Imperial College London

DrClaraLopes Novo

Faculty of MedicineDepartment of Metabolism, Digestion and Reproduction

Honorary Research Fellow
 
 
 
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c.lopes-novo

 
 
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Commonwealth BuildingHammersmith Campus

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Summary

 

Publications

Publication Type
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16 results found

Novo CL, Wong E, Hockings C, Poudel C, Sheekey E, Wiese M, Okkenhaug H, Boulton SJ, Basu S, Walker S, Schierle GSK, Narlikar GJ, Rugg-Gunn PJet al., 2022, Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells, Nature Communications, Vol: 13, Pages: 1-16, ISSN: 2041-1723

Heterochromatin maintains genome integrity and function, and is organised into distinct nuclear domains. Some of these domains are proposed to form by phase separation through the accumulation of HP1ɑ. Mouse heterochromatin contains noncoding major satellite repeats (MSR), which are highly transcribed in mouse embryonic stem cells (ESCs). Here, we report that MSR transcripts can drive the formation of HP1ɑ droplets in vitro, and modulate heterochromatin into dynamic condensates in ESCs, contributing to the formation of large nuclear domains that are characteristic of pluripotent cells. Depleting MSR transcripts causes heterochromatin to transition into a more compact and static state. Unexpectedly, changing heterochromatin’s biophysical properties has severe consequences for ESCs, including chromosome instability and mitotic defects. These findings uncover an essential role for MSR transcripts in modulating the organisation and properties of heterochromatin to preserve genome stability. They also provide insights into the processes that could regulate phase separation and the functional consequences of disrupting the properties of heterochromatin condensates.

Journal article

Lopes Novo C, 2021, A tale of two states: pluripotency regulation of telomeres, Frontiers in Cell and Developmental Biology, Vol: 9, ISSN: 2296-634X

Inside the nucleus, chromatin is functionally organized and maintained as a complex three-dimensional network of structures with different accessibility such as compartments, lamina associated domains, and membraneless bodies. Chromatin is epigenetically and transcriptionally regulated by an intricate and dynamic interplay of molecular processes to ensure genome stability. Phase separation, a process that involves the spontaneous organization of a solution into separate phases, has been proposed as a mechanism for the timely coordination of several cellular processes, including replication, transcription and DNA repair. Telomeres, the repetitive structures at the end of chromosomes, are epigenetically maintained in a repressed heterochromatic state that prevents their recognition as double-strand breaks (DSB), avoiding DNA damage repair and ensuring cell proliferation. In pluripotent embryonic stem cells, telomeres adopt a non-canonical, relaxed epigenetic state, which is characterized by a low density of histone methylation and expression of telomere non-coding transcripts (TERRA). Intriguingly, this telomere non-canonical conformation is usually associated with chromosome instability and aneuploidy in somatic cells, raising the question of how genome stability is maintained in a pluripotent background. In this review, we will explore how emerging technological and conceptual developments in 3D genome architecture can provide novel mechanistic perspectives for the pluripotent epigenetic paradox at telomeres. In particular, as RNA drives the formation of LLPS, we will consider how pluripotency-associated high levels of TERRA could drive and coordinate phase separation of several nuclear processes to ensure genome stability. These conceptual advances will provide a better understanding of telomere regulation and genome stability within the highly dynamic pluripotent background.

Journal article

Novo CL, Wong E, Hockings C, Poudel C, Sheekey E, Walker S, Schierle GK, Narlikar G, Rugg-Gunn Pet al., 2020, Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells, Publisher: bioRxiv

Summary Heterochromatin maintains genome integrity and function, and is organised into distinct nuclear domains. Some of these domains are proposed to form by phase separation through the accumulation of HP1α. Mammalian heterochromatin contains noncoding major satellite repeats (MSR), which are highly transcribed in mouse embryonic stem cells (ESCs). Here, we report that MSR transcripts can drive the formation of HP1α droplets in vitro , and scaffold heterochromatin into dynamic condensates in ESCs, leading to the formation of large nuclear domains that are characteristic of pluripotent cells. Depleting MSR transcripts causes heterochromatin to transition into a more compact and static state. Unexpectedly, changing heterochromatin’s biophysical properties has severe consequences for ESCs, including chromosome instability and mitotic defects. These findings uncover an essential role for MSR transcripts in modulating the organisation and properties of heterochromatin to preserve genome stability. They also provide new insights into the processes that could regulate phase separation and the functional consequences of disrupting the properties of heterochromatin condensates.

Working paper

Hockings C, Poudel C, Feeney K, Novo C, Hamouda M, Mela I, Fernandez-Antoran D, Vallejo-Ramirez P, Rugg-Gunn P, Chalut K, Kaminski C, Kaminski-Schierle Get al., 2020, Illuminating chromatin compaction in live cells and fixed tissues using SiR-DNA fluorescence lifetime, Publisher: BIOrXIV

The global compaction state of chromatin in a nucleus is an important component of cell identity that has been difficult to measure. We have developed a quantitative method to measure the chromatin compaction state in both live and fixed cells, without the need for genetic modification, using the fluorescence lifetime of SiR-DNA dye. After optimising this method using live cancer cell lines treated to induce chromatin compaction or decompaction, we observed chromatin compaction in differentiating epithelial cells in fixed tissue sections, as well as local decompaction foci that may represent transcription factories. In addition, we shed new light on chromatin decompaction during embryonic stem cell transition out of their naïve pluripotent state. This method will be useful to studies of nuclear architecture, and may be easy, cheap, and accessible enough to serve as a general assay of ‘stem-ness’.

Working paper

Lupo G, Nisi PS, Esteve P, Paul Y-L, Novo CL, Sidders B, Khan MA, Biagioni S, Liu H-K, Bovolenta P, Cacci E, Rugg-Gunn PJet al., 2018, Molecular profiling of aged neural progenitors identifies Dbx2 as a candidate regulator of age-associated neurogenic decline, Aging Cell, Vol: 17, Pages: 1-15, ISSN: 1474-9718

Adult neurogenesis declines with aging due to the depletion and functional impairment of neural stem/progenitor cells (NSPCs). An improved understanding of the underlying mechanisms that drive age-associated neurogenic deficiency could lead to the development of strategies to alleviate cognitive impairment and facilitate neuroregeneration. An essential step towards this aim is to investigate the molecular changes that occur in NSPC aging on a genomewide scale. In this study, we compare the transcriptional, histone methylation and DNA methylation signatures of NSPCs derived from the subventricular zone (SVZ) of young adult (3 months old) and aged (18 months old) mice. Surprisingly, the transcriptional and epigenomic profiles of SVZ-derived NSPCs are largely unchanged in aged cells. Despite the global similarities, we detect robust age-dependent changes at several hundred genes and regulatory elements, thereby identifying putative regulators of neurogenic decline. Within this list, the homeobox gene Dbx2 is upregulated in vitro and in vivo, and its promoter region has altered histone and DNA methylation levels, in aged NSPCs. Using functional in vitro assays, we show that elevated Dbx2 expression in young adult NSPCs promotes age-related phenotypes, including the reduced proliferation of NSPC cultures and the altered transcript levels of age-associated regulators of NSPC proliferation and differentiation. Depleting Dbx2 in aged NSPCs caused the reverse gene expression changes. Taken together, these results provide new insights into the molecular programmes that are affected during mouse NSPC aging, and uncover a new functional role for Dbx2 in promoting age-related neurogenic decline.

Journal article

Novo CL, Javierre B-M, Cairns J, Segonds-Pichon A, Wingett SW, Freire-Pritchett P, Furlan-Magaril M, Schoenfelder S, Fraser P, Rugg-Gunn PJet al., 2018, Long-range enhancer interactions are prevalent in mouse embryonic stem cells and are reorganized upon pluripotent state transition, Cell Reports, Vol: 22, Pages: 2615-2627, ISSN: 2211-1247

Transcriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target promoters using computational predictions. How promoter-SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, have not been reported. Here, we used promoter-capture Hi-C to identify promoters that interact with SEs in mouse embryonic stem cells (ESCs). We found that SEs form complex, spatial networks in which individual SEs contact multiple promoters, and a rewiring of promoter-SE interactions occurs between pluripotent states. We also show that long-range promoter-SE interactions are more prevalent in ESCs than in epiblast stem cells (EpiSCs) or Nanog-deficient ESCs. We conclude that SEs form cell-type-specific interaction networks that are partly dependent on core transcription factors, thereby providing insights into the gene regulatory organization of pluripotent cells.

Journal article

Novo CL, Rugg-Gunn P, 2016, Crosstalk between pluripotency factors and higher-order chromatin organization, Nucleus, Vol: 7, Pages: 447-452, ISSN: 1949-1034

Pluripotent cells are characterized by a globally open and accessible chromatin organization that is thought to contribute to cellular plasticity and developmental decision-making. We recently identified the pluripotency factor Nanog as a key regulator of this form of chromatin architecture in mouse embryonic stem cells. In particular, we demonstrated that the transcription factors Nanog and Sall1 co-dependently mediate the epigenetic state of pericentromeric heterochromatin to reinforce a more open and accessible organization in pluripotent cells. Here, we summarize our main findings and place the work into a broader context. We explore how heterochromatin domains could be targets of transcriptional networks in pluripotent cells and are coordinated with cell state. We propose this integration may be to balance the requirement for a dynamic and plastic chromatin organization in pluripotent cells, together with priming for a more restrictive nuclear compartmentalization that is triggered rapidly upon lineage commitment.

Journal article

Novo CL, Rugg-Gunn PJ, 2016, Chromatin organization in pluripotent cells: emerging approaches to study and disrupt function, Briefings in Functional Genomics, Vol: 15, Pages: 305-314, ISSN: 1473-9550

Translating the vast amounts of genomic and epigenomic information accumulated on the linear genome into three-dimensional models of nuclear organization is a current major challenge. In response to this challenge, recent technological innovations based on chromosome conformation capture methods in combination with increasingly powerful functional approaches have revealed exciting insights into key aspects of genome regulation. These findings have led to an emerging model where the genome is folded and compartmentalized into highly conserved topological domains that are further divided into functional subdomains containing physical loops that bring cis -regulatory elements to close proximity. Targeted functional experiments, largely based on designable DNA-binding proteins, have begun to define the major architectural proteins required to establish and maintain appropriate genome regulation. Here, we focus on the accessible and well-characterized system of pluripotent cells to review the functional role of chromatin organization in regulating pluripotency, differentiation and reprogramming.

Journal article

Novo CL, Tang C, Ahmed K, Djuric U, Fussner E, Mullin NP, Morgan NP, Hayre J, Sienerth AR, Elderkin S, Nishinakamura R, Chambers I, Ellis J, Bazett-Jones DP, Rugg-Gunn PJet al., 2016, The pluripotency factor <i>Nanog</i> regulates pericentromeric heterochromatin organization in mouse embryonic stem cells, GENES & DEVELOPMENT, Vol: 30, Pages: 1101-1115, ISSN: 0890-9369

Journal article

Zhdanova NS, Draskovic I, Minina JM, Karamysheva TV, Novo CL, Liu W-Y, Porreca RM, Gibaud A, Zvereva ME, Skvortsov DA, Rubtsov NB, Londono-Vallejo Aet al., 2014, Recombinogenic Telomeres in Diploid <i>Sorex granarius</i> (Soricidae, Eulipotyphla) Fibroblast Cells, MOLECULAR AND CELLULAR BIOLOGY, Vol: 34, Pages: 2786-2799, ISSN: 0270-7306

Journal article

Novo CL, Polese C, Matheus N, Decottignies A, Londono-Vallejo A, Castronovo V, Mottet Det al., 2013, A new role for histone deacetylase 5 in the maintenance of long telomeres, FASEB JOURNAL, Vol: 27, Pages: 3632-3642, ISSN: 0892-6638

Journal article

Kappei D, Butter F, Benda C, Scheibe M, Draskovic I, Stevense M, Novo CL, Basquin C, Araki M, Araki K, Krastev DB, Kittler R, Jessberger R, Londono-Vallejo JA, Mann M, Buchholz Fet al., 2013, HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment, The EMBO Journal, Vol: 32, Pages: 1681-1701, ISSN: 0261-4189

Telomeres are repetitive DNA structures that, together with the shelterin and the CST complex, protect the ends of chromosomes. Telomere shortening is mitigated in stem and cancer cells through the de novo addition of telomeric repeats by telomerase. Telomere elongation requires the delivery of the telomerase complex to telomeres through a not yet fully understood mechanism. Factors promoting telomerase–telomere interaction are expected to directly bind telomeres and physically interact with the telomerase complex. In search for such a factor we carried out a SILAC‐based DNA–protein interaction screen and identified HMBOX1, hereafter referred to as homeobox telomere‐binding protein 1 (HOT1). HOT1 directly and specifically binds double‐stranded telomere repeats, with the in vivo association correlating with binding to actively processed telomeres. Depletion and overexpression experiments classify HOT1 as a positive regulator of telomere length. Furthermore, immunoprecipitation and cell fractionation analyses show that HOT1 associates with the active telomerase complex and promotes chromatin association of telomerase. Collectively, these findings suggest that HOT1 supports telomerase‐dependent telomere elongation.

Journal article

Novo C, Arnoult N, Bordes W-Y, Castro-Vega L, Gibaud A, Dutrillaux B, Bacchetti S, Londono-Vallejo Aet al., 2013, The heterochromatic chromosome caps in great apes impact telomere metabolism, Nucleic Acids Research, Vol: 41, Pages: 4792-4801, ISSN: 0305-1048

In contrast with the limited sequence divergence accumulated after separation of higher primate lineages, marked cytogenetic variation has been associated with the genome evolution in these species. Studying the impact of such structural variations on defined molecular processes can provide valuable insights on how genome structural organization contributes to organismal evolution. Here, we show that telomeres on chromosome arms carrying subtelomeric heterochromatic caps in the chimpanzee, which are completely absent in humans, replicate later than telomeres on chromosome arms without caps. In gorilla, on the other hand, a proportion of the subtelomeric heterochromatic caps present in most chromosome arms are associated with large blocks of telomere-like sequences that follow a replication program different from that of bona fide telomeres. Strikingly, telomere-containing RNA accumulates extrachromosomally in gorilla mitotic cells, suggesting that at least some aspects of telomere-containing RNA biogenesis have diverged in gorilla, perhaps in concert with the evolution of heterochromatic caps in this species.

Journal article

Novo CL, Londono-Vallejo JA, 2013, Telomeres and the nucleus, SEMINARS IN CANCER BIOLOGY, Vol: 23, Pages: 116-124, ISSN: 1044-579X

Journal article

Royle NJ, Mendez-Bermudez A, Gravani A, Novo C, Foxon J, Williams J, Cotton V, Hidalgo Aet al., 2009, The role of recombination in telomere length maintenance, Symposium on DNA Damage - From Causes to Cures, Publisher: PORTLAND PRESS LTD, Pages: 589-595, ISSN: 0300-5127

Conference paper

Royle NJ, Foxon J, Jeyapalan JN, Mendez-Bermudez A, Novo CL, Williams J, Cotton VEet al., 2008, Telomere length maintenance - an ALTernative mechanism, CYTOGENETIC AND GENOME RESEARCH, Vol: 122, Pages: 281-291, ISSN: 1424-8581

Journal article

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