DNA fragmentation and quality control analysis Published: September, 2016 Abstract:
Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor®, Megaruptor®, and Fragment A... Read more »
Concurrent whole-genome haplotyping and copy-number profiling of single cells. Published: June, 2015 Abstract:
Methods for haplotyping and DNA copy-number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-geno... Read more »
Within-host diversity of MRSA antimicrobial resistances. Published: May, 2015 Abstract:
OBJECTIVES: MRSA is a major antimicrobial resistance (AMR) pathogen. The reservoir of infecting isolates is colonization, which is the site of evolutionary selection. The aim was to identify if AMRs in colonizing MRSA populations diversified and p... Read more »
Polyploidy can drive rapid adaptation in yeast. Published: March, 2015 Abstract:
Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood. Polyploidy, usually whole-genome duplication, is proposed to alter the rate of evolutionary adaptation. This could occur through comple... Read more »
Intermediate DNA methylation is a conserved signature of genome regulation. Published: February, 2015 Abstract:
The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 hum... Read more »
Epigenetic and transcriptional determinants of the human breast. Published: February, 2015 Abstract:
While significant effort has been dedicated to the characterization of epigenetic changes associated with prenatal differentiation, relatively little is known about the epigenetic changes that accompany post-natal differentiation where fully funct... Read more »
Genome-wide DNA methylation analysis in Graves' disease. Published: January, 2015 Abstract:
As an autoimmune disease, Graves' disease (GD) is associated with many genetic and environmental risk factors. Although the exact mechanism remains unclear, epigenetic determinants, such as DNA methylation, are thought to contribute to the pathoge... Read more »
Recurrent ETNK1 mutations in atypical chronic myeloid leukemia. Published: January, 2015 Abstract:
Despite the recent identification of recurrent SETBP1 mutations in atypical chronic myeloid leukemia (aCML), a complete description of the somatic lesions responsible for the onset of this disorder is still lacking. To find additional somatic abno... Read more »
Genetic evidence for ecological divergence in kokanee salmon. Published: January, 2015 Abstract:
The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has p... Read more »
Genome-wide methylation analysis in Silver-Russell syndrome patients. Published: January, 2015 Abstract:
Silver-Russell syndrome (SRS) is a clinically heterogeneous disorder characterised by severe in utero growth restriction and poor postnatal growth, body asymmetry, irregular craniofacial features and several additional minor malformations. The aet... Read more »
The human urine virome in association with urinary tract infections Published: January, 2015 Abstract:
While once believed to represent a sterile environment, the human urinary tract harbors a unique cellular microbiota. We sought to determine whether the human urinary tract also is home to viral communities whose membership might reflect urinary t... Read more »
Molecular Analysis of a Recurrent Sarcoma Identifies a Mutation in FAF1. Published: January, 2015 Abstract:
A patient presented with a recurrent sarcoma (diagnosed as leiomyosarcoma) 12 years after the removal of an initial cancer (diagnosed as extracompartmental osteosarcoma) distally on the same limb. Following surgery, the sarcoma and unaffected musc... Read more »
Genome-wide DNA methylation analysis in precursor B-cells. Published: December, 2014 Abstract:
DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order... Read more »
Evaluation of methods to detect CALR mutations in myeloproliferative neoplasms Published: November, 2014 Abstract:
The recent discovery of somatically acquired CALR mutations in a substantial proportion of patients with myeloproliferative neoplasms has provided a new marker of clonal disease, advancing both diagnosis and prognosis in these previously difficult... Read more »
Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. Published: November, 2014 Abstract:
Developmental history shapes the epigenome and biological function of differentiated cells. Epigenomic patterns have been broadly attributed to the three embryonic germ layers. Here we investigate how developmental origin influences epigenomes. We... Read more »
Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Published: November, 2014 Abstract:
DNA CpG methylation is a widespread epigenetic mark in high eukaryotes including mammals. DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and c... Read more »
A phylogenomic analysis of turtles. Published: November, 2014 Abstract:
Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved el... Read more »
MeDIP-on-Chip for Methylation Profiling Published: October, 2014 Abstract:
DNA methylation is an important regulatory step in gene expression. Knowledge of the alterations in DNA methylation at a whole genome scale improves our understanding of gene regulation and potential correlations with biological events or disease ... Read more »
Altered promoter nucleosome positioning is an early event in gene silencing. Published: October, 2014 Abstract:
Gene silencing in cancer frequently involves hypermethylation and dense nucleosome occupancy across promoter regions. How a promoter transitions to this silent state is unclear. Using colorectal adenomas, we investigated nucleosome positioning, DN... Read more »
A thermo-halo-tolerant and proteinase-resistant endoxylanase from Bacillus sp. HJ14. Published: September, 2014 Abstract:
A glycosyl hydrolase family 10 endoxylanase from Bacillus sp. HJ14 was grouped in a separated cluster with another six Bacillus endoxylanases which have not been characterized. These Bacillus endoxylanases showed less than 52% amino acid sequence ... Read more »
Hypomethylated pollen bypasses the interploidy hybridization barrier in Arabidopsis. Published: September, 2014 Abstract:
Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier that is established in the endosperm. Deregulated parent-of-origin specific genes cause the response to interploidy hybridizations, revealing an epigenet... Read more »
Y chromosomes of 40% Chinese descend from three Neolithic super-grandfathers. Published: August, 2014 Abstract:
Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-rec... Read more »
oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips. Published: August, 2014 Abstract:
DNA methylation analysis has become an integral part of biomedical research. For high-throughput applications such as epigenome-wide association studies, the Infinium HumanMethylation450 (450K) BeadChip is currently the platform of choice. However... Read more »
An improved method for including upper size range plasmids in metamobilomes. Published: August, 2014 Abstract:
Two recently developed isolation methods have shown promise when recovering pure community plasmid DNA (metamobilomes/plasmidomes), which is useful in conducting culture-independent investigations into plasmid ecology. However, both methods employ... Read more »
DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide. Published: July, 2014 Abstract:
Genomic DNA is under constant assault by endogenous and exogenous DNA damaging agents. DNA breakage can represent a major threat to genome integrity but can also be necessary for genome function. Here we present approaches to map DNA double-strand... Read more »
Homozygous missense variant in the human CNGA3 channel causes cone-rod dystrophy. Published: July, 2014 Abstract:
We assessed a large consanguineous Pakistani family (PKAB157) segregating early onset low vision problems. Funduscopic and electroretinographic evaluation of affected individuals revealed juvenile cone-rod dystrophy (CRD) with maculopathy. Other c... Read more »
Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa. Published: July, 2014 Abstract:
The filamentous fungus Neurospora crassa responds to light in complex ways. To thoroughly study the transcriptional response of this organism to light, RNA-seq was used to analyze capped and polyadenylated mRNA prepared from mycelium grown for 24 ... Read more »
Very small deletions within the NESP55 gene in pseudohypoparathyroidism type 1b. Published: July, 2014 Abstract:
Pseudohypoparathyroidism (PHP) is caused by reduced expression of genes within the GNAS cluster, resulting in parathormone resistance. The cluster contains multiple imprinted transcripts, including the stimulatory G protein α subunit (Gs-α) and NE... Read more »
Genome-wide analysis of DNA 5-hmC in peripheral blood of uremia by hMeDIP-chip. Published: July, 2014 Abstract:
Abstract Background: Treatment of uremia is now dominated by dialysis; in some cases, patients are treated with dialysis for decades, but overall outcomes are disappointing. A number of studies have confirmed the relevance of several experimental ... Read more »
A role for migration-linked genes and genomic islands in divergence of a songbird. Published: June, 2014 Abstract:
Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently there has been a debate around the role of 'genomic islands of divergence' (i.e. blocks of ... Read more »
Conservation of streptococcal CRISPRs on human skin and saliva. Published: June, 2014 Abstract:
BACKGROUND: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are utilized by bacteria to resist encounters with their viruses. Human body surfaces have numerous bacteria that harbor CRISPRs, and their content can provide clues a... Read more »
New lung cancer panel for high-throughput targeted resequencing. Published: June, 2014 Abstract:
We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total len... Read more »
Phylogenomics of the plant family Araceae. Published: June, 2014 Abstract:
The biogeography, chromosome number evolution, pollination biology and evolutionary history of the plant family Araceae have recently become much clearer (Cabrera et al., 2008; Chartier et al., 2013; Cusimano et al., 2011, 2012; Nauheimer et al., ... Read more »
Altered oral viral ecology in association with periodontal disease. Published: May, 2014 Abstract:
UNLABELLED: The human oral cavity is home to a large and diverse community of viruses that have yet to be characterized in patients with periodontal disease. We recruited and sampled saliva and oral biofilm from a cohort of humans either periodont... Read more »
Genomic analysis of the emergence of 20th century epidemic dysentery. Published: May, 2014 Abstract:
BACKGROUND: Shigella dysenteriae type 1 (Sd1) causes recurrent epidemics of dysentery associated with high mortality in many regions of the world. Sd1 infects humans at very low infectious doses (10 CFU), and treatment is complicated by the rapid ... Read more »
Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited. Published: May, 2014 Abstract:
• Premise of the study: New World Bambusoideae have only recently been studied in a phylogenomic context. Plastome sequences were determined and analyzed from Arundinaria appalachiana, A. tecta, and Olyra latifolia, to refine our knowledge of thei... Read more »
Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia. Published: April, 2014 Abstract:
BACKGROUND: Aberrant DNA methylation is frequently found in human malignancies including acute myeloid leukemia (AML). While most studies focus on later disease stages, the onset of aberrant DNA methylation events and their dynamics during leukemi... Read more »
Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids. Published: March, 2014 Abstract:
Pulmonary carcinoids are rare neuroendocrine tumours of the lung. The molecular alterations underlying the pathogenesis of these tumours have not been systematically studied so far. Here we perform gene copy number analysis (n=54), genome/exome (n... Read more »
Modelling mutational landscapes of human cancers in vitro. Published: March, 2014 Abstract:
Experimental models that recapitulate mutational landscapes of human cancers are needed to decipher the rapidly expanding data on human somatic mutations. We demonstrate that mutation patterns in immortalised cell lines derived from primary murine... Read more »
Large-scale analysis of tandem repeat variability in the human genome. Published: March, 2014 Abstract:
Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats c... Read more »
Fine mapping of genome activation in bovine embryos by RNA sequencing. Published: March, 2014 Abstract:
During maternal-to-embryonic transition control of embryonic development gradually switches from maternal RNAs and proteins stored in the oocyte to gene products generated after embryonic genome activation (EGA). Detailed insight into the onset of... Read more »
Sequencing and assembly of the 22-gb loblolly pine genome. Published: March, 2014 Abstract:
Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the lobloll... Read more »
PGC7 suppresses TET3 for protecting DNA methylation. Published: March, 2014 Abstract:
Ten-eleven translocation (TET) family enzymes convert 5-methylcytosine to 5-hydroxylmethylcytosine. However, the molecular mechanism that regulates this biological process is not clear. Here, we show the evidence that PGC7 (also known as Dppa3 or ... Read more »
C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells. Published: February, 2014 Abstract:
CCAAT/enhancer binding protein-α (C/EBPα) induces transdifferentiation of B cells into macrophages at high efficiencies and enhances reprogramming into induced pluripotent stem (iPS) cells when co-expressed with the transcription factors Oct4 (Pou... Read more »
Nonstochastic reprogramming from a privileged somatic cell state. Published: February, 2014 Abstract:
Reprogramming somatic cells to induced pluripotency by Yamanaka factors is usually slow and inefficient and is thought to be a stochastic process. We identified a privileged somatic cell state, from which acquisition of pluripotency could occur in... Read more »
A deterministic analysis of genome integrity during neoplastic growth in Drosophila. Published: February, 2014 Abstract:
The development of cancer has been associated with the gradual acquisition of genetic alterations leading to a progressive increase in malignancy. In various cancer types this process is enabled and accelerated by genome instability. While genome ... Read more »
Differential methylation of the TRPA1 promoter in pain sensitivity. Published: January, 2014 Abstract:
Chronic pain is a global public health problem, but the underlying molecular mechanisms are not fully understood. Here we examine genome-wide DNA methylation, first in 50 identical twins discordant for heat pain sensitivity and then in 50 further ... Read more »
Viral aetiology influenza like illnesses in Santa Cruz, Bolivia (2010-2012). Published: January, 2014 Abstract:
BACKGROUND: Acute respiratory infections represent a serious public health issue worldwide but virological aetiologies of Influenza Like Illnesses (ILIs) remain largely unknown in developing countries. This study represents the first attempt to ch... Read more »
Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Published: January, 2014 Abstract:
The contribution of cis-regulatory mutations to human disease remains poorly understood. Whole-genome sequencing can identify all noncoding variants, yet the discrimination of causal regulatory mutations represents a formidable challenge. We used ... Read more »
Suggestive linkage of familial mesial temporal lobe epilepsy to chromosome 3q26. Published: November, 2013 Abstract:
PURPOSE: To describe the clinical findings in a family with a benign form of mesial temporal lobe epilepsy and to identify the causative genetic factors. METHODS: All participants were personally interviewed and underwent neurologic examination. T... Read more »
Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques. Published: November, 2013 Abstract:
The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cos... Read more »
Fine-Mapping an Association of FSHR with Preterm Birth in a Finnish Population. Published: October, 2013 Abstract:
Preterm birth is a complex disorder defined by gestations of less than 37 weeks. While preterm birth is estimated to have a significant genetic component, relative few genes have been associated with preterm birth. Polymorphism in one such gene, f... Read more »
Diet Alters Both the Structure and Taxonomy of the Ovine Gut Microbial Ecosystem. Published: October, 2013 Abstract:
We surveyed the ruminal metagenomes of 16 sheep under two different diets using Illumina pair-end DNA sequencing of raw microbial DNA extracted from rumen samples. The resulting sequence data were bioinformatically mapped to known prokaryotic 16S ... Read more »
Mu-seq: Sequence-Based Mapping and Identification of Transposon Induced Mutations. Published: October, 2013 Abstract:
Mutations tagged by transposon insertions can be readily mapped and identified in organisms with sequenced genomes. Collections of such mutants allow a systematic analysis of gene function, and can be sequence-indexed to build invaluable resources... Read more »
Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Published: October, 2013 Abstract:
To uncover the function of and interplay between the mammalian cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), new techniques and advances in current technology are needed. To this end, we have developed oxidative... Read more »
Genome-Wide Analysis of DNA Methylation in Soybean. Published: September, 2013 Abstract:
Cytosine methylation is an important mechanism for dynamical regulation of gene expression. We identified 2162 differentially methylated regions in different soybean organs and further analyzed the interplays among DNA methylation, smRNA abundance... Read more »
The BTB-Containing Protein Kctd15 Is SUMOylated In Vivo. Published: September, 2013 Abstract:
Potassium Channel Tetramerization Domain containing 15 (Kctd15) has a role in regulating the neural crest (NC) domain in the embryo. Kctd15 inhibits NC induction by antagonizing Wnt signaling and by interaction with the transcription factor AP-2α ... Read more »
Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences. Published: September, 2013 Abstract:
Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the co... Read more »
Integrated virus-host methylome analysis in head and neck squamous cell carcinoma Published: September, 2013 Abstract:
One in six cancers worldwide is caused by infection and human papillomavirus (HPV) is one of the main culprits. To better understand the dynamics of HPV integration and its effect on both the viral and host methylomes, we conducted whole-genome DN... Read more »
Minotaur is critical for primary piRNA biogenesis. Published: August, 2013 Abstract:
Piwi proteins and their associated small RNAs are essential for fertility in animals. In part, this is due to their roles in guarding germ cell genomes against the activity of mobile genetic elements. piRNA populations direct Piwi proteins to sile... Read more »
DNA unmethylome profiling by covalent capture of CpG sites. Published: July, 2013 Abstract:
Dynamic patterns of cytosine-5 methylation and successive hydroxylation are part of epigenetic regulation in eukaryotes, including humans, which contributes to normal phenotypic variation and disease risk. Here we present an approach for the mappi... Read more »
An epigenetic trap stabilizes singular olfactory receptor expression. Published: July, 2013 Abstract:
The molecular mechanisms regulating olfactory receptor (OR) expression in the mammalian nose are not yet understood. Here, we identify the transient expression of histone demethylase LSD1 and the OR-dependent expression of adenylyl cyclase 3 (Adcy... Read more »
Senescence-associated lncRNAs: senescence-associated long noncoding RNAs. Published: June, 2013 Abstract:
Noncoding RNAs include small transcripts, such as microRNAs and piwi-interacting RNAs, and a wide range of long noncoding RNAs (lncRNAs). Although many lncRNAs have been identified, only a small number of lncRNAs have been characterized functional... Read more »
Global regulation of promoter melting in naive lymphocytes. Published: May, 2013 Abstract:
Lymphocyte activation is initiated by a global increase in messenger RNA synthesis. However, the mechanisms driving transcriptome amplification during the immune response are unknown. By monitoring single-stranded DNA genome wide, we show that the... Read more »
G-quadruplex structures are stable and detectable in human genomic DNA. Published: April, 2013 Abstract:
The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome for transcriptional regulation, DNA replication and genome stability, but the nature and distribution of G-quadruplexes... Read more »
Association between living environment and human oral viral ecology. Published: April, 2013 Abstract:
The human oral cavity has an indigenous microbiota known to include a robust community of viruses. Very little is known about how oral viruses are spread throughout the environment or to which viruses individuals are exposed. We sought to determin... Read more »
H2-independent growth of the hydrogenotrophic methanogen Methanococcus maripaludis. Published: February, 2013 Abstract:
UNLABELLED: Hydrogenotrophic methanogenic Archaea require reduced ferredoxin as an anaplerotic source of electrons for methanogenesis. H(2) oxidation by the hydrogenase Eha provides these electrons, consistent with an H(2) requirement for growth. ... Read more »
Mitochondrial phylogenomics of modern and ancient equids. Published: February, 2013 Abstract:
The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated... Read more »
Evolution of cichlid vision via trans-regulatory divergence. Published: December, 2012 Abstract:
ABSTRACT: BACKGROUND: Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within t... Read more »
A polycomb group protein is retained at specific sites on chromatin in mitosis. Published: December, 2012 Abstract:
Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states, but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionati... Read more »
Nano-MeDIP-seq: Methylome analysis using low DNA concentrations (Prot 58) Published: December, 2012 Abstract:
To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome - wide analysis should be embraced. This in turn requires a technique that balances accuracy, genome coverage, resolution and cost, yet is low in DNA i... Read more »
TET2 promotes histone O-GlcNAcylation during gene transcription. Published: December, 2012 Abstract:
Ten eleven translocation (TET) enzymes, including TET1, TET2 and TET3, convert 5-methylcytosine to 5-hydroxymethylcytosine and regulate gene transcription. However, the molecular mechanism by which TET family enzymes regulate gene transcription re... Read more »
Genome Sequence of OXA-48 Carbapenemase-Producing Klebsiella pneumoniae KpO3210. Published: December, 2012 Abstract:
Klebsiella pneumoniae KpO3210 is a OXA-48 carbapenemase-producing isolate obtained from a blood culture in the context of an outbreak in Hospital Universitario La Paz (Madrid, Spain) in 2010. It belongs to the major clone detected during the outbr... Read more »
The Many Landscapes of Recombination in Drosophila melanogaster. Published: October, 2012 Abstract:
Recombination is a fundamental biological process with profound evolutionary implications. Theory predicts that recombination increases the effectiveness of selection in natural populations. Yet, direct tests of this prediction have been restricte... Read more »
Oxidative stress-regulated lentiviral TK/GCV gene therapy for lung cancer treatment. Published: October, 2012 Abstract:
NRF2 is a transcription factor that regulates protection against a wide variety of toxic insults to cells, including cytotoxic cancer chemotherapeutic drugs. Many lung cancer cells harbor a mutation in either NRF2 or its inhibitor KEAP1 resulting ... Read more »
Read length versus Depth of Coverage for Viral Quasispecies Reconstruction. Published: October, 2012 Abstract:
Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus popula... Read more »
Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome. Published: October, 2012 Abstract:
ABSTRACT: BACKGROUND: Induction and promotion of liver cancer by exposure to non-genotoxic carcinogens coincides with epigenetic perturbations, including specific changes in DNA methylation. Here we investigate the genome-wide dynamics of 5-hydro... Read more »
The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine. Published: October, 2012 Abstract:
5-Hydroxymethylcytosine (5hmC) is a newly discovered DNA base present at detectable levels in most mammalian cell types and tissues. It is generated by Tet-enzyme-mediated oxidation of 5-methylcytosine (5mC). 5hmC is important both because of its ... Read more »
Draft Genome Sequence of Lactobacillus rossiae DSM 15814T. Published: October, 2012 Abstract:
The draft genome sequence of Lactobacillus rossiae DSM 15814(T) (CS1, ATCC BAA-88) was determined by a whole-genome shotgun approach. Reads were assembled to a 2.9-Mb draft version. RAST genome annotation evidenced 2,723 predicted coding sequences... Read more »
SATB1-mediated Functional Packaging of Chromatin into Loops. Published: July, 2012 Abstract:
Mammalian genomes are organized into multiple layers of higher-order chromatin structure, and in this organization chromatin looping is a striking and crucial feature that brings together distal genomic loci into close spatial proximity. Such thre... Read more »
Bovine polledness - an autosomal dominant trait with allelic heterogeneity. Published: June, 2012 Abstract:
The persistent horns are an important trait of speciation for the family Bovidae with complex morphogenesis taking place briefly after birth. The polledness is highly favourable in modern cattle breeding systems but serious animal welfare issues u... Read more »
Targeted re-sequencing of the allohexaploid wheat exome. Published: June, 2012 Abstract:
Bread wheat, Triticum aestivum, is an allohexaploid composed of the three distinct ancestral genomes, A, B and D. The polyploid nature of the wheat genome together with its large size has limited our ability to generate the significant amount of s... Read more »
Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation. Published: June, 2012 Abstract:
In female (XX) mammals, one of the two X chromosomes is inactivated to ensure an equal dose of X-linked genes with males (XY). X-chromosome inactivation in eutherian mammals is mediated by the non-coding RNA Xist. Xist is not found in metatherians... Read more »
Evolution of Burkholderia pseudomallei in Recurrent Melioidosis. Published: May, 2012 Abstract:
Burkholderia pseudomallei, the etiologic agent of human melioidosis, is capable of causing severe acute infection with overwhelming septicemia leading to death. A high rate of recurrent disease occurs in adult patients, most often due to recrudesc... Read more »
BIM promoter directly targeted by EBNA3C in polycomb-mediated repression by EBV. Published: May, 2012 Abstract:
Detailed analyses of the chromatin around the BIM promoter has revealed that latent Epstein-Barr virus (EBV) triggers the recruitment of polycomb repressive complex 2 (PRC2) core subunits and the trimethylation of histone H3 lysine 27 (H3K27me3) a... Read more »
Performance comparison of benchtop high-throughput sequencing platforms. Published: April, 2012 Abstract:
Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can gen... Read more »
Genetic and Epigenetic Determinants of Neurogenesis and Myogenesis. Published: March, 2012 Abstract:
The regulatory networks of differentiation programs have been partly characterized; however, the molecular mechanisms of lineage-specific gene regulation by highly similar transcription factors remain largely unknown. Here we compare the genome-wi... Read more »
Methylome analysis using MeDIP-seq with low DNA concentrations. Published: March, 2012 Abstract:
DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide analysis should be embraced. This in turn requires a t... Read more »
RHBDF2 mutations are associated with tylosis, a familial esophageal cancer syndrome. Published: February, 2012 Abstract:
Tylosis esophageal cancer (TOC) is an autosomal-dominant syndrome characterized by palmoplantar keratoderma, oral precursor lesions, and a high lifetime risk of esophageal cancer. We have previously localized the TOC locus to a small genomic inter... Read more »
RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. Published: January, 2012 Abstract:
ABSTRACT: BACKGROUND: The globe artichoke (Cynara cardunculus L. var. scolymus) genome is relatively poorly explored, especially compared to those of the other major Asteraceae crops sunflower and lettuce. No SNP markers are in the public domain.... Read more »
Adaptation to P element transposon invasion in Drosophila melanogaster. Published: December, 2011 Abstract:
Transposons evolve rapidly and can mobilize and trigger genetic instability. Piwi-interacting RNAs (piRNAs) silence these genome pathogens, but it is unclear how the piRNA pathway adapts to invasion of new transposons. In Drosophila, piRNAs are en... Read more »
A simple method for the parallel deep sequencing of full influenza A genomes. Published: December, 2011 Abstract:
Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this p... Read more »
Distinct Epigenomic Features in End-Stage Failing Human Hearts Published: November, 2011 Abstract:
Background—The epigenome refers to marks on the genome, including DNA methylation and histone modifications, that regulate the expression of underlying genes. A consistent profile of gene expression changes in end-stage cardiomyopathy led us to hy... Read more »
The draft genome and transcriptome of Cannabis sativa. Published: October, 2011 Abstract:
ABSTRACT: BACKGROUND: Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including... Read more »
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Published: October, 2011 Abstract:
Alternative splicing of pre-messenger RNA is a key feature of transcriptome expansion in eukaryotic cells, yet its regulation is poorly understood. Spliceosome assembly occurs co-transcriptionally, raising the possibility that DNA structure may di... Read more »
Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Published: July, 2011 Abstract:
Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, ∼50% of all CGIs are remote from annotated promoters but, nevertheless, o... Read more »
Tumour evolution inferred by single-cell sequencing. Published: April, 2011 Abstract:
Genomic analysis provides insights into the role of copy number variation in disease, but most methods are not designed to resolve mixed populations of cells. In tumours, where genetic heterogeneity is common, very important information may be los... Read more »
Tracing the domestication of a biofilm-forming bacterium. Published: April, 2011 Abstract:
Over the course of more than a century of laboratory experimentation, Bacillus subtilis has become "domesticated," losing its ability to carry out many behaviors characteristic of its wild ancestors. One such characteristic is the ability to form ... Read more »
Comprehensive analysis of DNA-methylation in mammalian tissues using MeDIP-chip. Published: February, 2011 Abstract:
Genome-wide mapping of epigenetic changes is essential for understanding the mechanisms involved in gene regulation during cell differentiation and embryonic development. DNA-methylation is one of these key epigenetic marks that is directly linked... Read more »
Local de novo assembly of RAD paired-end contigs using short sequencing reads. Published: January, 2011 Abstract:
Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using paired-end sequencing of restriction-si... Read more »
Identification of novel SNPs in glioblastoma using targeted resequencing. Published: January, 2011 Abstract:
High-throughput sequencing opens avenues to find genetic variations that may be indicative of an increased risk for certain diseases. Linking these genomic data to other "omics" approaches bears the potential to deepen our understanding of pathoge... Read more »
Targets and dynamics of promoter DNA methylation during early mouse development. Published: December, 2010 Abstract:
DNA methylation is extensively reprogrammed during the early phases of mammalian development, yet genomic targets of this process are largely unknown. We optimized methylated DNA immunoprecipitation for low numbers of cells and profiled DNA methyl... Read more »
Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. Published: November, 2010 Abstract:
BACKGROUND: To utilize the power of high-throughput sequencers, target enrichment methods have been developed. The majority of these require reagents and equipment that are only available from commercial vendors and are not suitable for the target... Read more »
Whole-genome DNA methylation profiling using MethylCap-seq. Published: November, 2010 Abstract:
MethylCap-seq is a robust procedure for genome-wide profiling of DNA methylation. The approach consists of the capture of methylated DNA using the MBD domain of MeCP2, and subsequent next-generation sequencing of eluted DNA. Elution of the capture... Read more »
Quantitative comparison of genome-wide DNA methylation mapping technologies. Published: October, 2010 Abstract:
DNA methylation plays a key role in regulating eukaryotic gene expression. Although mitotically heritable and stable over time, patterns of DNA methylation frequently change in response to cell differentiation, disease and environmental influences... Read more »
Conserved role of intragenic DNA methylation in regulating alternative promoters. Published: July, 2010 Abstract:
Although it is known that the methylation of DNA in 5' promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear. In mammals, tissue- and cell type-specific methylation is present in a small percentage of 5' CpG i... Read more »
Massively parallel sequencing, a new method for detecting adventitious agents. Published: May, 2010 Abstract:
There has been an upsurge of interest in developing new veterinary and human vaccines and, in turn, this has involved the development of new mammalian and insect cell substrates. Excluding adventitious agents from these cells can be problematic, p... Read more »
Unlocking short read sequencing for metagenomics. Published: January, 2010 Abstract:
BACKGROUND: Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved. METHODOLOGY/PR... Read more »
The epigenetic landscape of latent Kaposi sarcoma-associated herpesvirus genomes. Published: January, 2010 Abstract:
Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis o... Read more »
Global analysis of DNA methylation and transcription of human repetitive sequences Published: July, 2009 Abstract:
Half of the human genome consists of repetitive DNA sequences. Recent studies in various organisms highlight the role of chromatin regulation of repetitive DNA in gene regulation as well as in maintainance of chromosomes and genome integrity. Henc... Read more »
Improved Protocols for Illumina Sequencing Published: July, 2009 Abstract:
In this unit, we describe a set of improvements we have made to the standard Illumina protocols to make the sequencing process more reliable in a high-throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and ... Read more »
A link between RNA metabolism and silencing affecting Arabidopsis development. Published: June, 2008 Abstract:
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are abundant endogenous small RNAs (smRNAs) that control transcript expression through posttranscriptional gene silencing. Here, we show that concomitant loss of XRN4/EIN5, a 5'-3' exoribonucl... Read more »
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Published: May, 2008 Abstract:
Deciphering the multiple layers of epigenetic regulation that control transcription is critical to understanding how plants develop and respond to their environment. Using sequencing-by-synthesis technology we directly sequenced the cytosine methy... Read more »
Inactivation of a Human Kinetochore by Specific Targeting of Chromatin Modifiers Published: April, 2008 Abstract:
We have used a human artificial chromosome (HAC) to manipulate the epigenetic state of chromatin within an active kinetochore. The HAC has a dimeric α-satellite repeat containing one natural monomer with a CENP-B binding site, and one completely a... Read more »
Post-mortem genetic analysis in juvenile cases of sudden cardiac death Abstract:
Background The reason behind a sudden death of a young individual remains unknown in up to 50% of postmortem cases. Pathogenic mutations in genes encoding heart proteins are known to cause sudden cardiac death. Objective The aim of our study was... Read more »
A novel method for the genome-wide high resolution analysis of DNA damage. Abstract:
DNA damage occurs via endogenous and exogenous genotoxic agents and compromises a genome's integrity. Knowing where damage occurs within a genome is crucial to understanding the repair mechanisms which protect this integrity. This paper describes ... Read more »
AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay Abstract:
DNA methylation is an epigenetic mark linking DNA sequence and transcription regulation, and therefore plays an important role in phenotypic plasticity. The ideal whole genome methylation (methylome) assay should be accurate, affordable, high-thro... Read more »
SNP Discovery and Genotyping for Evolutionary Genetics Using RAD Sequencing Abstract:
Next-generation sequencing technologies are revolutionizing the field of evolutionary biology, opening the possibility for genetic analysis at scales not previously possible. Research in population genetics, quantitative trait mapping, comparative... Read more »
High-throughput whole-genome sequencing of E14 mouse embryonic stem cells Abstract:
Mouse E14 embryonic stem cells (ESCs) are the most used ESC line, often employed for genome-wide studies involving next generation sequencing analysis [1 – 5] . More than 2 × 10 E9 sequences made on Illumina platform derivedfromthegenomeofE14embry... Read more »
Methylation analysis by microarray. Abstract:
Differential methylation hybridization (DMH) is a high-throughput DNA methylation screening tool that utilizes methylation-sensitive restriction enzymes to profile methylated fragments by hybridizing them to a CpG island microarray. This array con... Read more »
Library preparation and data analysis packages for rapid genome sequencing. Abstract:
High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of o... Read more »
Short-read DNA Sequencing Yields Microsatellite Markers for Rheum Abstract:
Identifying and evaluating genetic diversity of culinary rhubarb (Rheum ×rhababarum) cultivars using morphological characteristics is challenging given the existence of synonyms and nomenclatural inconsistencies. Some cultivars with similar names ... Read more »
Mapping replication origin sequences in eukaryotic chromosomes. Abstract:
Recent advances in genome-sequencing technology have led to the complete mapping of DNA replication initiation sites in the human genome. This thorough origin mapping facilitates understanding of the relationship between replication initiation eve... Read more »
Consistency of metagenomic assignment programs in simulated and real data. Abstract:
BACKGROUND: Metagenomics is the genomic study of uncultured environmental samples, which has been greatly facilitated by the advent of shotgun-sequencing technologies. One of the main focuses of metagenomics is the discovery of previously uncultur... Read more »
Methylated DNA Immunoprecipitation (MeDIP) from Low Amounts of Cells. Abstract:
Methylated DNA immunoprecipitation (MeDIP) is an immunocapturing approach for unbiased enrichment of DNA that is methylated on cytosines. The principle is that genomic DNA is randomly sheared by sonication and immunoprecipitated with an antibody t... Read more »
Enrichment of Methylated DNA by Methyl-CpG Immunoprecipitation. Abstract:
Normal DNA methylation is an epigenetic modification required for proper development. Aberrant DNA methylation, in contrast, is frequently observed in many different malignancies including leukemias and lymphomas. Global DNA methylation profiling ... Read more »
