W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data

Summary: ChIP-based technology is becoming the leading technology to globally profile thousands of transcription factors and elucidate the transcriptional regulation mechanisms in living cells. It has evolved rapidly in recent years, from hybridization with spotted or tiling microarray (ChIP-chip), to pair-end tag sequencing (ChIP-PET), to current massively parallel sequencing (ChIP-seq). Although there are many tools available for identifying binding sites (peaks) for ChIP-chip and ChIP-seq, few of them are available as easy-accessible online web tools for processing both ChIP-chip and ChIP-seq data for the ChIP-based user community. As such, we have developed a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Our web tool W-ChIPeaks employed a probe-based (or bin-based) enrichment threshold to define peaks and applied statistical methods to control false discovery rate for identified peaks. The web tool includes two different web interfaces: PELT for ChIP-chip, BELT for ChIP-seq, where both were tested on previously published experimental data. The novel features of our tool include a comprehensive output for identified peaks with GFF, BED, bedGraph and .wig formats, annotated genes to which these peaks are related, a graphical interpretation and visualization of the results via a user-friendly web interface

Fluorescent Risedronate Analogues Reveal Bisphosphonate Uptake by Bone Marrow Monocytes and Localization Around Osteocytes In Vivo

Bisphosphonates are effective antiresorptive agents owing to their bone-targeting property and ability to inhibit osteoclasts. It remains unclear, however, whether any non-osteoclast cells are directly affected by these drugs in vivo. Two fluorescent risedronate analogues, carboxyfluorescein-labeled risedronate (FAM-RIS) and Alexa Fluor 647–labeled risedronate (AF647-RIS), were used to address this question. Twenty-four hours after injection into 3-month-old mice, fluorescent risedronate analogues were bound to bone surfaces. More detailed analysis revealed labeling of vascular channel walls within cortical bone. Furthermore, fluorescent risedronate analogues were present in osteocytic lacunae in close proximity to vascular channels and localized to the lacunae of newly embedded osteocytes close to the bone surface. Following injection into newborn rabbits, intracellular uptake of fluorescently labeled risedronate was detected in osteoclasts, and the active analogue FAM-RIS caused accumulation of unprenylated Rap1A in these cells. In addition, CD14high bone marrow monocytes showed relatively high levels of uptake of fluorescently labeled risedronate, which correlated with selective accumulation of unprenylated Rap1A in CD14+ cells, as well as osteoclasts, following treatment with risedronate in vivo. Similar results were obtained when either rabbit or human bone marrow cells were treated with fluorescent risedronate analogues in vitro. These findings suggest that the capacity of different cell types to endocytose bisphosphonate is a major determinant for the degree of cellular drug uptake in vitro as well as in vivo. In conclusion, this study shows that in addition to bone-resorbing osteoclasts, bisphosphonates may exert direct effects on bone marrow monocytes in vivo. © 2010 American Society for Bone and Mineral Researc

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology

Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for MBD-seq remain unclear and the data analysis remains challenging. In this study, we generated high depth MBD-seq data in MCF-7 cell and developed a bi-asymmetric-Laplace model (BALM) to perform data analysis. We found that optimal efficiency of MBD-seq experiments was achieved by sequencing ∼100 million unique mapped tags from a combination of 500 mM and 1000 mM salt concentration elution in MCF-7 cells. Clonal bisulfite sequencing results showed that the methylation status of each CpG dinucleotides in the tested regions was accurately detected with high resolution using the proposed model. These results demonstrated the combination of MBD-seq and BALM could serve as a useful tool to investigate DNA methylome due to its low cost, high specificity, efficiency and resolution

Transcription factor-associated combinatorial epigenetic pattern reveals higher transcriptional activity of TCF7L2-regulated intragenic enhancers

Abstract Background Recent studies have suggested that combinations of multiple epigenetic modifications are essential for controlling gene expression. Despite numerous computational approaches have been developed to decipher the combinatorial epigenetic patterns or “epigenetic code”, none of them has explicitly addressed the relationship between a specific transcription factor (TF) and the patterns. Methods Here, we developed a novel computational method, T-cep, for annotating chromatin states associated with a specific TF. T-cep is composed of three key consecutive modules: (i) Data preprocessing, (ii) HMM training, and (iii) Potential TF-states calling. Results We evaluated T-cep on a TCF7L2-omics data. Unexpectedly, our method has uncovered a novel set of TCF7L2-regulated intragenic enhancers missed by other software tools, where the associated genes exert the highest gene expression. We further used siRNA knockdown, Co-transfection, RT-qPCR and Luciferase Reporter Assay not only to validate the accuracy and efficiency of prediction by T-cep, but also to confirm the functionality of TCF7L2-regulated enhancers in both MCF7 and PANC1 cells respectively. Conclusions Our study for the first time at a genome-wide scale reveals the enhanced transcriptional activity of cell-type-specific TCF7L2 intragenic enhancers in regulating gene expression

Additional file 2: of Transcription factor-associated combinatorial epigenetic pattern reveals higher transcriptional activity of TCF7L2-regulated intragenic enhancers

Gene List associated with TF-states. (XLSX 330 kb

Three-dimensional gravity and magnetic modelling of the Irish sector of the NE Atlantic margin

A new 3D lithospheric model has been constructed using high-resolution gravity data from the Irish National Seabed Survey. The sedimentary component of the model incorporated density variations due to laterally varying overcompaction associated with Cenozoic denudation. After optimisation based on gravity inversion, regional crustal thickness variations were defined which are in reasonable agreement with the results of wide-angle seismic experiments. High crustal extension factors (β>5) characterise the deeper parts of the Rockall and Porcupine basins and in places the model indicates extreme stretching (β>10) beneath these basins. This could be because of instability in the gravity inversion, although other recent investigations have independently suggested similarly high extension factors. In contrast, the Hatton Basin is characterised by an apparent extension factor of about 2. The modelling resolves a pattern of NE- to NNE-trending local Mesozoic basins on the margins of the Rockall Trough, helping to delineate structures that were previously only sparsely sampled by seismic surveys. It appears possible that rifts with similar trends underlie the volcanic rocks which obscure the deeper parts of the Hatton Basin. The linear trends of the basins to the south and east of Ireland are interpreted to have been inherited from a basement fabric that was initially established during the late Precambrian assembly of this basement and subsequently subjected to Caledonian and Variscan reactivation. Magnetic modelling indicates that the variations in the thickness of the crystalline crust predicted by the gravity models can explain the regional magnetic anomaly patterns over the Rockall and Porcupine basins, but that significant additional magnetic material (probably igneous rocks of both Palaeogene and Cretaceous ages) is required to explain the anomalies in the Hatton Basin region. The magnetic signature of the Rockall Basin is distinctly different to that over the basement (of similar apparent thickness) formed during mid Cretaceous (C34N) opening of the ocean basin to the south. This is an impediment to hypotheses that invoke mid Cretaceous sea-floor spreading rather than intracontinental rifting to explain the development of the basin. The exception is in the extreme south of the basin where the volcanism associated with the Barra Volcanic Ridges combined with indications of relatively strong lithosphere could be evidence of incipient ocean opening