scholarly journals High-resolution TADs reveal DNA sequences underlying genome organization in flies

2017 ◽  
Author(s):  
Fidel Ramírez ◽  
Vivek Bhardwaj ◽  
José Villaveces ◽  
Laura Arrigoni ◽  
Björn A. Grüning ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Sequences ◽  
Spatial Organization ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Open Chromatin ◽  
Promoter Regions ◽  
Dna Motifs ◽  
3D Genome ◽  
Eukaryotic Chromatin

AbstractEukaryotic chromatin is partitioned into domains called TADs that are broadly conserved between species and virtually identical among cell types within the same species. Previous studies in mammals have shown that the DNA binding protein CTCF and cohesin contribute to a fraction of TAD boundaries. Apart from this, the molecular mechanisms governing this partitioning remain poorly understood. Using our new software, HiCExplorer, we annotated high-resolution (570 bp) TAD boundaries in flies and identified eight DNA motifs enriched at boundaries. Known insulator proteins bind five of these motifs while the remaining three motifs are novel. We find that boundaries are either at core promoters of active genes or at non-promoter regions of inactive chromatin and that these two groups are characterized by different sets of DNA motifs. Most boundaries are present at divergent promoters of constitutively expressed genes and the gene expression tends to be coordinated within TADs. In contrast to mammals, the CTCF motif is only present on 2% of boundaries in flies. We demonstrate that boundaries can be accurately predicted using only the motif sequences, along with open chromatin, suggesting that DNA sequence encodes the 3D genome architecture in flies. Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogeome.ie-freiburg.mpg.de.

scholarly journals Chromatin loop anchors contain core structural components of the gene expression machinery in maize

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Stéphane Deschamps ◽  
John A. Crow ◽  
Nadia Chaidir ◽  
Brooke Peterson-Burch ◽  
Sunil Kumar ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Transcriptional Activity ◽  
Spatial Organization ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Maize Genome ◽  
Chromatin Loop ◽  
Structural Components ◽  
Chromatin Loops

Abstract Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.

3D genome structure reconstruction from chromosomal contact data

2017 ◽  
Author(s):  
◽  
Tuan Anh Trieu
Keyword(s):  
High Resolution ◽  
Genome Structure ◽  
Cell Types ◽  
3D Models ◽  
Graphic User Interface ◽  
Soft Constraints ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Manual Adjustment ◽  
The Relationship

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Different cell types of an organism have the same DNA sequence, but they can function differently because their difference in 3D organization allows them to express different genes and has different cellular functions. Understanding the 3D organization of the genome is the key to understand functions of the cell. Chromosome conformation capture techniques like Hi-C and TCC that can capture interactions between proximal chromosome fragments have allowed the study of 3D genome organization in high resolution and high through-put. My work focuses on developing computational methods to reconstruct 3D genome structures from Hi-C data. I presented three methods to reconstruct 3D genome and chromosome structures. The first method can build 3D genome models from soft constraints of contacts and non-contacts. This method utilizes the concept of contact and non-contact to reconstruct 3D models without translating interaction frequencies into physical distances. The translation is commonly used by other methods even though it makes a strong assumption about the relationship between interaction frequencies and physical distances. In synthetic dataset, when the relationship was known, my method performed comparably with other methods assuming the relationship. This shows the potential of my method for real Hi-C datasets where the relationship is unknown. The limitation of the method is that it has parameters requiring manual adjustment. I developed the second method to reconstruct 3D genome models. This method utilizes a commonly used function to translate interaction frequencies to physical distances to build 3D models. I proposed a novel way to derive soft constraints to handle inconsistency in the data and to make the method robust. Building 3D models at high resolution is a more challenging problem as the number of constraints is small and the feasible space is larger. I introduced a third method to build 3D chromosome models at high resolution. The method reconstructs models at low resolution and then uses them to guide the reconstruction of models at high resolution. The last part of my work is the development of a comprehensive tool with intuitive graphic user interface to analyze Hi-C data, reconstruct and analyze 3D models.

scholarly journals DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

2020 ◽  
Author(s):  
Hanqing Liu ◽  
Jingtian Zhou ◽  
Wei Tian ◽  
Chongyuan Luo ◽  
Anna Bartlett ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mouse Brain ◽  
Spatial Organization ◽  
Brain Area ◽  
Cell Types ◽  
Regulatory Elements ◽  
Mammalian Brain ◽  
Open Chromatin ◽  
Cell Type ◽  
Single Nucleus

SummaryMammalian brain cells are remarkably diverse in gene expression, anatomy, and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. We carried out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single nucleus DNA methylation sequencing to profile 110,294 nuclei from 45 regions of the mouse cortex, hippocampus, striatum, pallidum, and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements, and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types, and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, an artificial neural network model was constructed that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data allowed prediction of high-confidence enhancer-gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse brain.

scholarly journals WhichTF is dominant in your open chromatin data?

2019 ◽  
Author(s):  
Yosuke Tanigawa ◽  
Ethan S. Dyer ◽  
Gill Bejerano
Keyword(s):  
Cell Fate ◽  
Molecular Mechanisms ◽  
Computational Prediction ◽  
Cell Types ◽  
Mouse Cell ◽  
Careful Consideration ◽  
Computational Method ◽  
Open Chromatin ◽  
Differential Analysis ◽  
Putative Gene

AbstractWe present WhichTF, a novel computational method to identify dominant transcription factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF integrates high-confidence genome-wide computational prediction of TF binding sites based on evolutionary sequence conservation, putative gene-regulatory models, and ontology-based gene annotations. Applying WhichTF, we find that the identified dominant TFs have been implicated as functionally important in well-studied cell types, such as NF-κB family members in lymphocytes and GATA factors in cardiac tissue. To distinguish the transcriptional regulatory landscape in closely related samples, we devise a differential analysis framework and demonstrate its utility in lymphocyte, mesoderm developmental, and disease cells. We also find TFs known for stress response in multiple samples, suggesting routine experimental caveats that warrant careful consideration. WhichTF yields biological insight into known and novel molecular mechanisms of TF-mediated transcriptional regulation in diverse contexts, including human and mouse cell types, cell fate trajectories, and disease-associated tissues.

scholarly journals ECOA-5. Integrative 3D spatial characterization of genomic and epigenomic intratumoral heterogeneity in glioblastoma

2021 ◽  
Vol 3 (Supplement_2) ◽  
pp. ii2-ii2
Author(s):  
Radhika Mathur ◽  
Qixuan Wang ◽  
Patrick Schupp ◽  
Stephanie Hilz ◽  
Chibo Hong ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Spatial Location ◽  
Cell Types ◽  
Intratumoral Heterogeneity ◽  
Tumor Evolution ◽  
Open Chromatin ◽  
Spatial Characterization

Abstract Treatment failure in glioblastoma is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and selection of therapy-resistant clones. While genomic alterations are known contributors to ITH, emerging studies highlight functional roles for epigenomic ITH which integrates differentiation status, stochastic events, and microenvironmental inputs. Here, we have established a novel platform for integrative characterization of genomic and epigenomic ITH of glioblastoma in three-dimensional (3-D) space. In collaboration with neurosurgeons and biomedical imaging experts, we utilize 3-D surgical neuro-navigation to safely acquire ~10 tumor samples per patient representing maximal anatomical diversity. We conduct whole-exome sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-Seq) on each sample. The spatial location of each sample is mapped by its 3-D coordinates, allowing 360-degree visualization of genomic and epigenomic ITH for each patient. We demonstrate this approach on 8 patients with primary IDH-WT glioblastoma (83 spatially mapped samples), providing unprecedented insight into their spatial organization at the genomic and epigenomic levels. We link genetically defined tumor subclones to patterns of open chromatin and gene regulation, revealing underlying transcription factor binding at active promoters and enhancers. We also identify ITH in whole-genome doubling and focal oncogene amplification events in multiple patients, which we then link with epigenomic ITH. Further, to study microenvironmental inputs and their contribution to epigenomic ITH, we conduct deconvolution of RNA sequencing and ATAC-Seq data by analyzing feature co-variation. We resolve the 3-D spatial organization of immune, neural, and other nontumor cell types present in glioblastoma, characterizing their functional states and interactions with tumor cells. This work provides the most comprehensive spatial characterization of genomic and epigenomic ITH to date in glioblastoma. As a resource for further investigation, we have developed an interactive data sharing platform – The 3D Glioma Atlas – that enables 360-degree visualization of both genomic and epigenomic ITH.

scholarly journals Molecular Aspects of Regeneration Mechanisms in Holothurians

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 250 ◽  
Author(s):  
Igor Yu. Dolmatov
Keyword(s):  
Spatial Organization ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Molecular Data ◽  
The Body ◽  
Matrix Remodeling ◽  
Oxygen Species ◽  
Morphological And Molecular Data ◽  
Molecular Aspects ◽  
Different Cell Types

Holothurians, or sea cucumbers, belong to the phylum Echinodermata. They show good regenerative abilities. The present review provides an analysis of available data on the molecular aspects of regeneration mechanisms in holothurians. The genes and signaling pathways activated during the asexual reproduction and the formation of the anterior and posterior parts of the body, as well as the molecular mechanisms that provide regeneration of the nervous and digestive systems, are considered here. Damage causes a strong stress response, the signs of which are recorded even at late regeneration stages. In holothurian tissues, the concentrations of reactive oxygen species and antioxidant enzymes increase. Furthermore, the cellular and humoral components of the immune system are activated. Extracellular matrix remodeling and Wnt signaling play a major role in the regeneration in holothurians. All available morphological and molecular data show that the dedifferentiation of specialized cells in the remnant of the organ and the epithelial morphogenesis constitute the basis of regeneration in holothurians. However, depending on the type of damage, the mechanisms of regeneration may differ significantly in the spatial organization of regeneration process, the involvement of different cell types, and the depth of reprogramming of their genome (dedifferentiation or transdifferentiation).

scholarly journals DNA methylation atlas of the mouse brain at single-cell resolution

Nature ◽  
2021 ◽  
Vol 598 (7879) ◽  
pp. 120-128 ◽  
Author(s):  
Hanqing Liu ◽  
Jingtian Zhou ◽  
Wei Tian ◽  
Chongyuan Luo ◽  
Anna Bartlett ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mouse Brain ◽  
Spatial Organization ◽  
Brain Area ◽  
Cell Types ◽  
Regulatory Elements ◽  
Mammalian Brain ◽  
Open Chromatin ◽  
Cell Type ◽  
Single Nucleus

AbstractMammalian brain cells show remarkable diversity in gene expression, anatomy and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. Here we carry out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single-nucleus DNA methylation sequencing1,2 to profile 103,982 nuclei (including 95,815 neurons and 8,167 non-neuronal cells) from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, we constructed an artificial neural network model that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data3 enabled prediction of high-confidence enhancer–gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments4. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse cerebrum.

scholarly journals Chromatin Loop Anchors Are Core Structural Components of the Gene Expression Machinery in Maize

2020 ◽  
Author(s):  
Stephane Deschamps ◽  
John A Crow ◽  
Nadia Chaidir ◽  
Brooke Peterson-Burch ◽  
Sunil Kumar ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Transcriptional Activity ◽  
Spatial Organization ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Chromatin Loop ◽  
Chromatin Loops

Abstract Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with transcriptional activity. Chromatin loops, made of two “anchors” flanking a loop “interior”, overlap with up to 90% of high-resolution interaction domains from a previous public maize interactome dataset. A majority of all anchors are shared between multiple loops, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analysis indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Up to 63% of all unique variants derived from a prior public maize eQTL datasets overlap with Hi-C loop anchors. Anchor annotation suggests that <7% of all loops detected from one Hi-C library are potentially devoid of any genes or regulatory elements. The overall conservation and organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions A majority of expressed genes and open chromatin regions co-locate with a conserved set of chromatin loop anchors. The results presented here will be a useful reference to further investigate the function of chromatin loop anchors and of the formation of interaction regions in the regulation of gene expression in maize.

Abstract 066: Enhancer Repertoires That Define Renin Cell Identity

Hypertension ◽  
2016 ◽  
Vol 68 (suppl_1) ◽  
Author(s):  
Maria F Martinez ◽  
Silvia Medrano ◽  
Masafumi Oka ◽  
Ellen S Pentz ◽  
Allan W Dickerman ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Cell Phenotype ◽  
Open Chromatin ◽  
Independent Manner ◽  
Cell Identity ◽  
Genome Wide ◽  
Renin Gene ◽  
Chromatin Configuration

Control of the renin cell phenotype is crucial for the regulation of blood pressure and fluid- electrolyte homeostasis. Enhancers are cis -acting DNA sequences that harbor distinct chromatin features and regulate gene expression in an orientation-independent manner. Recently, clusters of enhancers or super-enhancers (SE) highly enriched with master transcription factors, possessing open chromatin configuration and in close proximity to cell-identity genes have been proposed. We tested the hypothesis that renin cells have unique repertoires of enhancers and super-enhancers, distinct from other cell types. Those regulatory clusters may in turn confer the identity of renin cells. To define the genome-wide enhancer landscape characteristic of renin cells, we studied As4.1 cells, kidney tumor cells that express renin constitutively, and native renin cells sorted from the kidneys of Ren1cKO-YFP + mice. In these mice, the renin promoter drives YFP expression thus marking the renin cells. We used genome-wide ChIP-Seq for Med1 (subunit 1 of the Mediator complex), H3K27Ac (active enhancers) and Pol II (to visualize putative genomic areas undergoing transcription). The ROSE algorithm we used to ascertain super-enhancers. Chromatin accessibility genome-wide was assessed using ATAC-Seq. The results were compared to twenty-one other cell types that do not express renin. In As4.1 cells, we identified 14,871 enhancers based on H3K27Ac. Of those, 888 were classified as super-enhancers. The Med1 signal in As4.1 cells showed a SE localized 5kb upstream the Ren1 gene, which was ranked at position 25 among other SEs. The H3K27Ac signal showed highest occupancy in the same region. ChIP-Seq for H3K27Ac in YFP + cells showed 211 SEs of 2,987 peaks. The SE for the renin gene possessed the highest signal and ranked number 1, indicating its importance in renin cells. One hundred and thirteen SEs were unique to renin cells, including the SE associated with the renin gene. ATAC-Seq signals overlapped with the renin SE and the classical enhancer indicating that the chromatin was accessible for transcription. In summary, renin-expressing cells possess distinct repertoires of unique enhancers and super-enhancers that acting in concert are likely to determine the renin phenotype.

scholarly journals Systematic evaluation of chromosome conformation capture assays

2020 ◽  
Author(s):  
Betul Akgol Oksuz ◽  
Liyan Yang ◽  
Sameer Abraham ◽  
Sergey V. Venev ◽  
Nils Krietenstein ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Cell Types ◽  
Chromosome Conformation Capture ◽  
Chromatin Interaction ◽  
Systematic Evaluation ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Experimental Parameters ◽  
Genome Features ◽  
Multiple Cell

AbstractChromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of cross-linkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthens the compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results for multiple cell types and cell cycle stages. We find that cell type-specific quantitative differences in chromosome folding are not detected or underestimated by some protocols. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using conventional Hi-C, Micro-C and Hi-C 3.0 for commonly used cell lines in the 4D Nucleome Project.

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