scholarly journals MIGS: Methylation Interpolated Gene Signatures Determine Associations Between Differential Methylation and Gene Expression

2016 ◽  
Author(s):  
Christopher E Schlosberg ◽  
Nathan D VanderKraats ◽  
John R Edwards
Keyword(s):  
Gene Expression ◽  
Gene Promoter ◽  
Methylation Data ◽  
Expression Change ◽  
Gene Signatures ◽  
Genome Wide ◽  
Invaluable Tool ◽  
Genomic Studies ◽  
Specific Variation ◽  
Using Data

AbstractA large number of genomic studies are underway to determine which genes are abnormally regulated by methylation in disease. However, our understanding of how disease-specific methylation changes potentially affect expression is poorly understood. We need better tools to explain specific variation in methylation that potentially affects gene expression in clinical sequencing. We have developed a model, Methylation Interpolated Gene Signatures (MIGS), that captures the complexity of DNA methylation changes around a gene promoter. Using data from the Roadmap Epigenomics Project, we show that MIGS significantly outperforms current methods to use methylation data to predict differential expression. We find that methylation changes at the TSS and downstream ~2kb are most predictive of expression change. MIGS will be an invaluable tool to analyze genome-wide methylation data as MIGS produces a longer and more accurate list of genes with methylation-associated expression changes.

Abstract P098: An Epigenome-wide Study of Obesity in African American Youth and Young Adults: Novel Findings, Replication in Neutrophils and Relationship With Gene Expression

Circulation ◽  
2017 ◽  
Vol 135 (suppl_1) ◽  
Author(s):  
Xiaoling Wang ◽  
Yue Pan ◽  
Haidong Zhu ◽  
Guang Hao ◽  
Xin Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Older Adults ◽  
Dna Methylation ◽  
Young Adults ◽  
Methylation Data ◽  
Middle Aged ◽  
Cpg Sites ◽  
Genome Wide ◽  
Obesity Status ◽  
Youth And Young Adults

Background: Several large-scale epigenome wide association studies on obesity-related DNA methylation changes have been published and in total identified 46 CpG sites. These studies were conducted in middle-aged and older adults of Caucasians and African Americans (AAs) using leukocytes. To what extend these signals are independent of cell compositions as well as to what extend they may influence gene expression have not been systematically investigated. Furthermore, the high prevalence of obesity comorbidities in middle-aged or older population may hide or bias obesity itself related DNA methylation changes. Methods: In this study of healthy AA youth and young adults, genome wide DNA methylation data from leukocytes were obtained from three independent studies: EpiGO study (96 obese cases vs. 92 lean controls, aged 14-21, 50% females, test of interest is obesity status), LACHY study (284 participants from general population, aged 14-18, 50% females, test of interest is BMI), and Georgia Stress and Heart study (298 participants from general population, aged 18-38, 52% females, test of interest is BMI) using the Infinium HumanMethylation450 BeadChip. Genome wide DNA methylation data from purified neutrophils as well as genome wide gene expression data from leukocytes using Illumina HT12 V4 array were also obtained for the EpiGO samples. Results: The meta-analysis on the 3 cohorts identified 76 obesity related CpG sites in leukocytes with p<1х10 -7 . Out of the 46 previously identified CpG sites, 36 can be replicated in this AA youth and young adult sample with same direction and p<0.05. Out of the 107 CpG sites including the 36 replicated ones and the 71 newly identified ones, 71 CpG sites (66%) had their relationship with obesity replicated in purified neutrophils (p<0.05). The analysis on the cis regulation of the 107 CpG sites on gene expression showed that 59 CpG sites had at least one gene within 250kb having expression difference between obese cases and lean controls. Furthermore, out of the 59 CpG sites, 6 showed significantly negative correlations and 1 showed significantly positive correlation with the differentially expressed genes. These CpG sites located in SOCS3, CISH, ABCG1, PIM3 and PTGDS genes. Conclusion: In this study of AA youth and young adults, we identified novel CpG sites associated with obesity and replicated majority of the CpG sites previously identified in middle-aged and older adults. For the first time, we showed that majority of the obesity related CpG sites identified from leukocytes are not driven by cell compositions and provided the direct link between DNA methylation-gene expression-obesity status for 7 CpG sites in 5 genes.

scholarly journals Enrichment of genomic variation in pathways linked to autism

2020 ◽  
Author(s):  
Francisco J. Esteban ◽  
Peter J. Tonellato ◽  
Dennis P. Wall
Keyword(s):  
Gene Expression ◽  
Prior Knowledge ◽  
Neurological Disorders ◽  
Genetic Relationships ◽  
Genomic Variation ◽  
Large Numbers ◽  
Genome Wide ◽  
Genomic Studies ◽  
Biological Concepts ◽  
Novel Strategy

AbstractThe genetic heterogeneity of autism has stymied the search for causes and cures. Even whole-genomic studies on large numbers of families have yielded results of relatively little impact. In the present work, we analyze two genomic databases using a novel strategy that takes prior knowledge of genetic relationships into account and that was designed to boost signal important to our understanding of the molecular basis of autism. Our strategy was designed to identify significant genomic variation within a priori defined biological concepts and improves signal detection while lessening the severity of multiple test correction seen in standard analysis of genome-wide association data. Upon application of our approach using 3,244 biological concepts, we detected genomic variation in 68 biological concepts with significant association to autism in comparison to family-based controls. These concepts clustered naturally into a total of 19 classes, principally including cell adhesion, cancer, and immune response. The top-ranking concepts contained high percentages of genes already suspected to play roles in autism or in a related neurological disorder. In addition, many of the sets associated with autism at the DNA level also proved to be predictive of changes in gene expression within a separate population of autistic cases, suggesting that the signature of genomic variation may also be detectable in blood-based transcriptional profiles. This robust cross-validation with gene expression data from individuals with autism coupled with the enrichment within autism-related neurological disorders supported the possibility that the mutations play important roles in the onset of autism and should be given priority for further study. In sum, our work provides new leads into the genetic underpinnings of autism and highlights the importance of reanalysis of genomic studies of complex disease using prior knowledge of genetic organization.Author SummaryThe genetic heterogeneity of autism has stymied the search for causes and cures. Even whole-genomic studies on large numbers of families have yielded results of relatively little impact. In the present work, we reanalyze two of the most influential whole-genomic studies using a novel strategy that takes prior knowledge of genetic relationships into account in an effort to boost signal important to our understanding of the molecular structure of autism. Our approach demonstrates that these genome wide association studies contain more information relevant to autism than previously realized. We detected 68 highly significant collections of mutations that map to genes with measurable and significant changes in gene expression in autistic individuals, and that have been implicated in other neurological disorders believed to be closely related, and genetically linked, to autism. Our work provides leads into the genetic underpinnings of autism and highlights the importance of reanalysis of genomic studies of disease using prior knowledge of genetic organization.

scholarly journals Gene expression in African Americans and Latinos reveals ancestry-specific patterns of genetic architecture

2021 ◽  
Author(s):  
Angel C.Y. Mak ◽  
Linda Kachuri ◽  
Donglei Hu ◽  
Celeste Eng ◽  
Scott Huntsman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Architecture ◽  
Prediction Models ◽  
African Ancestry ◽  
Diverse Populations ◽  
Sequencing Data ◽  
Blood Gene Expression ◽  
Genome Wide ◽  
Genomic Studies

We explored the role of genetic ancestry in shaping the genetic architecture of whole blood gene expression using whole genome and RNA sequencing data from 2,733 African American and Hispanic/Latino children. We find that heritability of gene expression significantly increases with greater proportion of genome-wide African ancestry and decreases with higher levels of Indigenous American ancestry. Fine-mapping of expression quantitative trait loci (eQTLs) in individuals with predominantly African or Indigenous American ancestry revealed ancestry-specific eQTLs in over 30% of heritable genes. We leveraged our data to train genetically derived transcriptome prediction models, which identified significantly more associated genes when applied to 28 traits from a multi-ancestry population. Our findings underscore the importance of increasing representation from ancestrally diverse populations in genomic studies to enable new discoveries and ensure their equitable translation.

scholarly journals Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program

2018 ◽  
Author(s):  
Mónica Chagoyen ◽  
Juan F Poyatos
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Physiological State ◽  
Transcriptional Program ◽  
Expression Change ◽  
Regulatory Strategies ◽  
Genetic Perturbations ◽  
Specific Regulation ◽  
Using Data ◽  
The One

AbstractEnvironmental or genetic perturbations lead to gene expression changes. While most analyses of these changes emphasize the presence of qualitative differences on just a few genes, we now know that changes are widespread. This large-scale variation has been linked to the exclusive influence of a global transcriptional program determined by the new physiological state of the cell. However, given the sophistication of eukaryotic regulation, we expect to have a complex architecture of specific control affecting this program. Here, we examine this architecture. Using data of Saccharomyces cerevisiae expression in different nutrient conditions, we first propose a five-sector genome partition, which integrates earlier models of resource allocation, as a framework to examine the deviations from the global control. In this scheme, we recognize invariant genes, whose regulation is dominated by physiology, specific genes, which substantially depart from it, and two additional classes that contain the frequently assumed growth-dependent genes. Whereas the invariant class shows a considerable absence of specific regulation, the rest is enriched by regulation at the level of transcription factors (TFs) and epigenetic modulators. We nevertheless find markedly different strategies in how these classes deviate. On the one hand, there are TFs that act in a unique way between partition constituents, and on the other, the action of chromatin modifiers is significantly diverse. The balance between regulatory strategies ultimately modulates the action of the general transcription machinery and therefore limits the possibility of establishing a unifying program of expression change at a genomic scale.

scholarly journals Genome-Wide Analysis of DNA Methylation and the Gene Expression Change in Lung Cancer

2012 ◽  
Vol 7 (1) ◽  
pp. 20-33 ◽  
Author(s):  
Yong-Jae Kwon ◽  
Seog Joo Lee ◽  
Jae Soo Koh ◽  
Sung Han Kim ◽  
Hae Won Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Dna Methylation ◽  
Gene Expression Change ◽  
Expression Change ◽  
Genome Wide Analysis ◽  
Genome Wide

BTG1, a Gene Frequently Deleted in Pre-B ALL, Controls Glucocorticoid Receptor-Mediated Gene Expression.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3458-3458
Author(s):  
Frank N. van Leeuwen ◽  
Joost Casper van Galen ◽  
Roland P. Kuiper ◽  
Liesbeth van Emst ◽  
Marloes R Levers ◽  
...  
Keyword(s):  
Gene Expression ◽  
Conflicts Of Interest ◽  
Gene Promoter ◽  
Single Copy ◽  
Model Systems ◽  
Dependent Manner ◽  
Methyl Transferase ◽  
Genome Wide ◽  
Fold Reduction ◽  
Potential Tumor Suppressor

Abstract Abstract 3458 Poster Board III-346 Background By genome wide profiling we have found that about 10 % of pediatric pre-B ALL cases contain a (single copy) deletion of the B cell translocation gene 1 (BTG1) gene. BTG1 belongs to a family of potential tumor suppressor genes, which include BTG2, BTG3, TOB and TOB2. Proteins encoded by members of this gene family have been implicated in the induction of growth arrest or apoptosis in a variety of model systems. Moreover, BTG1 associates with and regulates the activity of the arginine methyl transferase PRMT1, a coactivator of nuclear receptor-mediated transcription. Hence we hypothesized that loss of BTG1 function, for instance due to deletion, may affect glucocorticoid induced therapy responses in ALL. Results Using RNA interference, we find that loss of BTG1 expression decreases sensitivity of pre-B ALL cells to the apoptosis-inducing effects of synthetic GCs about 10,000 fold (Figure). This acquired GC resistance is accompanied by a greater than 10 fold reduction in GR protein expression as well as a (near complete) loss of GC-induced gene expression. Conversely, re-expression of BTG1 restores GC sensitivity by potentiating GC-induced GR expression. By chromatin immunoprecipitations using anti PRMT1 antibodies we show that PRMT1 is recruited to the GR gene promoter in a BTG1-dependent manner, consistent with a role for this arginine methyl transferase in the regulation of GR-mediated gene expression. Conclusions Together, our results demonstrate the importance of the BTG1/PRMT1 complex in regulating GR-mediated gene expression and reveal how deregulation of the this complex can give rise to GC resistance. Targeting of these coactivators as part of the GR regulatory circuitry could offer novel opportunities for improving the efficacy of GC based therapies in ALL as well as other hematological malignancies. Disclosures No relevant conflicts of interest to declare.

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