Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence

AbstractSenescence is a state of stable proliferative arrest, generally accompanied by the senescence-associated secretory phenotype, which modulates tissue homeostasis. Enhancer-promoter interactions, facilitated by chromatin loops, play a key role in gene regulation but their relevance in senescence remains elusive. Here, we use Hi-C to show that oncogenic RAS-induced senescence in human diploid fibroblasts is accompanied by extensive enhancer-promoter rewiring, which is closely connected with dynamic cohesin binding to the genome. We find de novo cohesin peaks often at the 3′ end of a subset of active genes. RAS-induced de novo cohesin peaks are transcription-dependent and enriched for senescence-associated genes, exemplified by IL1B, where de novo cohesin binding is involved in new loop formation. Similar IL1B induction with de novo cohesin appearance and new loop formation are observed in terminally differentiated macrophages, but not TNFα-treated cells. These results suggest that RAS-induced senescence represents a cell fate determination-like process characterised by a unique gene expression profile and 3D genome folding signature, mediated in part through cohesin redistribution on chromatin.

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Transcription-driven cohesin repositioning rewires chromatin loops in cellular senescence

10.1101/823831 ◽

2019 ◽

Cited By ~ 2

Author(s):

Ioana Olan ◽

Aled J. Parry ◽

Stefan Schoenfelder ◽

Masako Narita ◽

Yoko Ito ◽

...

Keyword(s):

Gene Expression ◽

De Novo ◽

Three Dimensional ◽

Loop Formation ◽

Chromatin Loops ◽

Human Diploid Fibroblasts ◽

Domain Structures ◽

Binding Factor ◽

Macro Domain ◽

Cell Type Specific

AbstractSenescence is a phenotypic state of stable proliferative arrest, typically occurring in lineage-committed cells and triggered by various stimuli. It is generally accompanied by activation of a secretory program (senescence-associated secretory phenotype, SASP), which modulates both local (tissue microenvironment) and systemic (ageing) homeostasis1,2. Enhancer-promoter interactions play a key role in gene regulation3–5, facilitated by chromatin loops, mostly formed via CCCTC binding factor (CTCF) and cohesin tethering6–8. The three-dimensional chromatin structure of senescent cells has been characterised9–11 mostly in terms of macro-domain structures, but its relevance in gene expression remains elusive. Here, we use Hi-C and capture Hi-C12,13 to show that oncogenic HRAS-induced senescence (RIS) in human diploid fibroblasts (HDFs) is accompanied by extensive enhancer-promoter rewiring, which is closely connected with dynamic cohesin binding to the genome. We find de novo cohesin peaks at the 3’ end of a subset of active genes, reminiscent of the transcription-driven ‘cohesin islands’ recently discovered in mouse embryonic fibroblasts deficient in both CTCF and the cohesin release factor Wings apart-like (Wapl)14. RIS de novo cohesin peaks are also transcription-dependent and enriched for SASP genes, as exemplified by IL1B, where de novo cohesin binding is involved in new loop formation. Cytokine induction is associated with similar cohesin islands appearance and enhancer-promoter rewiring during the terminal differentiation of monocytes to macrophages15, but not upon acute TNFα treatment of HDFs16. These results suggest that RIS represents a fate-determined process in which gene expression is regulated beyond the cell type specific 3D chromatin framework, in part through cohesin redistribution.

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Differential Effects of Notch Ligands Delta-1 and Jagged-1 in Human Lymphoid Differentiation

Journal of Experimental Medicine ◽

10.1084/jem.194.7.991 ◽

2001 ◽

Vol 194 (7) ◽

pp. 991-1002 ◽

Cited By ~ 247

Author(s):

Ana C. Jaleco ◽

Hélia Neves ◽

Erik Hooijberg ◽

Paula Gameiro ◽

Nuno Clode ◽

...

Keyword(s):

T Cell ◽

Notch Signaling ◽

Cell Fate ◽

De Novo ◽

Cell Lineage ◽

Differential Effects ◽

Cell Lineages ◽

A Cell ◽

Fate Decision ◽

Notch Ligands

Notch signaling is known to differentially affect the development of lymphoid B and T cell lineages, but it remains unclear whether such effects are specifically dependent on distinct Notch ligands. Using a cell coculture assay we observed that the Notch ligand Delta-1 completely inhibits the differentiation of human hematopoietic progenitors into the B cell lineage while promoting the emergence of cells with a phenotype of T cell/natural killer (NK) precursors. In contrast, Jagged-1 did not disturb either B or T cell/NK development. Furthermore, cells cultured in the presence of either Delta-1 or Jagged-1 can acquire a phenotype of NK cells, and Delta-1, but not Jagged-1, permits the emergence of a de novo cell population coexpressing CD4 and CD8. Our results thus indicate that distinct Notch ligands can mediate differential effects of Notch signaling and provide a useful system to further address cell-fate decision processes in lymphopoiesis.

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Gene neighbourhood integrity disrupted by CTCF loss in vivo

10.1101/187393 ◽

2017 ◽

Cited By ~ 1

Author(s):

Dominic Paul Lee ◽

Wilson Lek Wen Tan ◽

Chukwuemeka George Anene-Nzelu ◽

Peter Yiqing Li ◽

Tuan Anh Luu Danh ◽

...

Keyword(s):

Large Scale ◽

De Novo ◽

Extrusion Process ◽

Mammalian Genome ◽

Ctcf Binding ◽

Ctcf Binding Site ◽

Loop Formation ◽

Chromatin Loops ◽

Genome Wide

The mammalian genome is coiled, compacted and compartmentalized into complex non-random three-dimensional chromatin loops in the nucleus1–3. At the core of chromatin loop formation is CCCTC-binding factor (CTCF), also described as a “weaver of the genome”45. Anchored by CTCF, chromatin loops are proposed to form through a loop extrusion process6, organising themselves into gene neighbourhoods2 that harbour insulated enhancer-promoter domains, restricting enhancer activities to genes within loops, and insulating genes from promiscuous interactions outside of loops2,7–9. Studies targeting CTCF binding site deletions at gene neighbourhood boundaries result in localised gene expression dysregulation8,10–12, and global CTCF depletion recently showed CTCF to be crucial for higher hierarchical chromatin organisation of topologically associating domains (TADs)13. However, the role for CTCF in maintaining sub-TAD CTCF gene neighbourhoods and how gene transcription is affected by CTCF loss remains unclear. In particular, how CTCF gene neighbourhoods govern genome-wide enhancer-promoter interactions require clarification. Here, we took an in vivo approach to assess the global dissolution of CTCF anchored structures in mouse cardiomyocyte-specific Ctcf-knockout (Ctcf-KO), and uncovered large-scale ectopic de novo Enhancer-Promoter (E-P) interactions. In vivo cardiomyocyte-specific Ctcf-KO leads to a heart failure phenotype14, but our analysis integrates genome-wide transcription dysregulation with aberrant E-P interactions in context of CTCF-loop structures, identifying how genes engage their E-P interactions, requiring CTCF looping for their maintenance. Our study points to a mammalian genome that possesses a strong propensity towards spontaneous E-P interactions in vivo, resulting in a diseased transcriptional state, manifest as organ failure. This work solidifies the role of CTCF as the central player for specifying global E-P connections.

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Faculty Opinions recommendation of A positive-feedback-based bistable 'memory module' that governs a cell fate decision.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1014093.206673 ◽

2004 ◽

Author(s):

Hiten Madhani

Keyword(s):

Cell Fate ◽

Positive Feedback ◽

Cell Fate Decision ◽

Memory Module ◽

A Cell ◽

Fate Decision

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

Nature ◽

10.1038/s41586-021-03460-z ◽

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.

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Cellular Senescence and Mammalian Healthspan

Innovation in Aging ◽

10.1093/geroni/igaa057.2655 ◽

2020 ◽

Vol 4 (Supplement_1) ◽

pp. 742-742

Author(s):

Judith Campisi

Keyword(s):

Growth Factors ◽

Cell Fate ◽

Cellular Senescence ◽

Complex Cell ◽

Transgenic Mouse Models ◽

Bioactive Lipids ◽

Age Related ◽

Mammalian Tissues ◽

Secretory Phenotype ◽

Near Future

Abstract Cellular senescence is a complex cell fate, often induced by stress or damage, that can be beneficial or deleterious, depending on the physiological context and age of the organism. A prominent feature of senescent cells is a multi-faceted senescence-associated secretory phenotype (SASP), which includes growth factors, cytokine and chemokines, growth factors, proteases, bioactive lipids and metabolites. Senescent cells increase with age in most, if not all, mammalian tissues. Through the use of transgenic mouse models, senescent cells are now known to causally drive numerous age-related pathologies, largely through the SASP. Eliminating senescent cells, genetically or through the use of senolytic/senomorphic agents, can improve the health span, at least in mice, and hold promise for extension to humans in the near future.

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Order and stochasticity in the folding of individual Drosophila genomes

Nature Communications ◽

10.1038/s41467-020-20292-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Sergey V. Ulianov ◽

Vlada V. Zakharova ◽

Aleksandra A. Galitsyna ◽

Pavel I. Kos ◽

Kirill E. Polovnikov ◽

...

Keyword(s):

Random Walk ◽

High Resolution ◽

3D Genome ◽

Topologically Associating Domains ◽

Chromatin Folding ◽

A Cell ◽

Single Nucleus ◽

High Level ◽

Cell To Cell Variability

AbstractMammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome.

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DNA methylation in 5-aza-2'-deoxycytidine-resistant variants of C3H 10T1/2 C18 cells

Molecular and Cellular Biology ◽

10.1128/mcb.4.10.2098-2102.1984 ◽

1984 ◽

Vol 4 (10) ◽

pp. 2098-2102

Author(s):

E Flatau ◽

F A Gonzales ◽

L A Michalowsky ◽

P A Jones

Keyword(s):

Cell Line ◽

Cytosine Methylation ◽

De Novo ◽

Lethal Dose ◽

Cytotoxic Effects ◽

Drug Treatments ◽

A Cell ◽

Mouse Cells ◽

Low Levels ◽

Dna Cytosine Methylation

A cell line (T17) was derived from C3H 10T1/2 C18 cells after 17 treatments with increasing concentrations of 5-aza-2'-deoxycytidine. The T17 cell line was very resistant to the cytotoxic effects of 5-aza-2'-deoxycytidine, and the 50% lethal dose for 5-aza-2'-deoxycytidine was ca. 3 microM, which was 30-fold greater than that of the parental C3H 10T1/2 C18 cells. Increased drug resistance was not due to a failure of the T17 cell line to incorporate 5-aza-2'-deoxycytidine into DNA. The cells were also slightly cross-resistant to 5-azacytidine. The percentage of cytosines modified to 5-methylcytosine in T17 cells was 0.7%, a 78% decrease from the level of 3.22% in C3H 10T1/2 C18 cells. The DNA cytosine methylation levels in several clones isolated from the treated lines were on the order of 0.7%, and clones with methylation levels lower than 0.45% were not obtained even after further drug treatments. These highly decreased methylation levels appeared to be unstable, and DNA modification increased as the cells divided in the absence of further drug treatment. The results suggest that it may not be possible to derive mouse cells with vanishingly low levels of 5-methylcytosine and that considerable de novo methylation can occur in cultured lines.

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A regulatory network of microRNAs confers lineage commitment during early developmental trajectories of B and T lymphocytes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2104297118 ◽

2021 ◽

Vol 118 (46) ◽

pp. e2104297118

Author(s):

Sameena Nikhat ◽

Anurupa D. Yadavalli ◽

Arpita Prusty ◽

Priyanka K. Narayan ◽

Dasaradhi Palakodeti ◽

...

Keyword(s):

Gene Expression ◽

T Lymphocytes ◽

Cell Fate ◽

T Lymphocyte ◽

De Novo ◽

Gene Expression Pattern ◽

Lymphocyte Development ◽

Motif Analysis ◽

Differentiation Potential ◽

B And T Lymphocytes

The commitment of hematopoietic multipotent progenitors (MPPs) toward a particular lineage involves activation of cell type–specific genes and silencing of genes that promote alternate cell fates. Although the gene expression programs of early–B and early–T lymphocyte development are mutually exclusive, we show that these cell types exhibit significantly correlated microRNA (miRNA) profiles. However, their corresponding miRNA targetomes are distinct and predominated by transcripts associated with natural killer, dendritic cell, and myeloid lineages, suggesting that miRNAs function in a cell-autonomous manner. The combinatorial expression of miRNAs miR-186-5p, miR-128-3p, and miR-330-5p in MPPs significantly attenuates their myeloid differentiation potential due to repression of myeloid-associated transcripts. Depletion of these miRNAs caused a pronounced de-repression of myeloid lineage targets in differentiating early–B and early–T cells, resulting in a mixed-lineage gene expression pattern. De novo motif analysis combined with an assay of promoter activities indicates that B as well as T lineage determinants drive the expression of these miRNAs in lymphoid lineages. Collectively, we present a paradigm that miRNAs are conserved between developing B and T lymphocytes, yet they target distinct sets of promiscuously expressed lineage-inappropriate genes to suppress the alternate cell-fate options. Thus, our studies provide a comprehensive compendium of miRNAs with functional implications for B and T lymphocyte development.

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