A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.National Human Genome Research Institute (U.S.)National Institutes of Health (U.S.

A User\u27s Guide to the Encyclopedia of DNA Elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome

Nucleosome positioning: resources and tools online

Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info

Doctor of Philosophy

dissertationRNA Polymerase III (Pol III) transcribes small noncoding RNAs that are important in protein synthesis. Genome-wide analysis of Pol III and associated transcription factors (TFIIIC, BRF1, and BRF2) localization in various human cell lines was performed using chromatin immunoprecipitation followed by highthroughput sequencing (ChIP-seq). These analyses show that Pol III binds only to a fraction of all its annotated target genes. Comparison of Pol III-bound regions to known chromatin and transcription factor data shows that Pol III localization in a cell is guided by the chromatin landscape setup by Pol II. We believe Pol III binding is opportunistic and relies on a cell's pool of transcription factors and chromatin landscapes to bind its target genes. To understand Pol III localization in a cell line of high interest, human embryonic stem cells (hESCs), we performed Pol III and TFIIIC ChIP-seq analyses in H1 cells. We hoped to understand the role of open chromatin and pluripotency transcription factors in hESC, on Pol III occupancy. We observed that there are significantly more Pol III-bound regions in hESCs when compared to differentiated cells types. We also observe that these Pol III-bound regions correlated positively with active chromatin marks and Pol II. Interestingly, we also observed that pluripotency transcription factors, NANOG (in hESCs) and OCT4 ! iv! (in mESCs), correlated with Pol III-bound regions. We also observed regional H3K27me3 at Pol III-bound regions. We observe Pol II and H3K4me3 peaks situated in between the Pol III and H3K27me3 peaks. We postulate that active chromatin setup by Pol II insulates the Pol III transcription unit from H3K27me3 repression. We also identified several novel Pol III-bound regions in hESCs. This is the first analysis of Pol III in hESCs and our results are consistent with Pol III binding and activity being regulated by active chromatin that is shaped in part by the pluripotency transcription factor network

A User\u27s Guide to the Encyclopedia of DNA Elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome

Transcriptional Regulation by DAX-1 in Pluripotent and Differentiated Cells

DAX-1, an orphan nuclear hormone receptor, acts mainly as a repressor through transcriptional protein complexes. Its unique structure and specific expression raises questions as to what its precise interactions are and how it mediates its repressive function. While it is known to play a role in sexual development and adrenal insufficiency, expression in certain types of cancer suggests additional functions and interactions. Knock in of DAX-1 into a low-DAX-1 expressing cancer cell line has been previously observed to increase apoptosis, while, inversely, down in a high-DAX-1 expressing cancer cell line shows a decrease in apoptosis. Target genes that belong to the TNFα and BCL-2 families have shown changes in expression correlating to the modified levels of DAX-1 in knock-down experiments. Direct regulation of BCL-2, one of the target genes of interest, was investigated further based on mirrored expression changes of DAX-1 in knock-down and knock in experiments through ChIP experiments. These findings emphasize a significant role of DAX-1 in moderating apoptosis in a breast cancer cell line. In the context of undifferentiated mouse embryonic stem cells, Dax-1 is highly expressed and has been shown to be an important contributor to the pluripotent state. Potential downstream targets of Dax-1 were previously identified based on significant changes in expression when Dax-1 expression was down regulated. Two methods, siRNA and CRISPR-Cas9, were used to decrease Dax-1 expression in the E14 mouse embryonic stem cell line. Direct interactions and other novel stem cell factors were confirmed using analysis of publically available ChiP-seq data. Ultimately, while Dax-1 is not a master regulator, its transcriptional control of specific genes that are key in the maintenance of pluripotency is an important component of stem cell growth and differentiation. Bioinformatic analysis of ChIP-seq experiments brought to light general patterns as to how Dax-1 contributes to pluripotency, and additional ontologies of Dax-1 target genes for future studies

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

We develop a statistical framework to study the relationship between chromatin features and gene expression. This can be used to predict gene expression of protein coding genes, as well as microRNAs. We demonstrate the prediction in a variety of contexts, focusing particularly on the modENCODE worm datasets. Moreover, our framework reveals the positional contribution around genes (upstream or downstream) of distinct chromatin features to the overall prediction of expression levels