scholarly journals Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective

2021 ◽  
Vol 9 ◽  
Author(s):  
Suresh Kumar ◽  
Simardeep Kaur ◽  
Karishma Seem ◽  
Santosh Kumar ◽  
Trilochan Mohapatra
Keyword(s):  
Gene Expression ◽  
Environmental Stress ◽  
Genome Organization ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Regulatory Elements ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Chromatin Architecture ◽  
Capture Techniques

The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.

scholarly journals The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 289 ◽  
Author(s):  
Ping Hong ◽  
Hao Jiang ◽  
Weize Xu ◽  
Da Lin ◽  
Qian Xu ◽  
...  
Keyword(s):  
Target Genes ◽  
High Efficiency ◽  
New Technology ◽  
Three Dimensional ◽  
Large Data ◽  
Regulatory Elements ◽  
Chromosome Conformation Capture ◽  
Genome Chromosome ◽  
Chromosome Conformation ◽  
3D Genome

It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.

scholarly journals The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains

2018 ◽  
Author(s):  
TR Luperchio ◽  
MEG Sauria ◽  
VE Hoskins ◽  
X Wong ◽  
E DeBoy ◽  
...  
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Nuclear Lamina ◽  
Early Event ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Dynamic Relationship ◽  
Organizational Principles

AbstractThree-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.

scholarly journals Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells

2019 ◽  
Author(s):  
Vijay Ramani ◽  
Xinxian Deng ◽  
Ruolan Qiu ◽  
Choli Lee ◽  
Christine M Disteche ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Organization ◽  
Single Cells ◽  
Three Dimensional ◽  
Population Based ◽  
Order Structure ◽  
Chromosome Conformation ◽  
3D Genome ◽  
A Cell ◽  
Cell To Cell Variability

AbstractThe highly dynamic nature of chromosome conformation and three-dimensional (3D) genome organization leads to cell-to-cell variability in chromatin interactions within a cell population, even if the cells of the population appear to be functionally homogeneous. Hence, although Hi-C is a powerful tool for mapping 3D genome organization, this heterogeneity of chromosome higher order structure among individual cells limits the interpretive power of population based bulk Hi-C assays. Moreover, single-cell studies have the potential to enable the identification and characterization of rare cell populations or cell subtypes in a heterogeneous population. However, it may require surveying relatively large numbers of single cells to achieve statistically meaningful observations in single-cell studies. By applying combinatorial cellular indexing to chromosome conformation capture, we developed single-cell combinatorial indexed Hi-C (sci-Hi-C), a high throughput method that enables mapping chromatin interactomes in large number of single cells. We demonstrated the use of sci-Hi-C data to separate cells by karytoypic and cell-cycle state differences and to identify cellular variability in mammalian chromosomal conformation. Here, we provide a detailed description of method design and step-by-step working protocols for sci-Hi-C.

Umi-4C: A Quantitative, Robust and Multiplexed Method to Study the Regulatory Three Dimensional Chromatin Organization - Application for the Mgakaryocytic-Eythroid Lineage

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1183-1183
Author(s):  
Omer Schwartzman ◽  
Zohar Mukamel ◽  
Shai Izraeli ◽  
Amos Tanay
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Regulatory Elements ◽  
Chromatin Organization ◽  
Leukemia Cells ◽  
High Complexity ◽  
Physical Proximity ◽  
Specific Priming

Abstract Background: The role of the spatial three dimensional (3D) chromatin organization in regulation of gene expression is at the forefront of epigenetic research. Chromatin Conformation Capture (3C) technologies are increasingly being used to map physical proximity between distal regulatory elements. The underlying principal is similar in all these assays and involves chromatin cross-linking, digestion, and ligation. The proximity ligation junctions are then analyzed as a proxy to physical proximity. These methods vary in terms of scope and resolution, from Hi-C, which allows whole-genome coverage but requires massive sequencing burden, to traditional 3C which is simpler but allows only pairwise contact mapping. Of particular recent interest are methods allowing targeted sequencing of ligation products such as 4C-seq. However, 4C is heavily dependent on PCR amplification and requires elaborate statistical models to account for biases introduced. Consequently, a major drawback of all current methodologies is the lack of precise quantitation. To control for these drawbacks we developed a new simple and directly quantitative 4C methodology applying the concept of Unique Molecular Identifiers (UMI). Methods: We have developed a modified 4C-seq protocol (see figure). After the standard fixation, digestion and ligation, the chromatin DNA is sonicated, resulting in random breakpoints that are exploited as bona-fida UMIs. To target specific loci we utilize a version of ligation mediated (LM)-PCR, ligating a universal adapter to one end of the insert and a target-specific primer, to focus on the region of interest, to the other end. In addition, we developed a novel computational framework to process the data and filter potential artifacts and non-specific priming events. We applied this highly quantitative method to study the chromatin spatial landscape of important megakaryocytic and eryhtroid genes - GATA1, ANK1 and the HBB region. We generated high-complexity contact profiles of these regions in six cell lines - four Megaerythroid cell lines (CMK, CMY, K562 and CHRF), that express these genes at variable levels, and a T-ALL cell line (DND41) and primary human fibroblasts where these loci are silenced. Results: We are able to recover on average 5,000-20,000 ligation events per 1μg of starting 4C template. Estimating the sequencing requirement by inference and subsampling, we find that 500,000 reads are enough to recover more than 90% of the ligation events. By applying our assay to GATA1 locus we were able to detect and precisely quantify hotspots of differential contact intensity, likely to reflect differences in the contacting probabilities between erythroid and megakaryocytic cells. These regions coincided with active histone marks in either of the cell types. Next, we interrogated ANK1 promoter region and detected differential contact intensity of the promoter with enhancer elements -15kb, and -27kb upstream and +15kb downstream of the transcription start site (TSS). The differences were also correlated with the expression pattern of ANK1 in these cells. Finally we utilized our assay to multiplex different regions in the HBB locus and generated very high complexity contact profiles of the region revealing activity-associated hierarchical looping structure that was previously not described. Conclusions: We have developed a powerful sensitive methodology to study the chromatin structure of specific targets in a multiplexed, cost-effective and simple manner. We applied it to a variety of regions and cells and were able to precisely detect and quantify minute differences in contact intensities between cells belonging to related but different lineages. We suggest UMI-4C as a precise and practical tool to study 3D epigenetic regulation of gene expression. Figure 1. A scheme of the UMI-4C methodology and a snapshot of the GATA1 locus in CMK megakaryocytic-eryhthroid and K562 erythroid leukemia cells. Figure 1. A scheme of the UMI-4C methodology and a snapshot of the GATA1 locus in CMK megakaryocytic-eryhthroid and K562 erythroid leukemia cells. Disclosures No relevant conflicts of interest to declare.

scholarly journals Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages

2018 ◽  
Author(s):  
Evelien M. Bunnik ◽  
Kate B. Cook ◽  
Nelle Varoquaux ◽  
Gayani Batugedara ◽  
Jacques Prudhomme ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Genome Organization ◽  
Genome Structure ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Gene Families ◽  
Specific Gene ◽  
Heterochromatin Protein 1 ◽  
Malaria Parasites

ABSTRACTThe development of malaria parasites throughout their various life cycle stages is controlled by coordinated changes in gene expression. We previously showed that the three-dimensional organization of the P. falciparum genome is strongly associated with gene expression during its replication cycle inside red blood cells. Here, we analyzed genome organization in the P. falciparum and P. vivax transmission stages. Major changes occurred in the localization and interactions of genes involved in pathogenesis and immune evasion, erythrocyte and liver cell invasion, sexual differentiation and master regulation of gene expression. In addition, we observed reorganization of subtelomeric heterochromatin around genes involved in host cell remodeling. Depletion of heterochromatin protein 1 (PfHP1) resulted in loss of interactions between virulence genes, confirming that PfHP1 is essential for maintenance of the repressive center. Overall, our results suggest that the three-dimensional genome structure is strongly connected with transcriptional activity of specific gene families throughout the life cycle of human malaria parasites.

scholarly journals Three-Dimensional Genome Organization and Virulence in Apicomplexan Parasites

2019 ◽  
Vol 12 ◽  
pp. 251686571987943
Author(s):  
Todd Lenz ◽  
Karine G Le Roch
Keyword(s):  
Gene Expression ◽  
Genome Organization ◽  
Three Dimensional ◽  
Plasmodium Species ◽  
Babesia Microti ◽  
3 Dimensional ◽  
Apicomplexan Parasites ◽  
3D Genome ◽  
3D Architecture ◽  
Eukaryotic Organisms

Mounting evidence supports the idea that epigenetic, and the overall 3-dimensional (3D) architecture of the genome, plays an important role in gene expression for eukaryotic organisms. We recently used Hi-C methodologies to generate and compare the 3D genome of 7 different apicomplexan parasites, including several pathogenic and less pathogenic malaria parasites as well as related human parasites Babesia microti and Toxoplasma gondii. Our goal was to understand the possible relationship between genome organization, gene expression, and pathogenicity of these infectious agents. Collectively, our results demonstrate that spatial genome organization in most Plasmodium species is constrained by the colocalization of virulence genes that are unique in their effect on chromosome folding, indicating a link between genome organization and gene expression in more virulent pathogens.

scholarly journals Dynamics of the 4D genome during lineage specification, differentiation and maturation in vivo

2019 ◽  
Author(s):  
A. Marieke Oudelaar ◽  
Robert A. Beagrie ◽  
Matthew Gosden ◽  
Sara de Ornellas ◽  
Emily Georgiades ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Erythroid Differentiation ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Integrated Analysis ◽  
Chromosome Conformation ◽  
High Resolution Data ◽  
Chromatin Architecture

AbstractMammalian gene expression patterns are controlled by regulatory elements, which interact within Topologically Associating Domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. We developed Tiled-C, a low-input Chromosome Conformation Capture (3C) approach, to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of matched chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. In contrast to previous reports, our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity. Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development.

scholarly journals Unraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation

2021 ◽  
Author(s):  
Yi Zheng ◽  
Lingkai Zhang ◽  
Long Jin ◽  
Pengfei Zhang ◽  
Fuyuan Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Three Dimensional ◽  
Higher Order ◽  
Self Renewal ◽  
Chromosome Conformation ◽  
Chromatin Dynamics ◽  
Chromatin Architecture ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Chromatin Structural

Spermatogonial stem cells (SSCs) are able to undergo self-renewal and differentiation. Unlike the self-renewal that replenishes the SSC and progenitor pool, the differentiation is an irreversible process committed to meiosis. While the preparations for meiotic events in differentiating spermatogonia (Di-SG) are likely to be accompanied by alterations in chromatin structure, the three-dimensional (3D) chromatin architectural difference between SSCs and Di-SG, and the higher-order chromatin dynamics during spermatogonial differentiation, have not been systematically investigated. Here, we performed in situ high throughput chromosome conformation capture (Hi-C), RNA-sequencing (RNA-seq) and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses on porcine undifferentiated spermatogonia (Un-SG, which consist of SSCs and progenitors) and Di-SG. By integrating and analyzing these data, we identified that Di-SG exhibited increased disorder but weakened compartmentalization and topologically associating domains (TADs) in comparison with Un-SG, suggesting that diminished higher-order chromatin architecture in meiotic cells, as shown by recent reports, is preprogramed in Di-SG. Our data also revealed that A/B compartments and TADs were related to dynamic gene expression during spermatogonial differentiation. We further unraveled the contribution of promoter-enhancer interactions (PEIs) to pre-meiotic transcriptional regulation, which has not been accomplished in previous studies due to limited cell input and resolution. Together, our study uncovered the 3D chromatin structure of SSCs/progenitors and Di-SG, as well as the interplay between higher-order chromatin architecture and dynamic gene expression during spermatogonial differentiation, providing novel insights into the mechanisms for SSC self-renewal and differentiation and having implications for diagnosis and treatment of male sub-/infertility.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungusEpichloë festucae

2018 ◽  
Author(s):  
David J Winter ◽  
Austen RD Ganley ◽  
Carolyn A Young ◽  
Ivan Liachko ◽  
Christopher L Schardl ◽  
...  
Keyword(s):  
Genome Structure ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
In Planta ◽  
Repeat Elements ◽  
Symbiotic Relationships ◽  
3D Genome ◽  
Transcriptional Changes

AbstractStructural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organization influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus,Epichloë festucae. Coupling it with RNAseq and HiC data, we investigate how the structure of the genome contributes to the suite of transcriptional changes that anEpichloëspecies needs to maintain symbiotic relationships with its grass host. Our results reveal a unique “patchwork” genome, in which repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences. In contrast to other species, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.

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