John A. Stamatoyannopoulos - US grants

DESCRIPTION (provided by applicant): The overall aim of this research proposal is to combine computational and functional methodologies to develop a set of algorithms with high positive predictive value for identifying and classifying candidate cis-regulatory sequences sites in the vicinity of any gene of interest. The underlying hypothesis is that functional non-coding sequences - particularly those governing a set of tissue-specific genes - will evince common features at the sequence level that can be identified computationally and modeled with sufficient precision to enable accurate de novo predictions. However, it is expected that the overall predictive value of computational approaches alone will be comparatively low. Rather, employed as a screening tool in combination with a high throughput functional validation methodology, computational approaches of even low (10-20%) predictive potential would be of enormous value, enabling rapid culling of tens of thousands of cis-regulatory sequences from the human genome. The strategy employed will commence with development of a catalogue of functional non-coding sequences for a set of tissue- and lineage-specific human genes. This will be achieved by precise localization of DNaseI hypersensitive sites (HSs) surrounding 100 erythroid-specific and 100 lymphoid lineage -restricted genes. Both tissues represent highly developed experimental systems, and a substantial amount of information has already come to light concerning both cis- and trans-regulatory mechanisms operative within these cell types. DNaseI hypersensitivity in vivo is the sine qua non of a diverse cast of transcriptional regulatory elements including enhancers, promoters, insulators, and locus control regions. The utility of the nuclease hypersensitivity assay for identification of in vivo-functional regulatory sequences is unmatched: it is a mature, functionally-based approach validated by a vast literature and decades of highly productive studies encompassing hundreds of human and other eukaryotic genes. A comprehensive catalogue of HSs surrounding any gene would therefore be expected to encompass the majority - if not all - of its cognate transcriptional control elements active in the tissues under study. Next, a significant data mining effort will be undertaken. This phase will involve (i) structural comparisons among identified functional elements; (ii) identification of candidate transcription factor binding sites within HS sequences using motif analysis methodologies; (iii) identification of correlations with ancillary genomic features such as transcriptional start sites, CpG islands, and certain classes of repetitive sequences; and (iv) structural comparisons between in vivo functional sequences and evolutionarily conserved sequences within the study regions. A major focus will be application of model techniques such as hidden Markov models, technology from gene prediction programs, and classifier kernel methods such as support vector machines. Based on these analyses, initial models for prospective detection of cis-regulatory regions will be developed. Finally, these models will be tested in and out of sample for sensitivity and specificity. Positive feedback from successfully confirmed sites will be utilized to refine the information collected above, thereby enhancing the basic model. Predictive techniques will then be applied systematically to discover cis-regulatory sequences surrounding erythroid, lymphoid, and diverse other classes of human genes. The resulting database will be of incalculable value in furthering the study of the regulation of human genes and the computational methodologies employed therein.

DESCRIPTION (provided by applicant): The overall aim of this research proposal is to localize and analyze a comprehensive catalogue of transcriptional regulatory elements affecting a broad spectrum of inflammatory response genes, with the goal of identifying genetic determinants of inter-individual variability in inflammatory response. The strategy employed will commence with precise localization of all DNasel hypersensitive sites (HSs) within 100kb of 200 inflammatory response genes for which substantial genetic variation data exist. A novel, tested high-throughput methodology developed by the investigators - Quantitative Chromatin Profiling (QCP) - will be applied to chart the cz's-regulatory landscapes of these gene loci (Specific Aim 1). This approach is capable of creating high-resolution maps of DNasel sensitivity across genomic distances and of sequence-specific localization of DNase HSs. Targeted re-sequencing of 1000 identified HS elements will be undertaken in 96 unrelated individuals to produce a comprehensive catalogue of genetic variation within candidate regulatory regions (Specific Aim 2). The size of the survey sample will permit identification of substantially all (99.99%) alleles of >5% frequency and >87% of 1% frequency alleles. To ensure timely dissemination of both polymorphism and HS data to the scientific community, a robust dedicated web-based project resource will be implemented (Specific Aim 3). It is expected that the results of this study will provide a rich supply of novel information concerning the genetics of gene regulation, and will provide a springboard for subsequent population-based studies surrounding a gene set of major clinical importance.

DESCRIPTION (provided by applicant): The overall aim of this proposal is to establish a comprehensive, high-quality catalogue of human DNaseI hypersensitive sites (DHSs) spanning all major tissue lineages. We plan to map DNaseI hypersensitive sites at physiological resolution across the genome with high sensitivity and specificity. The major focus of our production effort will be on data quality, a strategy that served the Human Genome Project well. Accordingly, samples will be rigorously screened in a pipeline fashion, with only a select set advancing to whole-genome data collection (Specific Aim 1). To ensure the broadest possible coverage of both unique and non-unique genomic territories, a synergistic combination of three technologies (DNase-array, digital mapping of DNAasel cleave site sequences, and Quantitative Chromatin Profiling) will be applied (Specific Aim 2). This combination will enable mapping of >95% of the DHSs in the genome of each cell type. Independent validation provides the ultimate quality standard. We therefore plan to validate the DHS catalogue in a statistically rigorous fashion using hypersensitivity Southerns, a well-established, gold standard assay (Specific Aim 3). Since DNAasel hypersensitive sites are generic markers of a broad spectrum of human cis-regulatory sequences, the utility of the catalogue will be greatly enhanced by the classification of DHSs into major functional categories including promoters, distal elements (enhancers, LCRs), and insulators (Specific Aim 4). Validation of DHS functional classes will be accomplished using well-tested cell and transgenic assays of biological function (Specific Aim 5).

DESCRIPTION (provided by applicant): The overall aim of this proposal is to establish an integrated Center for creating high-quality reference maps of key epigenotypes in pluripotent, differentiating, and primary differentiated human cells and tissues. The Northwest Reference Epigenome Mapping Center aggregates leading experts in human embryonic stem cell (hESC) biology, lineage-specific differentiation of hESCs, and well-established differentiating and differentiated adult primary tissue systems to establish a substantial capacity for the production of purified cells and tissues for large-scale epigenomic studies. The Center integrates this capacity with an existing high-throughput genomics and informatics infrastructure operating at scale, creating unique synergies that enable genome-scale epigenetic analyses of high-value human primary and progenitor cell types. The Center will perform high-resolution, whole-genome profiling of foundational epigenotypes in project cell types including high-resolution quantification of chromatin structural remodeling, and analysis of DNA methylation at both actively remodeled and silenced regulatory DNA templates. The Center will also profile both small RNA species and conventional gene expression from all study cell types. The Center's informatics and analytical arm will manage project data and its release into consortium and public repositories, and will perform integrative analyses to elucidate the connection between major epigenotypes and dynamic cellular programming of gene expression.

DESCRIPTION (provided by applicant): The goal of this project is to produce comprehensive, high-definition maps of mouse regulatory DNA marked by DNaseI hypersensitive sites to parallel the human catalogue currently under production by the ENCODE Project. Digital DNaseI technology enables efficient genome-wide mapping of accessible chromatin and DNaseI hypersensitive sites. The core regions of DNaseI hypersensitive sites are constitutively populated by regulatory factor binding sites, the nucleotide-resolution footprints of which may be systematically exposed on a genome-wide scale by ultra-deep sequencing. DNaseI hypersensitive sites exhibit marked cell-type variability;accordingly, production of a comprehensive catalog will require surveying a wide range of cell types. Cell types targeted under this proposal include murine analogues of the ENCODE Tier 1 and Tier 2 common reference cell lines;a broad spectrum of primary adult tissues;embryonic stem cells;and sentinel tissues amenable to sequential temporal profiling during development. The production of a parallel, high-quality, high-resolution compendium of mouse regulatory DNA will greatly enhance the value of the human ENCODE project and will provide a rich independent and unique resource for evolutionary, functional, and model organism genomics. PUBLIC HEALTH RELEVANCE: Relevance to Public Health Understanding the genetic basis of human disease requires detailed knowledge of the functional elements of the human genome which may be subject to polymorphism. The ENCODE Project seeks to identify all of the functional elements in the human genome, and present project seeks to greatly increase the value of the ENCODE data by providing a parallel catalogue of regulatory DNA in the mouse genome. This project is therefore expected to provide key insights into the importance of elements in the human genome, and to provide an unprecedented resource for rational functional modeling of human disease in the mouse.

DESCRIPTION (provided by applicant): We plan to develop a high-throughput, high-resolution in vivo footprinting method based on next generation single molecule DNA sequencing technology. Single molecule sequencing will be used in place of conventional methods to detect cleavage induced by three modifying agents: DMS (dimethyl sulfate), DNase I and UV light. With a simple modification to standard ligation-mediated PCR (LM-PCR), the precise sequence of protein binding sites can be determined by sequencing short cleavage signature tags and simply counting the number of times a tag terminates at each nucleotide position within a designated 'footprint window'. This counting method will convert the cumbersome, 'band intensity'analysis of classical footprinting methods to an absolute, frequency-based approach that can be readily analyzed by an automated analysis pipeline. The project commences with the development and demonstration of the technology and its large-scale use. First, optimal conditions will be developed and applied to generate cleavage maps of previously footprinted 'control'segments (DMS, DNase I and UV) in a multiplexed format. With optimized parameters established, the assay will be used for the de novo footprinting of putative cis regulatory elements, as indicated by DNase I hypersensitivity. Within this aim we will also determine the sensitivity and specificity of the HD (High Definition) tag footprinting assay as well as assess the biological and technical reproducibility of the system. >100 tag-generated footprints will be validated each year by classical footprinting techniques to ensure accuracy of the data. Finally, we will determine the scalability of the HD tag footprinting system and apply it on a large scale to the analysis of putative functional elements within the ENCODE regions. DNase I hypersensitive sites identified from four cell types will be footprinted and data compared to existing ENCODE data types. A high-throughput method capable of generating high resolution DNase I, DMS and UV footprints will provide a powerful tool for identifying the protein interacting sequences within novel cis-regulatory elements of any eukaryotic genome. High-resolution tag footprinting will contribute to the goals of the ENCODE project by complementing existing assays and creating a large volume of precise sequence-based data that can be used to further annotate functional elements in the genome.

The genome of an organism encodes not only genes and their RNA and protein products, but also the integrated programs that define when, where, and to what extent different genes are activated or silenced. At the DNA level, gene regulatory signals are encoded by regulatory elements that comprise clustered recognition sites for DNA binding proteins. However, the location and function of the vast majority of Arabidopsis regulatory sequences is currently obscure. In this project, novel high-throughput epigenomic technologies--Digital DNaseI Mapping and Digital Genomic Footprinting--will be applied to map and characterize regulatory DNA across the A. thaliana genome at nucleotide resolution. These technologies are capable of mapping the locations of regulatory DNA sequences, and delineating the specific sites of regulatory factor binding within such regions. Because gene regulatory programs vary widely both between different cell types and within a cell type during differentiation, the project will encompass multiple developmental stages and tissues of a reference strain. As sessile organisms, plants integrate many cues into appropriate developmental and stress responses, most of which rely on major re-programming gene regulatory responses. Regulatory DNA involved in such responses will therefore be mapped through study of standard stress conditions. At the population level, most phenotypic variation is likely to derive from non-coding genetic variation. By systematically extending maps of regulatory DNA across both diverse A. thaliana accessions and related species, the project will expose relationships between genotypic variation and gene regulatory programs on a genome-wide scale. The resulting data will provide unprecedented insight into endogenous and environmentally-responsive plant regulatory programs, and will significantly accelerate the identification of functional non-coding variation underlying relevant phenotypic variation.

Broader impacts. This project has the potential to change fundamentally the landscape of gene regulation research in A. thaliana and in plants generally, both as it applies to basic mechanisms and in its application to solve diverse quantitatively varying phenotypes. The availability of comprehensive, high-resolution regulatory DNA maps for A. thaliana stages, tissues, treatments, accessions, and evolutionarily related species will immediately bring A. thaliana to the forefront of regulatory genomics, and will provide a powerful attraction for bringing dynamic new investigators to the field. The comprehensive annotation of A. thaliana regulatory regions and transcription factor binding sites targeted under this project will be of use to the entire plant biology community, and will develop significant data resources that will potentiate experimental approaches to determining gene function. The project will foster the advancement of plant regulatory genomics through rapid dissemination of data to the public domain via genomic databases as well as relevant analytical tools to assist in its utilization by diverse investigators. The project will also encompass a significant educational component aimed at training next-generation leaders in plant regulatory genomics, and recruitment and training of talented undergraduate and graduate scientists from diverse backgrounds.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This is a failed project that attempted to look at proteins that are interacting with CTCF using a pulldown approach with biotinylated antibody. The main issues with this were keratin contamination and poor CTCF signal. This experiment further supported the difficulties in identifying low abundance proteins using a shotgun proteomics approach.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The previous project using chromatographic intensities from the FT-ICR and crawdad to identify proteins in nuclei that were changing between cell lines identified several hundred proteins. However, only 10 of these were transcription factors. Consequently, we sought to utilize the increased sampling speed of the LTQ-VELOS in order to better identify low abundant nuclear proteins, such as transcription factors. Whole cell extracts and nuclear extracts from BJ, SKNSH, HepG2 and K562 cell lines were run in multiple replicates and analyzed using a data dependent acquisition (DDA) approach. This experiment was able to identify several dozen more transcription factors (TFs) in the nuclear samples of each of these cell lines. Additionally, these experiments were able to identify several transcription factors that were unique to the whole cell extract. These transcription factors correspond to proteins that are known to be predominately cytoplasmic under the growth conditions. One startling finding was the discrepancy between the cell-lines in total number of TFs identified. BJ nuclear extracts showed only a fraction of the number of TFs found in K562 nuclear extracts. This finding is thought to be due to the higher dynamic range of proteins present in BJ versus K562 nuclear extracts. As shown in the previous experiment. BJ nuclei contain an elevated amount of structural proteins that are most likely "hogging" the exclusion list in a DDA run.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project represents a number of different ways that were tested to better identify transcription factors (TFs) in nuclear protein samples. In this study, a peptide inclusion list was created that contained a large number of peptides corresponding to TFs. Although the inclusion list was overly large, the results oddly showed an increase in the number of TFs identified. I am still not entirely sure why this method worked better than the standard DDA approach, but have set up future experiments to better understand this. My current hypothesis is that I may be able to replicate these results by just doing a DDA experiment where I tell the instrument to ignore the top 2 highest abundant peaks.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project is a companion to project 2039. These experiments were designed to elucidate factors that were contaminating the nuclear preps, as well as to test different nuclear prep methods. Whole cell and nuclear extracts from K562 and HepG2 were run in the FT-ICR (same column). This data suggests that the nuclear enrichments are void of most cytoplasmic proteins, but still contain mitochondrial membrane proteins. Additionally, a nuclear enrichment protocol that is commonly used in the literature was also tested for cytoplasmic contamination. This protocol gives a "cytoplasmic protein" fraction, a "nuclear protein" fraction and an insoluble pellet. This data suggests that the nuclear fraction obtained by this protocol contains a large amount of cytoplasmic proteins, and that the insoluble pellet contains a large number of nuclear proteins. Given the outcomes of this experiment, this nuclear protein protocol has been discarded from future use.

Core Unit C will assist the individual projects by providing the following functions :1) Genome-wide profiling of DNase I Hypersensitive Sites (DHSs). In support of Project 1, Core Unit C will profile the DHSs of fetal human erythroid cells and adult CD34 cell-derived erythroblasts and will provide the data from all other lineages and cell lines required for the identification of the insulator elements of the human genome. In support of Project 2, the unit will profile the DHSs of the thalassemia-derived iPS cells and the erythroid cells derived from differentiation of IPS cells. In support of Project 4, the Unit will provide access to comprehensive data on DHS in human hemopoietic cells to be used to further characterize the correlation between VIS and DHS in the setting of clinical samples. 2) Genome-wide mapping of specific protein-DNA binding sites (Chip-seq). In support of Project 1, Genomics Core Unit C will perform the high-throughput sequencing associated with the genome-wide ChlP-seq analysis of USF1/2 and CTCF binding sites. This will include the ligation of P5 and P7 primers, template amplification, sequencing on the Solexa platform, mapping of sequence tags, and calculation of binding hotspots. 3) Assisting with the informatics and automated cloning and sequencing needs. Core Unit C will provide assistance with informatics needs related to genomics analysis in support of all projects as they develop during the course of the PPG. This will include in part the mapping and correlation of VIS and genomics properties in support of Project 4, and the correlation between several genomics properties related to the identification of candidate chromatin insulators in support of Project 1. The Core Unit will also provide assistance with physical aspects of automated cloning and sequencing in support of all projects as they develop during the course of this PPG.

DESCRIPTION (provided by applicant): The current proposal requests funds for the purchase of an ABI SOLiD V3 sequencer, a next- generation, and massively parallel sequencing platform. The ultra-high throughput of next- generation instruments, coupled with substantially reduced sequencing costs have made these the platforms of choice for interrogating genome sequence and function. Massively parallel sequencing is particularly well-suited for epigenomic and functional genomics studies, including chromatin structure, histone modifications and variants, regulatory factor localization;DNA methylation;transcription;and quantification of genome modifications such as localization of retroviral vector integrations. With 2-base encoding, the SOLiD V3 system is capable of generating highly accurate sequence data, with an output of >20 gigabases of mappable data per run, from >400 million mappable reads from the two slides with each run of the instrument. This output is roughly double that of other short read sequencers currently on the market, and, with read lengths expected to reach 100 bases by early 2010, the raw sequence output will double again. Demand for next-generation sequencing capacity is experiencing explosive growth as more investigators realize the potential of the technology to impact and accelerate their research. The new instrument will be deployed in the context of a well-established, self- supporting core facility that already provides substantial epigenomics-focused next-generation sequencing services and associated bioinformatics support, and is therefore ideally positioned to rapidly translate the SOLiD V3's potential to meet the needs of specific investigator projects as well as those of the general research community. PUBLIC HEALTH RELEVANCE: The current proposal requests funding to purchase an ABI SOLiD v3 massively parallel sequencing platform. The new instrument will be deployed in the context of an existing core facility, and will address substantial demand for epigenomic and functional genomics sequencing applications including mapping and analysis of chromatin structure, regulatory factors, and DNA methylation. The instrument will also support gene therapy programs by providing a platform to map genomic sites of therapeutic vector integration in model and patient cells.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project is composed of a large number of experiments designed at treating nuclei in such a manner that transcription factors are selectively enriched from them. Most of the experiments were designed using protocols from papers in the 1960s-1970s. The conditions that were varied include: salt concentration, sucrose concentration, EDTA/EGTA presence, Sucrose fractionation, Spermidine and DNAse concentration. One of the main findings from these experiments was that the salt concentration had the largest effect on the transcription factor recovery. Additionally, it was observed that the MCX cartridges were not fully cleaning up the NP-40 from the samples, which was probably causing the chromatographic contamination that was observed in experiment 2.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Subsequent to the previous findings that different transcription factors (TFs) are released with different salt concentrations, I sought to test a gradient of different salt concentrations and see the profile of TFs that are released by each step. Additionally, I sought to replicate a finding from Henikoff et. al. Genome Research 2009 that showed that if you treat nuclei with MNAse, and subsequently do salt fractionation, the low salt fractions correspond to active transcriptional elements in the human genome. Unfortunately, the concentration of DNAse that I used was not sufficient to digest the nuclei, so the DNAse data is analogous to the salt data. This project provided many interesting results that are currently being validated using SRM, ChIP-seq and SILAC like approaches.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Selective reaction monitoring (SRM) has the potential to revolutionize the field of proteomics by providing sensitive, specific, reproducible and quantifiable assays for every protein in the proteome. This need is most evident for low abundance proteins such as transcription factors, a class of proteins that bind to and regulate the genome, which are often left undetected by traditional shotgun proteomic approaches. However, the main challenge in targeted proteomics is identifying which peptides and fragment ions should be monitored from a given protein. Consequently, the main goal of this project is to empirically identify for ~550 transcription factors in the human proteome a set of peptides and their fragment ion signatures that can be easily and reproducibly identified from complex mixtures.

The overall aim of this proposal is to establish a comprehensive, high-quality, high-resolution catalogues of human and mouse DNasel hypersensitive sites (DHSs) spanning all major tissue lineages. Building on the prior success of the UW ENCODE center, we plan to localize DNasel hypersensitive sites, to define the locations of DNasel footprints therein, and to continue to provide relevant synergistic annotations including RNA-seq, histone modifications, and CTCF, as well as DNA methylation. The overriding focus of our production effort has been on data quality. Accordingly, samples will be rigorously screened in a pipeline fashion, with only a select set advancing to whole-genome data collection. To ensure the broadest possible coverage of both unique and non-unique genomic territories, we will employ a higher resolution, higher coverage sequencing strategy than the prior project period, significantly enhancing the information content of the data. This proposal integrates the UW-FHCRC Mouse ENCODE Center, which will be closely aligned with the human project to generate a comparative catalogue of regulatory DNA in carefully matched cells and tissues, providing an unparalleled resource. Since DNasel hypersensitive sites are generic markers of a broad spectrum of human cis-regulatory sequences, the utility of the catalogue will be greatly enhanced by the classification of DHSs into major functional categories including promoters, distal elements (enhancers, LCRs), and insulators. We plan to systematically connect distal DHSs with their cognate promoters and to perform in vivo validation of these connections using nuclease-mediated knockouts of distal DHSs in somatic cells.

DESCRIPTION (provided by applicant): Our current understanding of how endocrine-disrupting chemicals (EDCs), such as the hormone mimics ('xenoestrogens') modify and maintain chromatin states, gene expression patterns and alter genomic nuclear receptor binding and chromatin structural patterns is nascent. Chromatin accessibility plays a major role in shaping the binding landscape of nuclear hormone receptors and all transcription factors. DNaseI hypersensitivity mapping provides a powerful approach for global, generic, and precise delineation of regulatory DNA. In this proposal, we aim to apply these powerful approaches to map alterations in the regulatory DNA landscape associated with EDCs, and to define the impact of EDC exposure on transcriptional control networks. Focusing on xenoestrogens, we aim to characterize systematically the impact of exposure on the regulatory DNA landscape using model cell lines as well as specialized primary cell and primary human tissue culture systems. We will also address major outstanding questions concerning transient exposures to EDCs giving rise to lasting phenotypic effects, and analyze transcriptional regulatory networks perturbed by EDCs.

DESCRIPTION (provided by applicant): The current proposal requests funds for the purchase of Illumina HiSeq 2500 sequencer, a next- generation, massively parallel sequencing platform. The ultra-high throughput of Illumina instruments, coupled with substantially reduced sequencing costs have made this a platform of choice for interrogating regulatory genomic sequences and function. Massively parallel sequencing is particularly well-suited for epigenomic and functional genomic studies, including chromatin structure, Chromatin accessibility, histone modifications and variants, regulatory factor localization; DNA methylation; transcription; and quantification of genome modifications such as localization of retroviral vector integrations. HiSeq2500 sequencer has dual flow cells with high density clusters generated in each channel that produces high quality passing filter data of 600 GB per 2X100 bp run. The two flow cells can be operated independently using different chemistries. The sequencer has the capability to operate in dual mode; in rapid run mode the clusters are generated on the sequencer, allows producing up to single or paired end 150 base long reads, and run times are several fold shorter , while in high output mode the sequence yields are up to 600 Gb per run. This allows tailoring the sequence run to the desired outcome in terms of speed vs. significantly large data output. The advances in Illumina sequencing technologies and chemistries, the price per Mb sequence output has made HiSeq a platform of choice for functional genomics research, These advances have led to explosive growth in demand for massively parallel sequencing, as more investigators realize the potential of the technology to impact and accelerate their research. The new instrument will be deployed in the context of a well-established, self-supporting core facility that already provides substantial epigenomics-focused next-generation sequencing services and associated bioinformatics support, and is therefore ideally positioned to rapidly translate the HiSeq 2500 potential to meet the needs of specific investigator projects as well as those of the general research community.

Connecting genetic variation with gene expression and other phenotypes is a major goal of genomic science. Gene expression patterns vary widely among different cell and tissue types, and also regionally within a tissue. The impact of genetic variation on gene expression patterns is thus expected to differ substantially between tissues. The Genotype-Tissue Expression (GTEx) is establishing resource databases to enable comprehensive analysis of tissue gene expression profiles and their connection with individual genotypes. Most variants linked to individual variation in human gene expression lie in non-coding regions of the genome; of these, a proportion is expected to directly impact gene regulation through perturbation of regulatory DNA regions. Systematic understanding of the impact of genetic variation on gene expression will thus require both comprehensive delineation of regulatory DNA, and an understanding of the degree to which actuation of individual regulatory regions varies at the population level. In this proposal we aim to empower the central goal of GTEx -- connecting genotype to gene expression patterns -- for diverse human tissues by comprehensively delineating regulatory DNA at very high resolution, and systematically identifying genetic variants that impact its function through abrogation of regulatory factor binding and perturbation of local chromatin architecture. We will apply high-resolution genome-scale mapping of DNaseI hypersensitive sites to comprehensively delineate regulatory DNA within tissue samples from a multi-ethnic population accrued by the GTEx project. We will also apply genomic DNaseI footprinting at genome-scale and in a targeted fashion to map transcription factor occupancy within regulatory DNA at nucleotide resolution.

DESCRIPTION (provided by applicant): The vast majority (>90%) of disease- and trait-associated variants emerging from genome-wide association studies (GWAS) lie in non-coding regions of the genome, and currently all but a handful lack molecular mechanisms that explain the observed associations with complex traits. Superimposition of the human regulatory DNA catalogue with GWAS data reveals a striking concentration of disease-associated variation precisely within regulatory DNA regions defined by DNaseI hypersensitive sites. We will fully understand gene regulation and mis-regulation only if we are able to examine genetic variants in their biological chromatin context in otherwise isogenic cells. TALE nuclease (TALEN) platforms can alter the DNA sequence of cells in a precise, targeted manner. We have already established the feasibility of single-TALEN- mediated homologous recombination for efficient knockout of individual regulatory DNA regions. In R21 phase, we will model candidate disease/trait-associated variants in regulatory DNA in vivo using engineered templates at 10 individual regulatory regions. We will test the feasibility and determine the salient operating characteristics of a scalable implementation of a TALEN genomic modification pipeline using K562 cells, and demonstrate knockout feasibility and specific allele insertion in primary hematopoietic cells and document efficiencies. We will test the efficiency of a using single or multiple TALENs flanking an editing site. In the R33 phase, we will scale the TALEN pipeline process to efficiently characterize sites identified in GWAS studies as associated with red blood cell phenotypes. These studies will provide a direct proof for the role of regulatory elements and demonstrate the relevance of GWAS associated SNPs as causative for the observed phenotypes.

? DESCRIPTION (provided by applicant): This application seeks support for the conference Epigenomics 2015: A Roadmap to the Living Genome. This application follows the successful inaugural conference that took place in Boston on October 20-21 2013. This biennial conference series will bring together an international group of scientists to (l) present and discuss new developments in epigenomics and its diverse applications; and (ll) provide a hands-on workshop for junior and established scientists on key methodologies and resources for epigenomic research. These components will ultimately catalyze epigenomic research and accelerate pace of discovery. The conference is anticipated to take place in Seattle, Washington in the late spring of 2015.

? DESCRIPTION (provided by applicant): The mission of the Center for Photogenomics is to develop revolutionary technologies that enable the direct visualization and functional profiling of human regulatory regions at the resolution of individual chromatin templates in intact cells, and to leverage the extraordinary cell selectivity and information content of regulatory DNA to pioneer novel biological and translational applications. The Center will specifically (i) develop technology to simultaneously visualize and localize in highly multiplexed fashion, regulatory DNA regions on individual chromatin templates within the intact cell nucleus; (ii) develop technology for activity-based profiling of regulatory regions; (iii) pioneer structural, functional and integrative applications of photogenomics using super-resolution nanoscopic techniques; (iv) enable photogenomics through development of revolutionary instrumentation for high-throughput, high-speed super-resolution microscopy; and (v) lay the foundation for translation of photogenomic techniques to solving common problems in the modern clinical diagnostic laboratory by integrating with existing clinical workflows. This will ensure that photogenomics wil bring the power of genomic analysis to the understanding of cells within the context of their tissue environment. In keeping with the mission of the CEGS program of training and outreach, this Center proposal outlines a strong multi-disciplinary post- doctoral program that will create a new breed of genomics researcher with expertise in genomics as well as advanced imaging techniques and analysis. In addition, through innovative and interactive programs, the Center will expose non-genomics researchers and pre-doctoral students to this new field.

ABSTRACT    The  overall  mission  of  this  Mapping  Center  is  to  create  and  disseminate  open  access,  comprehensive,  high-­quality,  high-­resolution  reference  maps  of  DNase  I  hypersensitive  sites  (DHSs)  in  the  human  and  mouse  genomes,  at  previously  unattainable  levels  of  cellular  and  anatomical  definition.  Regulatory  DNA  is  actuated  in  an  exceptionally  state-­specific  manner;?  accordingly,  achieving  a  comprehensive  map  of  DHSs  necessitates  the  interrogation  of  an  expansive  and  finely  partitioned  range  of  cell  and  tissue  samples.  Progressive  technical  improvements and recent innovations have resulted in dramatic (>100x) decreases in requisite  input  biological  sample  quantities  coupled  with  equally  dramatic  (>100x)  increases  in  assay  throughput, and corresponding decreases in the incremental cost of generating reference-­quality  DHS maps.  These advances have in turn opened the possibility of systematically addressing all  well-­defined  physiologically  and  disease-­relevant  anatomic  and  cellular  compartments.  Four  major Specific Aims are targeted: (1) To create open access, comprehensive high-­quality, high-­ resolution reference maps of human DNase I hypersensitive sites;? (2) To create and disseminate  comprehensive  high-­quality,  high-­resolution  reference  maps  of  mouse  DNase  I  hypersensitive  sites;?  (3)  To  maintain  and  disseminate  reference  indices  of  DNase  I  hypersensitive  sites  and  footprints in the human and mouse genomes;? and (4) To enable large-­scale intake of Consortium  and Community samples for high-­quality, high-­throughput DHS mapping.