Summary ChIP-seq combines chromatin immunoprecipitation with massively parallel short-read sequencing. While it can profile genome-wide in vivo transcription factor-DNA association with higher sensitivity, specificity, and spatial resolution than ChIP-chip, it poses new challenges for statistical analysis that derive from the complexity of the biological systems characterized and from variability and biases in its sequence data. We propose a method called PICS (Probabilistic Inference for ChIP-seq) for identifying regions bound by transcription factors from aligned reads. PICS identifies binding event locations by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model. It uses precalculated, whole-genome read mappability profiles and a truncated t-distribution to adjust binding event models for reads that are missing due to local genome repetitiveness. It estimates uncertainties in model parameters that can be used to define confidence regions on binding event locations and to filter estimates. Finally, PICS calculates a per-event enrichment score relative to a control sample, and can use a control sample to estimate a false discovery rate. Using published GABP and FOXA1 data from human cell lines, we show that PICS' predicted binding sites were more consistent with computationally predicted binding motifs than the alternative methods MACS, QuEST, CisGenome, and USeq. We then use a simulation study to confirm that PICS compares favorably to these methods and is robust to model misspecification.

False Discovery Rate

Chromatin immunoprecipitation

DNA binding site

Synthetic data

10.1111/j.1541-0420.2010.01441.x

Cite

Citations (70)

MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures

Nature Communications (2015)

Tanmoy Mondal Santhilal Subhash Roshan Vaid Stefan Enroth Sireesha Uday

Abstract Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin, but how they target chromatin remains poorly understood. We have used chromatin RNA immunoprecipitation-coupled high-throughput sequencing to identify 276 lncRNAs enriched in repressive chromatin from breast cancer cells. Using one of the chromatin-interacting lncRNAs, MEG3 , we explore the mechanisms by which lncRNAs target chromatin. Here we show that MEG3 and EZH2 share common target genes, including the TGF-β pathway genes. Genome-wide mapping of MEG3 binding sites reveals that MEG3 modulates the activity of TGF-β genes by binding to distal regulatory elements. MEG3 binding sites have GA-rich sequences, which guide MEG3 to the chromatin through RNA–DNA triplex formation. We have found that RNA–DNA triplex structures are widespread and are present over the MEG3 binding sites associated with the TGF-β pathway genes. Our findings suggest that RNA–DNA triplex formation could be a general characteristic of target gene recognition by the chromatin-interacting lncRNAs.

MEG3

10.1038/ncomms8743

Cite

Citations (593)

PARTICULATE MATTER EMISSIONS FROM ROADS IN BIRMINGHAM

Derek Williamson Steven J.M. Jones Stephanie Kirby A. Flora

Air quality concerns continue to pose a challenge to the transportation industry. This project investigated the extent to which traffic flow impacted particulate emissions from roadways in Birmingham, Alabama. Through repeated measurements at five locations, it was determined that truck flow is a controlling influence on roadway particulate emissions. In particular, queuing of trucks greatly increases emissions. Therefore, emissions and planning models and activities must include a description of truck operational mode to accurately describe roadway contributions. If roadway particulate emissions are to be minimized, optimizing traffic flow on high truck (not necessarily high average daily traffic) routes needs to be considered.

Source

Cite

Citations (1)

Preclinical Activity of VX-787, a First-in-Class, Orally Bioavailable Inhibitor of the Influenza Virus Polymerase PB2 Subunit

Antimicrobial Agents and Chemotherapy (2014)

Randal A. Byrn Steven J.M. Jones Hamilton B. Bennett Chris Bral Michael P. Clark

ABSTRACT VX-787 is a novel inhibitor of influenza virus replication that blocks the PB2 cap-snatching activity of the influenza viral polymerase complex. Viral genetics and X-ray crystallography studies provide support for the idea that VX-787 occupies the 7-methyl GTP (m 7 GTP) cap-binding site of PB2. VX-787 binds the cap-binding domain of the PB2 subunit with a K D (dissociation constant) of 24 nM as determined by isothermal titration calorimetry (ITC). The cell-based EC 50 (the concentration of compound that ensures 50% cell viability of an uninfected control) for VX-787 is 1.6 nM in a cytopathic effect (CPE) assay, with a similar EC 50 in a viral RNA replication assay. VX-787 is active against a diverse panel of influenza A virus strains, including H1N1pdm09 and H5N1 strains, as well as strains with reduced susceptibility to neuraminidase inhibitors (NAIs). VX-787 was highly efficacious in both prophylaxis and treatment models of mouse influenza and was superior to the neuraminidase inhibitor, oseltamivir, including in delayed-start-to-treat experiments, with 100% survival at up to 96 h postinfection and partial survival in groups where the initiation of therapy was delayed up to 120 h postinfection. At different doses, VX-787 showed a 1-log to >5-log reduction in viral load (relative to vehicle controls) in mouse lungs. Overall, these favorable findings validate the PB2 subunit of the viral polymerase as a drug target for influenza therapy and support the continued development of VX-787 as a novel antiviral agent for the treatment of influenza infection.

Neuraminidase inhibitor

Oseltamivir

10.1128/aac.04623-14

Cite

Citations (174)

Identification and analysis of internal promoters in Caenorhabditis elegans operons

Genome Research (2007)

Peiming Huang Erin Pleasance Jason S Maydan Rebecca Hunt-Newbury Nigel J. O’Neil

The current Caenorhabditis elegans genomic annotation has many genes organized in operons. Using directionally stitched promoter∷GFP methodology, we have conducted the largest survey to date on the regulatory regions of annotated C. elegans operons and identified 65, over 25% of those studied, with internal promoters. We have termed these operons “hybrid operons.” GFP expression patterns driven from internal promoters differ in tissue specificity from expression of operon promoters, and serial analysis of gene expression data reveals that there is a lack of expression correlation between genes in many hybrid operons. The average length of intergenic regions with putative promoter activity in hybrid operons is larger than previous estimates for operons as a whole. Genes with internal promoters are more commonly involved in gene duplications and have a significantly lower incidence of alternative splicing than genes without internal promoters, although we have observed almost all trans -splicing patterns in these two distinct groups. Finally, internal promoter constructs are able to rescue lethal knockout phenotypes, demonstrating their necessity in gene regulation and survival. Our work suggests that hybrid operons are common in the C. elegans genome and that internal promoters influence not only gene organization and expression but also operon evolution.

10.1101/gr.6824707

Cite

Citations (42)

Production and characterization of monoclonal antibodies against different epitopes of Ebola virus antigens

Journal of Virological Methods (2007)

Soraya Shahhosseini Dipankar Das Xiangguo Qiu Heinz Feldmann Steven J.M. Jones

Epitope mapping

Linear epitope

Ebolavirus

10.1016/j.jviromet.2007.02.004

Cite

Citations (50)

Sequencing the genome of the Atlantic salmon (Salmo salar)

Genome biology (2010)

William S. Davidson Ben F. Koop Steven J.M. Jones Patricia Iturra Rodrigo Vidal

The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in the Atlantic salmon genome and acts as a reference sequence for other salmonids.

Sequence (biology)

Sequence assembly

Human genetics

10.1186/gb-2010-11-9-403

Cite

Citations (287)

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

Molecular Ecology Resources (2011)

Armando Geraldes Johnson Pang Nina Thiessen Timothée Cezard Richard A. Moore

Abstract The western black cottonwood ( Populus trichocarpa ) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high‐throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26 595 genes that are expressed in developing secondary xylem. More than two‐thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar.

Populus trichocarpa

Sequence assembly

Illumina dye sequencing

10.1111/j.1755-0998.2010.02960.x

Cite

Citations (109)

Subsea Well Annular Integrity Repair Using Coiled Tubing and Pressure Activated Sealant

SPE/ICoTA Well Intervention Conference and Exhibition (2023)

Joel Johns Chris Anderson Juan A. Anguiano Steven J.M. Jones

Abstract Production from a subsea well was halted due to hurricane activity in the Gulf of Mexico. When the well was returned to production, the annulus experienced a loss of pressure integrity. To achieve regulatory compliance and return the well to production, annular integrity had to be restored in a safe, expeditious manner. This paper will describe the process of operations undertaken to cure this well integrity issue utilizing pressure activated sealant deployed via coiled tubing. Pressure activated sealants have been utilized for a number of years to efficiently cure leaks in a wide variety of applications. One of the first challenges to be addressed when considering a sealant repair is the method of getting the material to the leak site. For the purpose of the subsea well in question, coiled tubing was used to convey the sealant to the sea floor from a service vessel. An ROV then connected the coil to an external tree cap via a flying lead after which the sealant was introduced to the annulus by lube and bleed pressure cycles. The annular integrity issue was analyzed in an effort to determine leak severity and location. Pressure trends noted at annular pressures of 4000 psi indicated a leak ranging from 0.15 – 1.5 lit/min. Gradient analysis indicated that the leak was deep in the completion potentially at a liner lap or the packer. Based on this information a sealant blend approximately 2 ppg heavier than the completion fluid was developed for the purpose of curing the leak. An external tree cap was installed on the well in order to provide access to the annulus of the well via a hot stab connection. About eleven cubic meters of sealant was transferred to the annulus through 2" coiled tubing extended to the sea floor connected to the well via a flying lead. A series of lubricate and bleed cycles were performed to accomplish this without exceeding predetermined pressure limits. After allowing the sealant to settle on the packer, annular pressure was maintained to allow the sealant to cure at the leak site. The pressure differential at the leak caused the liquid sealant to form an elastomeric seal. A positive pressure test was obtained shortly after the process and the well was returned to production. An example of how using pressure activated sealants designed to polymerize only at a leak site affords options to expensive workovers on subsea wells will be provided herein. The use of this technology in concert with coiled tubing deployment represents an expeditious, economic approach to solving complex well integrity issues.

Subsea

Coiled tubing

10.2118/212925-ms

Cite

Citations (1)