Unraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation

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.

Download Full-text

Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells

Protein & Cell ◽

10.1007/s13238-020-00794-8 ◽

2020 ◽

Author(s):

Lei Chang ◽

Mengfan Li ◽

Shipeng Shao ◽

Chen Li ◽

Shanshan Ai ◽

...

Keyword(s):

Nuclear Periphery ◽

Three Dimensional ◽

Higher Order ◽

Order Structure ◽

Chromatin Dynamics ◽

Lamin B1 ◽

Chromatin Architecture ◽

Chromatin Interactions ◽

Molecular Machinery

Abstract The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood. Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to detachment of lamina-associated domains (LADs) from the nuclear periphery accompanied with global chromatin redistribution and decompaction. Consequently, the inter-chromosomal as well as inter-compartment interactions are increased, but the structure of topologically associating domains (TADs) is not affected. Using live-cell genomic loci tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm. Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, chromatin compaction, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.

Download Full-text

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

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.774719 ◽

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.

Download Full-text

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

Genome Research ◽

10.1101/gr.201624.115 ◽

2016 ◽

Vol 26 (9) ◽

pp. 1188-1201 ◽

Cited By ~ 48

Author(s):

A. Rasim Barutcu ◽

Bryan R. Lajoie ◽

Andrew J. Fritz ◽

Rachel P. McCord ◽

Jeffrey A. Nickerson ◽

...

Keyword(s):

Gene Expression ◽

Epithelial Cells ◽

Chromatin Structure ◽

Mammary Epithelial Cells ◽

Higher Order ◽

Mammary Epithelial

Download Full-text

Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells

10.1101/569004 ◽

2019 ◽

Author(s):

Mengyi Sun ◽

Jianzhi Zhang

Keyword(s):

Gene Expression ◽

Mammalian Cells ◽

Three Dimensional ◽

Sequencing Data ◽

Chromatin Dynamics ◽

Gene Expression Noise ◽

Genes Encoding ◽

The Face ◽

Allele Specific ◽

Genomic Scale

ABSTRACTGene expression is subject to stochastic noise, but to what extent and by which means such stochastic variations are coordinated among different genes are unclear. We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics, and verify it at the genomic scale using allele-specific single-cell RNA-sequencing data of mouse cells. Unexpectedly, the co-fluctuation extends to genes that are over 60 million bases apart. We provide evidence that this long-range effect arises in part from chromatin co-accessibilities of linked loci attributable to three-dimensional proximity, which is much closer intra-chromosomally than inter-chromosomally. We further show that genes encoding components of the same protein complex tend to be chromosomally linked, likely resulting from natural selection for intracellular among-component dosage balance. These findings have implications for both the evolution of genome organization and optimal design of synthetic genomes in the face of gene expression noise.

Download Full-text

DNA methylation in transposable elements disrupts the connection between three-dimensional chromatin organization and gene expression upon rice genome duplication.

10.1101/2021.12.15.472849 ◽

2021 ◽

Author(s):

Zhenfei Sun ◽

Yunlong Wang ◽

Zhaojian Song ◽

Hui Zhang ◽

Min Ma ◽

...

Keyword(s):

Gene Expression ◽

Transposable Elements ◽

Genome Duplication ◽

Rice Genome ◽

Three Dimensional ◽

Plant Evolution ◽

Chromatin Organization ◽

Regulatory Sequences ◽

Chromosome Conformation ◽

Significant Difference

Polyploidy serves as a major force in plant evolution and domestication of cultivated crops. However, the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene expression upon rice genome duplication is largely unknown. Here we compared the 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice by high-throughput chromosome conformation capture analysis, and found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor. Moreover, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domain (TAD) and loops uncouple from gene expression. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are not related to their expressions. Importantly, in contrast to that there was no significant difference of methylation levels in TEs in promoters of differentially expressed genes (DEGs) and non-DEGs between 2C and 4C rice, we found that the hypermethylated transposable elements across genes in compartment A/B switched regions and TAD boundaries suppress the expression of these genes. We propose that the rice genome doubling might modulate TE methylation which results in the disconnection between the alteration of 3D chromatin structure and gene expression.

Download Full-text

Chromatin-lamin B1 interaction promotes genomic compartmentalization and constrains chromatin dynamics

10.1101/601849 ◽

2019 ◽

Cited By ~ 2

Author(s):

Lei Chang ◽

Mengfan Li ◽

Shipeng Shao ◽

Boxin Xue ◽

Yingping Hou ◽

...

Keyword(s):

Higher Order ◽

Order Structure ◽

Chromatin Dynamics ◽

Lamin B1 ◽

Structure And Dynamics ◽

Chromatin Architecture ◽

Topologically Associating Domains ◽

Chromosomal Territory ◽

Molecular Machinery

AbstractThe eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized chromatin architecture and dynamics remains poorly understood. Here by combining imaging and Hi-C sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to chromatin redistribution and decompaction. Consequently, the inter-chromosomal interactions and overlap between chromosome territories are increased. Moreover, Hi-C data revealed that lamin B1 is required for the integrity and segregation of chromatin compartments but not for the topologically associating domains (TADs). We further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nuclear interior. Taken together, our data suggest that chromatin-lamin B1 interactions promote chromosomal territory segregation and genomic compartmentalization, and confine chromatin dynamics, supporting its crucial role in chromatin higher-order structure and dynamics.

Download Full-text

The ISWI Chromatin-Remodeling Protein Is Required for Gene Expression and the Maintenance of Higher Order Chromatin Structure In Vivo

Molecular Cell ◽

10.1016/s1097-2765(00)80430-x ◽

2000 ◽

Vol 5 (2) ◽

pp. 355-365 ◽

Cited By ~ 238

Author(s):

Renate Deuring ◽

Laura Fanti ◽

Jennifer A Armstrong ◽

Melinda Sarte ◽

Ophelia Papoulas ◽

...

Keyword(s):

Gene Expression ◽

Chromatin Remodeling ◽

Chromatin Structure ◽

Higher Order

Download Full-text

Abstract 355: Systems Epigenomics of Chromatin Structure in the Heart

Circulation Research ◽

10.1161/res.111.suppl_1.a355 ◽

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.

Download Full-text