Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.Postprint (published version

The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what measures meaningfully evaluate performance are open questions. We address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. We find that imputation evaluations are challenging and confounded by distributional shifts from differences in data collection and processing over time, the amount of available data, and redundancy among performance measures. Our analyses suggest simple steps for overcoming these issues and promising directions for more robust research

The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what measures meaningfully evaluate performance are open questions. We address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. We find that imputation evaluations are challenging and confounded by distributional shifts from differences in data collection and processing over time, the amount of available data, and redundancy among performance measures. Our analyses suggest simple steps for overcoming these issues and promising directions for more robust research

Expanded encyclopaedias of DNA elements in the human and mouse genomes

All data are available on the ENCODE data portal: www.encodeproject. org. All code is available on GitHub from the links provided in the methods section. Code related to the Registry of cCREs can be found at https:// github.com/weng-lab/ENCODE-cCREs. Code related to SCREEN can be found at https://github.com/weng-lab/SCREEN.© The Author(s) 2020. The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.This work was supported by grants from the NIH under U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

Characterization of Mammalian Cellular Memory.

Abstract Cellular differentiation is accompanied by the coordinated activation and silencing of specific subsets of genes and associated alterations in chromatin structure. This process, which is under the control of extrinsic and intrinsic cellular signals, results in the establishment of lineage-specific domain structures that must be maintained during dynamic nuclear events, such as cell division. The propagation of specific patterns of gene expression is termed “cellular memory”. Our goal is to identify the elements that are involved in the establishment and propagation of transcription states and to determine the molecular basis of memory establishment in mammals. To this end, K562 cells were transfected with a γ-globin promoter-GFP-metallothionein response element (MRE) cassette (GGM cassettes) and, using a procedure to derive stably transfected cells in the absence of selection, multiple stable transformants harboring a single copy of the cassette were obtained. In most clones, zinc (Zn) induction resulted in transition of the transgene from the silent to the active state, with the maintenance of the active state dependent on continuous exposure to Zn. However, at one genomic site (clone 6177), a high level of GFP expression was maintained even after Zn removal. Characterization of epigenetic marks of this transgene, including CpG methylation, histone modifications and nuclear localization, at various stages of GFP expression may provide insight into the molecular mechanisms of mammalian cellular memory. In initial experiments, Na-bisulfite conversion/sequencing revealed that, prior to the establishment of memory, up to 8% of CpGs in the GFP gene are methylated, and after memory establishment, no CpG methylation is detectable. However, pretreatment of 6177 cells with a DNA methylation inhibitor, 5-dAzaC for 48hs before Zn induction resulted in no change in the memory establishment program, suggestiong that reduction of CpG methylation is not a cause of memory establishment in 6177 cells. We also have examined the relationship between cellular memory and histone modifications. Comparison of the histone modification status of the active GFP gene in cells before and after memory establishment revealed that H4 K20 dimethylation is present in the both the inactive and active GFP gene prior to memory establishment, but is significantly reduced upon memory establishment. Interestingly, this mark is known to be associated with silenced regions of euchromatin and the chromocenter, but not with active genes, in Drosophila. Thus, these results have revealed a unique nature of histone modification at the 6177 site: a marker of silenced chromatin co-exists with active transcription prior to the establishment of cellular memory. This co-existence may be the mechanism by which the establishment of memory of the active state is prevented at stage II. Currently, we are cloning the 6177 integration site to identify cellular memory elements, the function of which will be further analyzed at defined genomic sites.</jats:p