Abstract 355: Systems Epigenomics of Chromatin Structure in the Heart

2012 ◽  
Vol 111 (suppl_1) ◽  
Author(s):  
Sarah Franklin ◽  
Haodong Chen ◽  
Elaheh Karbassi ◽  
Emma Monte ◽  
Thomas M Vondriska
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Chromatin Structure ◽  
Genomic Structure ◽  
Structural Proteins ◽  
Basic Question ◽  
Cell Type ◽  
Chromatin Structural ◽  
Genomic Scale ◽  
Cell Type Specific

Except during metaphase, endogenous chromatin structure is unknown. DNA - invariant between cells - and the cell type-specific modifiers of the genome establish chromatin structural features, both local (e.g. at the scale of individual nucleosomes) and global (e.g. chromosomal territories). A fundamental question is how these cell type-specific modifiers, including DNA modification, non-coding RNAs, and proteins, establish the chromatin environment conducive to gene expression for the correct cell type: in cardiac muscle, how is the genome structurally poised to confer cardiac (and not, say, renal) transcriptomes and proteomes, and what physical reprogramming events occur during disease? To address these questions, we are conducting a systems analysis of the epigenetic features of the healthy and diseased heart. In adult mice, we have used quantitative mass spectrometry to dissect distinct fractions of the nucleus and reveal the itineraries of chromatin structural proteins, enzymatic nucleosome remodelers, histone molecules and histone post-translational modifications. These studies have revealed rules for global reprogramming of gene expression, which involve altered abundance of non-histone chromatin structural proteins, a shift from hetero- towards euchromatic post-translational marks and a decreased linker to core histone ratio in heart failure. Furthermore, interrogation of genome-wide binding patterns of known cardiac transcription factors within the genes that encode proteins operative in cardiac genomic structure reveals hierarchical relationships between these protein, transcript and gene networks. Complementary investigations in isolated myocytes are characterizing the global rearrangement of chromatin following hypertrophic agonist treatment using conventional and super-resolution microscopy to directly visualize the chromatin backbone. Lastly, a combination of multiple genomic scale sequencing studies have revealed regions under control of specific chromatin structural proteins. Together, these studies aim to address the basic question of how global chromatin structure is maintained in cardiac myocytes and how diseases like heart failure result from deranged chromatin structure on a genomic scale.

Abstract 115: Cell-type-specific Gene Expression And Transcriptional Networks Reveal Adamts2 As A Powerful Regulator Of Cardiac Homeostasis During Heart Failure

2021 ◽  
Vol 129 (Suppl_1) ◽  
Author(s):  
Caitlin Lahue ◽  
Douglas Chapski ◽  
Manuel Rosa Garrido ◽  
Shuxun Ren ◽  
Thomas M Vondriska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Careful Examination ◽  
Transcriptional Networks ◽  
Tunel Staining ◽  
Specific Gene ◽  
Paracrine Signaling ◽  
Cell Type ◽  
Specific Gene Expression ◽  
Cell Type Specific

Background: Heart failure (HF) is a highly heterogeneous disorder characterized by the interactions of multiple genetic and environmental factors as well as the interaction of different cell types in the heart. Although reductionistic approaches have successfully identified many genes involved in HF, heritability studies suggest that many genes have resisted discovery through these approaches. By utilizing cell-type-specific gene expression paired with transcriptomic data from a large cohort of mice, we sought to identify important drivers of HF using a systems genetics approach. Methods and Results: Mice from 93 unique inbred lines of the Hybrid Mouse Diversity Panel were given 30 ug/g/day of isoproterenol for three weeks via osmotic minipump to induce heart failure. Transcriptomes were generated from these mice and the weighted Maximal Information Component Analysis (wMICA) algorithm was applied to generate transcriptomic gene networks. Cardiomyocytes and Fibroblasts were isolated from both control and isoproterenol-treated adult C57BL/6J hearts using a Langendorff apparatus (n=3 per sex/treatment) and transcriptomes were generated. Significantly differentially expressed genes were identified using DESEQ2 and used to query the wMICA-derived network, identifying the gene Adamts2 as a potential regulator of cardiac hypertrophy. Follow-up in vitro and in vivo work has demonstrated that Adamts2 knockdown significantly blunts the hypertrophic effect of isoproterenol on cardiomyocytes while simultaneously reducing fibroblast proliferation and increasing apoptosis as measured by TUNEL staining. Careful examination of the gene network reveals evidence of paracrine signaling between cardiomyocytes and fibroblasts and suggests a key trans-cell-type role of Adamts2 in the regulation of HF after catecholamine stimulation. Conclusion: Co-expression network algorithms combined with cell-type-specific transcriptomics identified Adamts2 as a driver of HF. Adamts2 plays an important role via paracrine signaling in the proliferative response of fibroblasts and the hypertrophic response of cardiomyocytes to catecholamines. Further mechanistic analysis of Adamts2 will further reveal its role in the progression of heart failure.

Analysis of Gene Expression Directed by a Thymic Locus Control in Transgenic Mice: Mechanisms and Application to Vectors for Gene Therapy

1996 ◽  
Vol 54 ◽  
pp. 22-23
Author(s):  
BJ Aronow ◽  
CA Ley ◽  
KC Ess ◽  
DP Witte
Keyword(s):  
Gene Expression ◽  
Gene Therapy ◽  
T Cells ◽  
Transgenic Mice ◽  
Chromatin Structure ◽  
Base Pair ◽  
Regulatory Elements ◽  
Gene Copy ◽  
Cell Type ◽  
Cell Type Specific

The formation of peripheral T cells from thymocyte progenitors is an intricate developmental process that requires the organized and coordinate expression of multiple genes. Adenosine deaminase (ADA) is an example of a gene that is subject to strong developmental regulation in T-cell precursors and is essential for the subsequent formation of T-cells in humans. We have sought to understand the mechanisms of ADA gene regulation from a basic point of view as well as to employ this to potential vectors for gene therapy.Using transgenic mice have shown that the first intron of the ADA gene contains a powerful locus control region that directs high level gene expression within cortical thymocytes. Based on extensive mutational analysis of the regulatory region and analyses of gene expression that include quantitative gene expression, in situ hybridization, and biochemical characterizations of chromatin structure, we have demonstrated that the intronic locus control region (LCR) consists of a hierarchically structured 2300 base pairs of DNA sequence (Figure 1). The LCR is composed of a series of regulatory elements that include a centrally positioned 300 base pair classical enhancer domain within which there is a critical 30 base pair enhancer core. Within this core, there is a single binding site for the transcription factor c-Myb that is required for activity of the enhancer core, the enhancer, and the intact LCR. Beyond the 300 bp enhancer core on either side the LCR contains novel and puzzling 1 kb non-enhancer sequences that we have termed facilitators. These sequences enable gene copy proportional expression by facilitating the ability of the enhancer to function in chromatin. The effects of the facilitators are evidenced by their ability to allow for insertion-site-independent and gene-copy-proportional expression and they prevent variegated expression among similarly differentiated cell types (Figure 2). Thus, total gene expression does not indicate proper cell type specific expression. The facilitators also allow for the formation of a strong tissue and cell type specific DNAse I hypersensitive site at the enhancer. This suggests that the formation of a discrete organized chromatin structure as a function of developmental differentiation requires extensive DNA sequences, only some of which are of the enhancer type. The capabilities of the facilitators to activate a chromatin domain may also suggest their potential usefulness in vectors for gene therapy of both ADA deficiency and possibly other human genetic diseases. However, the distance and non-enhancer nature of the facilitators suggest that they may act differently than conventional regulatory elements. In support of this, the facilitators obey a strict position and orientation rules with respect to the enhancer.

scholarly journals Single-cell dissection of live human hearts in ischemic heart disease and heart failure reveals cell-type-specific driver genes and pathways

2021 ◽  
Author(s):  
Suvi Linna-Kuosmanen ◽  
Eloi Schmauch ◽  
Kyriakitsa Galani ◽  
Carles A. Boix ◽  
Lei Hou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Heart Disease ◽  
Ischemic Heart Disease ◽  
Single Cell ◽  
Human Heart ◽  
Cell Types ◽  
Ischemic Heart ◽  
Cell Type ◽  
Cell Type Specific

Ischemic heart disease is the single most common cause of death worldwide with an annual death rate of over 9 million people. Genome-wide association studies have uncovered over 200 genetic loci underlying the disease, providing a deeper understanding of the causal mechanisms leading to it. However, in order to understand ischemic heart disease at the cellular and molecular level, it is necessary to identify the cell-type-specific circuits enabling dissection of driver variants, genes, and signaling pathways in normal and diseased tissues. Here, we provide the first detailed single-cell dissection of the cell types and disease-associated gene expression changes in the living human heart, using cardiac biopsies collected during open-heart surgery from control, ischemic heart disease, and ischemic and non-ischemic heart failure patients. We identify 84 cell types/states, grouped in 12 major cell types. We define markers for each cell type, providing the first extensive reference set for the live human heart. These major cell types include cardiovascular cells (cardiomyocytes, endothelial cells, fibroblasts), rarer cell types (B lymphocytes, neurons, Schwann cells), and rich populations of previously understudied layer-specific epicardial and endocardial cells. In addition, we reveal substantial differences in disease-associated gene expression at the cell subtype level, revealing arterial pericytes as having a central role in the pathogenesis of ischemic heart disease and heart failure. Our results demonstrate the importance of high-resolution cellular subtype mapping in gaining mechanistic insight into human cardiovascular disease.

scholarly journals Boundary sequences flanking the mouse tyrosinase locus ensure faithful pattern of gene expression

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Davide Seruggia ◽  
Almudena Fernández ◽  
Marta Cantero ◽  
Ana Fernández-Miñán ◽  
José Luis Gomez-Skarmeta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Cell Type ◽  
Chromosome Conformation ◽  
Control Of Gene Expression ◽  
Cell Type Specific

Abstract Control of gene expression is dictated by cell-type specific regulatory sequences that physically organize the structure of chromatin, including promoters, enhancers and insulators. While promoters and enhancers convey cell-type specific activating signals, insulators prevent the cross-talk of regulatory elements within adjacent loci and safeguard the specificity of action of promoters and enhancers towards their targets in a tissue specific manner. Using the mouse tyrosinase (Tyr) locus as an experimental model, a gene whose mutations are associated with albinism, we described the chromatin structure in cells at two distinct transcriptional states. Guided by chromatin structure, through the use of Chromosome Conformation Capture (3C), we identified sequences at the 5′ and 3′ boundaries of this mammalian gene that function as enhancers and insulators. By CRISPR/Cas9-mediated chromosomal deletion, we dissected the functions of these two regulatory elements in vivo in the mouse, at the endogenous chromosomal context, and proved their mechanistic role as genomic insulators, shielding the Tyr locus from the expression patterns of adjacent genes.

scholarly journals Boundary sequences flanking the mouse tyrosinase locus ensure faithful pattern of gene expression

2020 ◽  
Author(s):  
Davide Seruggia ◽  
Almudena Fernández ◽  
Marta Cantero ◽  
Ana Fernández-Miñán ◽  
José Luis Gomez-Skarmeta ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Regulatory Sequences ◽  
Cell Type ◽  
Chromosome Conformation ◽  
Control Of Gene Expression ◽  
Cell Type Specific

ABSTRACTControl of gene expression is dictated by cell-type specific regulatory sequences that physically organize the structure of chromatin, including promoters, enhancers and insulators. While promoters and enhancers convey cell-type specific activating signals, insulators prevent the cross-talk of regulatory elements within adjacent loci and safeguard the specificity of action of promoters and enhancers towards their targets in a tissue specific manner. Using the mouse tyrosinase (Tyr) locus as an experimental model, a gene whose mutations are associated with albinism, we described the chromatin structure in cells at two distinct transcriptional states. Guided by chromatin structure, through the use of Chromosome Conformation Capture (3C), we identified sequences at the 5’ and 3’ boundaries of this mammalian gene that function as enhancers and insulators. By CRISPR/Cas9-mediated chromosomal deletion, we dissected the functions of these two regulatory elements in vivo in the mouse, at the endogenous chromosomal context, and proved their role as genomic insulators, shielding the Tyr locus from the expression patterns of adjacent genes.

scholarly journals Cortical structural differences in major depressive disorder correlate with cell type-specific transcriptional signatures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jiao Li ◽  
Jakob Seidlitz ◽  
John Suckling ◽  
Feiyang Fan ◽  
Gong-Jun Ji ◽  
...  
Keyword(s):  
Gene Expression ◽  
Major Depressive Disorder ◽  
Depressive Disorder ◽  
Structural Changes ◽  
Brain Regions ◽  
Cell Type ◽  
Major Depressive ◽  
Structural Differences ◽  
Neuroimaging Data ◽  
Cell Type Specific

AbstractMajor depressive disorder (MDD) has been shown to be associated with structural abnormalities in a variety of spatially diverse brain regions. However, the correlation between brain structural changes in MDD and gene expression is unclear. Here, we examine the link between brain-wide gene expression and morphometric changes in individuals with MDD, using neuroimaging data from two independent cohorts and a publicly available transcriptomic dataset. Morphometric similarity network (MSN) analysis shows replicable cortical structural differences in individuals with MDD compared to control subjects. Using human brain gene expression data, we observe that the expression of MDD-associated genes spatially correlates with MSN differences. Analysis of cell type-specific signature genes suggests that microglia and neuronal specific transcriptional changes account for most of the observed correlation with MDD-specific MSN differences. Collectively, our findings link molecular and structural changes relevant for MDD.

scholarly journals Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
John A. Halsall ◽  
Simon Andrews ◽  
Felix Krueger ◽  
Charlotte E. Rutledge ◽  
Gabriella Ficz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Histone Modifications ◽  
Expression Patterns ◽  
Cell Types ◽  
Cell Type ◽  
Bar Code ◽  
Genes Encoding ◽  
Cell Type Specific ◽  
Rolling Windows

AbstractChromatin configuration influences gene expression in eukaryotes at multiple levels, from individual nucleosomes to chromatin domains several Mb long. Post-translational modifications (PTM) of core histones seem to be involved in chromatin structural transitions, but how remains unclear. To explore this, we used ChIP-seq and two cell types, HeLa and lymphoblastoid (LCL), to define how changes in chromatin packaging through the cell cycle influence the distributions of three transcription-associated histone modifications, H3K9ac, H3K4me3 and H3K27me3. We show that chromosome regions (bands) of 10–50 Mb, detectable by immunofluorescence microscopy of metaphase (M) chromosomes, are also present in G1 and G2. They comprise 1–5 Mb sub-bands that differ between HeLa and LCL but remain consistent through the cell cycle. The same sub-bands are defined by H3K9ac and H3K4me3, while H3K27me3 spreads more widely. We found little change between cell cycle phases, whether compared by 5 Kb rolling windows or when analysis was restricted to functional elements such as transcription start sites and topologically associating domains. Only a small number of genes showed cell-cycle related changes: at genes encoding proteins involved in mitosis, H3K9 became highly acetylated in G2M, possibly because of ongoing transcription. In conclusion, modified histone isoforms H3K9ac, H3K4me3 and H3K27me3 exhibit a characteristic genomic distribution at resolutions of 1 Mb and below that differs between HeLa and lymphoblastoid cells but remains remarkably consistent through the cell cycle. We suggest that this cell-type-specific chromosomal bar-code is part of a homeostatic mechanism by which cells retain their characteristic gene expression patterns, and hence their identity, through multiple mitoses.

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