assays. Here we apply a sequence capture approach to enrich Hi-C libraries for >22,000 annotated mouse promoters to identify statistically significant, long-range interactions at restriction fragment resolution, assigning long-range interacting elements to their target genes genome-wide in embryonic stem cells and fetal liver cells. The distal sites contacting active genes are enriched in active histone modifications and transcription factor occupancy, whereas inactive genes contact distal sites with repressive histone marks, demonstrating the regulatory potential of the distal elements identified. Furthermore, we find that coregulated genes cluster nonrandomly in spatial interaction networks correlated with their biological function and expression level. Interestingly, we find the strongest gene clustering in ES cells between transcription factor genes that control key developmental processes in embryogenesis. The results provide the first genome-wide catalog linking gene promoters to their long-range interacting elements and highlight the complex spatial regulatory circuitry controlling mammalian gene expression.

Mitochondrial disease genetic diagnostics: optimized whole-exome analysis for all MitoCarta nuclear genes and the mitochondrial genome

Discovering causative genetic variants in individual cases of suspected mitochondrial disease requires interrogation of both the mitochondrial (mtDNA) and nuclear genomes. Whole-exome sequencing can support simultaneous dual-genome analysis, although currently available capture kits do not target the mtDNA genome and provide insufficient capture for some nuclear-encoded mitochondrial genes. To optimize interrogation of nuclear and mtDNA genes relevant to mitochondrial biology and disease, a custom SureSelect "Mito-Plus" whole-exome library was formulated by blending RNA "baits" from three separate designs: (A) Agilent Technologies SureSelectXT 50 Mb All Exon PLUS Targeted Enrichment Kit, (B) 16-gene nuclear panel targeting sequences for known MitoCarta proteins not included in the 50 Mb All Exon design, and (C) sequences targeting the entire mtDNA genome. The final custom formulations consisted of a 1:1 ratio of nuclear baits to which a 1 to 1,000-fold diluted ratio of mtDNA genome baits were blended. Patient sample capture libraries were paired-end sequenced on an Illumina HiSeq 2000 system using v3.0 SBS chemistry. mtDNA genome coverage varied depending on the mtDNA:nuclear blend ratio, where a 1:100 ratio provided optimal dual-genome coverage with 10X coverage for over 97.5% of all targeted nuclear regions and 1,000X coverage for 99.8% of the mtDNA genome. mtDNA mutations were reliably detected to at least an 8% heteroplasmy level, as discriminated both from sequencing errors and potential contamination from nuclear mtDNA transcripts (Numts). The "1:100 Mito-Plus Whole-Exome" Agilent capture kit offers an optimized tool for whole-exome analysis of nuclear and mtDNA genes relevant to the diagnostic evaluation of mitochondrial disease.

Abstract 5095: CGH+SNP microarrays for copy-neutral aberration detection in cancer research

Advances in cancer research have greatly benefited from high resolution copy number (CN) measurements provided by oligo array Comparative Genomic Hybridization (aCGH). The addition of single nucleotide polymorphism (SNP) measurements to CGH microarrays enables the detection of copy-neutral loss of heterozygosity (cnLOH) events and allelic imbalances arising from genomic instability during cancer development and progression. Nonetheless, cancer studies face challenges associated with genomes’ aneuploidy, polyclonality and mosaicism due to the admixtures of tumor and normal cells. In the quest to decipher tumor complexity, the power and sensitivity of Agilent's CGH+SNP platform has been expanded with new computational methods capable of determining clonal fraction, total CN and allele-specific CN in aneuploid samples. Genomic DNA from hematology-oncology samples, cell lines and a genotyped control sample was digested with AluI and RsaI restriction endonucleases to allow for SNP profiling at the enzymes’ restriction sites. Experimental and reference samples were differentially labeled and hybridized to the Agilent Cancer CGH+SNP microarray, containing ∼20K cancer associated CGH probes, ∼100K backbone probes and ∼60K SNP probes. The data were analyzed using algorithms with extended capability to determine clonal fraction, total and allele-specific CN of the aberrant clone. As expected, significant diversity was found in different chronic lymphocytic leukemia (CLL) tumors. In one CLL sample a small homozygous deletion and cnLOH were identified on chromosome 13. In another CLL case a trisomy of the entire chromosome 12 was observed, together with a small hemizygous deletion and cnLOH on chromosome 18. An Acute Lymphoblastic Leukemia (ALL) tumor sample was found to harbor an amplification on chromosome 6, as well as two small amplifications on chromosome X. To assess the ability of detecting low level mosaicism, we conducted a mixed sample experiment whereby a sample with a known aberration was mixed at known ratios with a matched sample not containing the aberration. The computed clonal fraction, total and allele-specific CN matched the expected values. We have shown that the new algorithms developed for cancer sample analysis determined the genotypes, total copy numbers and clonal fractions in aneuploid samples highly mixed with normal cell populations.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5095. doi:1538-7445.AM2012-5095

Abstract 1256: Profiling protein-coding RNA and thousands of large non-coding RNAs from nanogram amounts of total RNA using a single microarray design

Large intergenic non-coding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes, yet determining the function of individual lincRNAs remains challenging. Recently, more than 8,000 human lincRNAs were annotated and cataloged from more than 4 billion RNA-Seq reads across 24 tissues and cell types by scientists at the Broad Institute of MIT and Harvard. Data from this project indicates that lincRNA expression is highly tissue-specific as compared to protein coding gene expression. As researchers continue to investigate the function of lincRNAs, there is a need for tools that can rapidly and accurately measure the expression of the recently annotated lincRNAs along with mRNA expression. We have previously developed and recently updated the content of the human SurePrint G3 microarrays so that they are comprised of all known protein-coding mRNAs and lincRNAs, to enable systematic profiling and simultaneous detection of coding and non-coding gene expression from a single sample. To demonstrate the utility of the new microarray design we used low nanogram amounts RNA from matched tumor and adjacent normal tissues to produce cyanine-labeled cRNA. The labeled cRNA was applied to the microarrays to detect differences in coding and non-coding gene expression profiles. Using the GeneSpring GX software we are able to identify differentially expressed lincRNAs and protein-coding RNAs in the tumor and normal samples in less than two days. Comparisons of probe signals from technical replicate samples demonstrated high reproducibility with wide dynamic ranges and high sensitivity. Data from the microarrays correlates well with whole transcriptome sequencing of the same matched tumor/normal samples. Using this approach we show that lincRNA expression coincides with key genes known to regulate biological processes involved in cancer progression and this work demonstrates how profiling mRNA and lincRNA from matched tumor and adjacent normal samples can enable researchers to further define the role of lincRNAs in gene regulation.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1256. doi:1538-7445.AM2012-1256

Myofibrillar myopathy caused by a mutation in the motor domain of mouse MyHC IIb

Ariel is a mouse mutant that suffers from skeletal muscle myofibrillar degeneration due to the rapid accumulation of large intracellular protein aggregates. This fulminant disease is caused by an ENU-induced recessive mutation resulting in an L342Q change within the motor domain of the skeletal muscle myosin protein MYH4 (MyHC IIb). Although normal at birth, homozygous mice develop hindlimb paralysis from Day 13, consistent with the timing of the switch from developmental to adult myosin isoforms in mice. The mutated myosin (MYH4(L342Q)) is an aggregate-prone protein. Notwithstanding the speed of the process, biochemical analysis of purified aggregates showed the presence of proteins typically found in human myofibrillar myopathies, suggesting that the genesis of ariel aggregates follows a pathogenic pathway shared with other conformational protein diseases of skeletal muscle. In contrast, heterozygous mice are overtly and histologically indistinguishable from control mice. MYH4(L342Q) is present in muscles from heterozygous mice at only 7% of the levels of the wild-type protein, resulting in a small but significant increase in force production in isolated single fibres and indicating that elimination of the mutant protein in heterozygotes prevents the pathological changes observed in homozygotes. Recapitulation of the L342Q change in the functional equivalent of mouse MYH4 in human muscles, MYH1, results in a more aggregate-prone protein.

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations

Utilizing the full power of next-generation sequencing often requires the ability to perform large-scale multiplex enrichment of many specific genomic loci in multiple samples. Several technologies have been recently developed but await substantial improvements. We report the 10,000-fold improvement of a previously developed padlock-based approach, and apply the assay to identifying genetic variations in hypermutable CpG regions across human chromosome 21. From approximately 3 million reads derived from a single Illumina Genome Analyzer lane, approximately 94% (approximately 50,500) target sites can be observed with at least one read. The uniformity of coverage was also greatly improved; up to 93% and 57% of all targets fell within a 100- and 10-fold coverage range, respectively. Alleles at >400,000 target base positions were determined across six subjects and examined for single nucleotide polymorphisms (SNPs), and the concordance with independently obtained genotypes was 98.4%-100%. We detected >500 SNPs not currently in dbSNP, 362 of which were in targeted CpG locations. Transitions in CpG sites were at least 13.7 times more abundant than non-CpG transitions. Fractions of polymorphic CpG sites are lower in CpG-rich regions and show higher correlation with human-chimpanzee divergence within CpG versus non-CpG sites. This is consistent with the hypothesis that methylation rate heterogeneity along chromosomes contributes to mutation rate variation in humans. Our success suggests that targeted CpG resequencing is an efficient way to identify common and rare genetic variations. In addition, the significantly improved padlock capture technology can be readily applied to other projects that require multiplex sample preparation.

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

Studies of epigenetic modifications would benefit from improved methods for high-throughput methylation profiling. We introduce two complementary approaches that use next-generation sequencing technology to detect cytosine methylation. In the first method, we designed approximately 10,000 bisulfite padlock probes to profile approximately 7,000 CpG locations distributed over the ENCODE pilot project regions and applied them to human B-lymphocytes, fibroblasts and induced pluripotent stem cells. This unbiased choice of targets takes advantage of existing expression and chromatin immunoprecipitation data and enabled us to observe a pattern of low promoter methylation and high gene-body methylation in highly expressed genes. The second method, methyl-sensitive cut counting, generated nontargeted genome-scale data for approximately 1.4 million HpaII sites in the DNA of B-lymphocytes and confirmed that gene-body methylation in highly expressed genes is a consistent phenomenon throughout the human genome. Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions.

A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids

Oligonucleotide microarrays or oDNA chips are effective decoding and analytical tools for genomic sequences and are useful for a broad range of applications. Therefore, it is desirable to have synthesis methods of DNA chips that are highly flexible in sequence design and provide high quality and general adoptability. We report herein, DNA microarray synthesis based on a flexible biochip method. Our method simply uses photogenerated acid (PGA) in solution to trigger deprotection of the 5'-OH group in conventional nucleotide phosphoramidite monomers (i.e. PGA-gated deprotection), with the rest of the reactions in the synthesis cycle the same as those used for routine synthesis of oligonucleotides. The complete DNA chip synthesis process is accomplished on a regular DNA synthesizer that is coupled with a UV-VIS projection display unit for performing digital photolithography. Using this method, oDNA chips containing probes of newly discovered genes can be quickly and easily synthesized at high yields in a conventional laboratory setting. Furthermore, the PGA-gated chemistry should be applicable to microarray syntheses of a variety of combinatorial molecules, such as peptides and organic molecules.

Characterization of oligodeoxyribonucleotide synthesis on glass plates

Achieving high fidelity chemical synthesis on glass plates has become increasingly important, since glass plates are substrates widely used for miniaturized chemical and biochemical reactions and analyses. DNA chips can be directly prepared by synthesizing oligonucleotides on glass plates, but the characterization of these micro-syntheses has been limited by the sub-picomolar amount of material available. Most DNA chip syntheses have been assayed using in situ coupling of fluorescent molecules to the 5'-OH of the synthesized oligonucleotides. We herein report a systematic investigation of oligonucleotide synthesis on glass plates with the reactions carried out in an automated DNA synthesizer using standard phosphoramidite chemistry. The analyses were performed using (32)P gel electrophoresis of the oligonucleotides cleaved from glass plates to provide product distribution profiles according to chain length of oligonucleotides. 5'-Methoxythymidine was used as the chain terminator, which permits assay of coupling reaction yields as a function of chain length growth. The results of this work reveal that a major cause of lower fidelity synthesis on glass plates is particularly inefficient reactions of the various reagents with functional groups close to glass plate surfaces. These problems cannot be detected by previous in situ fluorescence assays. The identification of this origin of low fidelity synthesis on glass plates should help to achieve improved synthesis for high quality oligonucleotide microarrays.

Digital light-directed synthesis. A microarray platform that permits rapid reaction optimization on a combinatorial basis

Solution reactions using photogenerated reagents (Gao, X.; Yu, P.; LeProust, E.; Sonigo, L.; Pellois, J. P.; Zhang, H. J. Am. Chem. Soc. 1998, 120, 12698) are a potentially powerful means for combinatorial parallel synthesis of addressable molecular microarrays. In this report, we demonstrate that this chemistry permits combinatorial screening of reaction conditions on a microarray platform. Using this method of optimization and our reaction apparatus, efficient photogenerated acids and reaction conditions suitable for removal of the acid labile protection group on 5'-O of nucleotides are identified in a short period of time. The chemistry platform demonstrated opens new avenues for rapid, simultaneous investigation of multiple reactions using different reagents and reaction parameters directly on a solid support (e.g., a glass plate). The combinatorial screening method described may be extended to include general organic reactions employing photogenerated and conventional reagents as well as a microarray reaction device. This should be especially valuable for efficient synthesis of addressable organic compound libraries.

An efficient and economic site-specific deuteration strategy for NMR studies of homologous oligonucleotide repeat sequences

We describe herein the use of a 2H-labeling strategy to achieve specific assignments of considerably overlapped cross peaks in the 1H-NMR spectrum of a DNA trinucleotide repeat sequence. Our strategy focuses on site-specific 2H-labeling of base moieties to simplify the NMR spectral regions which contain the major portion of the structural information. To achieve efficient preparation of 2H8- or 2H6-labeled DNA and RNA nucleosides and nucleotides, the existing synthetic and purification procedures were significantly improved. Our experiments demonstrate that pyrimidine H6 deuteration reactions may be carried out using non-deuterated base reagents with DMSO-d6 as a 2H donor. These reactions are simple and economic to perform and produce base deuterated nucleosides and nucleotides in high yield. The 2H-labeled residues have been incorporated into oligonucleotides with minor modifications of the existing reaction conditions. Using the homologous CGG repeat sequence, d(CGG)5, as an example, the effectiveness of the site-specific base deuteration strategy is demonstrated. In the otherwise extensively overlapped spectra of d(CGG)5, 2H-labeling has permitted unambiguous identification of a sequential connectivity at a central CG step and confirmation of several other NOE assignments. This information is critical for elucidation of the structure and the folding of the CGG repeat sequences and will contribute to the intensive effort to understand the mechanisms of triplet expansion, which has been implicated in the development of a number of hereditary neurodegenerative diseases. In addition to the two dimensional spectral simplification in a key spectral region using site-specific 2H8/2H6-labeling, the potential applications of the prescribed strategy in homonuclear three dimensional experiments are also discussed.