scholarly journals Deciphering the species-level structure of topologically associating domains

2021 ◽  
Author(s):  
Rohit Singh ◽  
Bonnie Berger
Keyword(s):  
Cell Fate ◽  
Chromatin Structure ◽  
Time Course ◽  
Level Structure ◽  
Species Level ◽  
Cell Type ◽  
Systematic Analysis ◽  
Chromosome Conformation ◽  
Gene Coexpression ◽  
Topologically Associating Domains

Chromosome conformation capture technologies such as Hi-C have revealed a rich hierarchical structure of chromatin, with topologically associating domains (TADs) as a key organizational unit, but experimentally reported TAD architectures, currently determined separately for each cell type, are lacking for many cell/tissue types. A solution to address this issue is to integrate existing epigenetic data across cells and tissue types to develop a species-level consensus map relating genes to TADs. Here, we introduce the TAD Map, a bag-of-genes representation that we use to infer, or "impute", TAD architectures for those cells/tissues with limited Hi-C experimental data. The TAD Map enables a systematic analysis of gene coexpression induced by chromatin structure. By overlaying transcriptional data from hundreds of bulk and single-cell assays onto the TAD Map, we assess gene coexpression in TADs and find that expressed genes cluster into fewer TADs than would be expected by chance, and show that time-course and RNA velocity studies further reveal this clustering to be strongest in the early stages of cell differentiation; it is also strong in tumor cells. We provide a probabilistic model to summarize any scRNA-seq transcriptome in terms of its TAD activation profile, which we term a TAD signature, and demonstrate its value for cell type inference, cell fate prediction, and multimodal synthesis. More broadly, our work indicates that the TAD Map's comprehensive, quantitative integration of chromatin structure and scRNA-seq data should play a key role in epigenetic and transcriptomic analyses. Software availability: https://tadmap.csail.mit.edu

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 Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast

2017 ◽  
Author(s):  
Giuliano G Stirparo ◽  
Thorsten Boroviak ◽  
Ge Guo ◽  
Jennifer Nichols ◽  
Austin Smith ◽  
...  
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Cell Fate ◽  
Time Course ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Preimplantation Embryos ◽  
Integrated Analysis ◽  
Cell Type ◽  
Type Assignment

AbstractSingle-cell profiling techniques create opportunities to delineate cell fate progression in mammalian development. Recent studies provide transcriptome data from human preimplantation embryos, in total comprising nearly 2000 individual cells. Interpretation of these data is confounded by biological factors such as variable embryo staging and cell-type ambiguity, as well as technical challenges in the collective analysis of datasets produced with different sample preparation and sequencing protocols. Here we address these issues to assemble a complete gene expression time course spanning human preimplantation embryogenesis. We identify key transcriptional features over developmental time and elucidate lineage-specific regulatory networks. We resolve post hoc cell-type assignment in the blastocyst, and define robust transcriptional prototypes that capture epiblast and primitive endoderm lineages. Examination of human pluripotent stem cell transcriptomes in this framework identifies culture conditions that sustain a naïve state pertaining to the inner cell mass. Our approach thus clarifies understanding both of lineage segregation in the early human embryo and of in vitro stem cell identity, and provides an analytical resource for comparative molecular embryology.

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 Chromatin Manipulation and Editing: Challenges, New Technologies and Their Use in Plants

2021 ◽  
Vol 22 (2) ◽  
pp. 512
Author(s):  
Kateryna Fal ◽  
Denisa Tomkova ◽  
Gilles Vachon ◽  
Marie-Edith Chabouté ◽  
Alexandre Berr ◽  
...  
Keyword(s):  
Cell Fate ◽  
Dna Sequence ◽  
Zinc Finger ◽  
Chromatin Structure ◽  
New Technologies ◽  
Dna Interaction ◽  
The Other ◽  
Proof Of Concept ◽  
Epigenetic Marks ◽  
Molecular Events

An ongoing challenge in functional epigenomics is to develop tools for precise manipulation of epigenetic marks. These tools would allow moving from correlation-based to causal-based findings, a necessary step to reach conclusions on mechanistic principles. In this review, we describe and discuss the advantages and limits of tools and technologies developed to impact epigenetic marks, and which could be employed to study their direct effect on nuclear and chromatin structure, on transcription, and their further genuine role in plant cell fate and development. On one hand, epigenome-wide approaches include drug inhibitors for chromatin modifiers or readers, nanobodies against histone marks or lines expressing modified histones or mutant chromatin effectors. On the other hand, locus-specific approaches consist in targeting precise regions on the chromatin, with engineered proteins able to modify epigenetic marks. Early systems use effectors in fusion with protein domains that recognize a specific DNA sequence (Zinc Finger or TALEs), while the more recent dCas9 approach operates through RNA-DNA interaction, thereby providing more flexibility and modularity for tool designs. Current developments of “second generation”, chimeric dCas9 systems, aiming at better targeting efficiency and modifier capacity have recently been tested in plants and provided promising results. Finally, recent proof-of-concept studies forecast even finer tools, such as inducible/switchable systems, that will allow temporal analyses of the molecular events that follow a change in a specific chromatin mark.

scholarly journals Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development

2021 ◽  
Author(s):  
Ragini S Phansalkar ◽  
Josephine Krieger ◽  
Mingming Zhao ◽  
Sai Saroja Kolluru ◽  
Robert C Jones ◽  
...  
Keyword(s):  
Blood Vessels ◽  
Cell Fate ◽  
Adult Mouse ◽  
Coronary Vessels ◽  
Lineage Tracing ◽  
Specific Gene ◽  
Cell Type ◽  
Functional Differences ◽  
Coronary Blood Vessels ◽  
Two Populations

Most cell fate trajectories during development follow a diverging, tree-like branching pattern, but the opposite can occur when distinct progenitors contribute to the same cell type. During this convergent differentiation, it is unknown if cells "remember" their origins transcriptionally or whether this influences cell behavior. Most coronary blood vessels of the heart develop from two different progenitor sources-the endocardium (Endo) and sinus venosus (SV)-but whether transcriptional or functional differences related to origin are retained is unknown. We addressed this by combining lineage tracing with single-cell RNA sequencing (scRNAseq) in embryonic and adult mouse hearts. Shortly after coronary development begins, capillary ECs transcriptionally segregated into two states that retained progenitor-specific gene expression. Later in development, when the coronary vasculature is well-established but still remodeling, capillary ECs again segregated into two populations, but transcriptional differences were related to tissue localization rather than lineage. Specifically, ECs in the heart septum expressed genes indicative of increased local hypoxia and decreased blood flow. Adult capillary ECs were more homogeneous and lacked indications of either lineage or location. In agreement, SV- and Endo-derived ECs in adult hearts displayed similar responses to injury. Finally, scRNAseq of developing human coronary vessels indicated that the human heart followed similar principles. Thus, over the course of development, transcriptional heterogeneity in coronary ECs is first influenced by lineage, then by location, until heterogeneity disappears in the homeostatic adult heart. These results highlight the plasticity of ECs during development, and the validity of the mouse as a model for human coronary development.

scholarly journals Cell Type-Specific Role of RNA Nuclease SMG6 in Neurogenesis

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3365
Author(s):  
Gabriela Maria Guerra ◽  
Doreen May ◽  
Torsten Kroll ◽  
Philipp Koch ◽  
Marco Groth ◽  
...  
Keyword(s):  
Stem Cells ◽  
Cell Fate ◽  
Cortical Neurons ◽  
Embryonic Stem ◽  
Normal Structure ◽  
Mutant Mice ◽  
Cell Type ◽  
Nonsense Mediated Mrna Decay ◽  
A Cell ◽  
Cell Type Specific

SMG6 is an endonuclease, which cleaves mRNAs during nonsense-mediated mRNA decay (NMD), thereby regulating gene expression and controling mRNA quality. SMG6 has been shown as a differentiation license factor of totipotent embryonic stem cells. To investigate whether it controls the differentiation of lineage-specific pluripotent progenitor cells, we inactivated Smg6 in murine embryonic neural stem cells. Nestin-Cre-mediated deletion of Smg6 in mouse neuroprogenitor cells (NPCs) caused perinatal lethality. Mutant mice brains showed normal structure at E14.5 but great reduction of the cortical NPCs and late-born cortical neurons during later stages of neurogenesis (i.e., E18.5). Smg6 inactivation led to dramatic cell death in ganglionic eminence (GE) and a reduction of interneurons at E14.5. Interestingly, neurosphere assays showed self-renewal defects specifically in interneuron progenitors but not in cortical NPCs. RT-qPCR analysis revealed that the interneuron differentiation regulators Dlx1 and Dlx2 were reduced after Smg6 deletion. Intriguingly, when Smg6 was deleted specifically in cortical and hippocampal progenitors, the mutant mice were viable and showed normal size and architecture of the cortex at E18.5. Thus, SMG6 regulates cell fate in a cell type-specific manner and is more important for neuroprogenitors originating from the GE than for progenitors from the cortex.

DNA loop extrusion by human cohesin

Science ◽  
2019 ◽  
Vol 366 (6471) ◽  
pp. 1338-1345 ◽  
Author(s):  
Iain F. Davidson ◽  
Benedikt Bauer ◽  
Daniela Goetz ◽  
Wen Tang ◽  
Gordana Wutz ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Atpase Activity ◽  
Chromatin Structure ◽  
Adenosine Triphosphatase ◽  
Gene Recombination ◽  
Loop Formation ◽  
Base Pairs ◽  
Topologically Associating Domains ◽  
Dna Loop ◽  
Eukaryotic Genomes

Eukaryotic genomes are folded into loops and topologically associating domains, which contribute to chromatin structure, gene regulation, and gene recombination. These structures depend on cohesin, a ring-shaped DNA-entrapping adenosine triphosphatase (ATPase) complex that has been proposed to form loops by extrusion. Such an activity has been observed for condensin, which forms loops in mitosis, but not for cohesin. Using biochemical reconstitution, we found that single human cohesin complexes form DNA loops symmetrically at rates up to 2.1 kilo–base pairs per second. Loop formation and maintenance depend on cohesin’s ATPase activity and on NIPBL-MAU2, but not on topological entrapment of DNA by cohesin. During loop formation, cohesin and NIPBL-MAU2 reside at the base of loops, which indicates that they generate loops by extrusion. Our results show that cohesin and NIPBL-MAU2 form an active holoenzyme that interacts with DNA either pseudo-topologically or non-topologically to extrude genomic interphase DNA into loops.

Cell Stress Signaling Cascades Regulating Cell Fate

2018 ◽  
Vol 24 (27) ◽  
pp. 3176-3183 ◽  
Author(s):  
Rohit Gundamaraju ◽  
Ravichandra Vemuri ◽  
Wai Chin Chong ◽  
Dominic P. Geraghty ◽  
Rajaraman Eri
Keyword(s):  
Cell Death ◽  
Cell Fate ◽  
Stress Responses ◽  
Cellular Stress ◽  
Cell Stress ◽  
Signaling Cascades ◽  
Stress Signaling ◽  
Cell Type ◽  
Induce Cell Death ◽  
Stressed Cell

Initiating anti-apoptotic signaling or triggering cell death depends to a great extent on the nature or source of cellular stress and cell type. Interplay between each stress response eventually determines the fate of stressed cell. Numerous factors induce cell death by a number of pathways including apoptosis, autophagy and necrosis. Not surprisingly, some of the pathways are interrelated to each other through a mediator that could articulate the entire mechanism. The present review attempts to consolidate all the pathways included in intrinsic cellular stress such as oxidative stress and autophagy, endoplasmic reticular stress (ERS) and mitophagy and apoptosis as fate in cell stress. These stress responses are a hallmark of numerous diseases including neurodegenerative diseases, diabetes and cancer. Understanding the cross-talk between different intrinsic cell stress responses will help to develop new therapeutic targets and hence lead to the development of new therapeutics.

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