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Chromatin remodeling

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lightbulbAbout this topic
Chromatin remodeling refers to the dynamic structural changes in chromatin that regulate access to DNA, influencing gene expression and cellular processes. This involves the repositioning, restructuring, or removal of nucleosomes, facilitated by various protein complexes, thereby altering the chromatin architecture and its interaction with transcription factors and other regulatory proteins.
lightbulbAbout this topic
Chromatin remodeling refers to the dynamic structural changes in chromatin that regulate access to DNA, influencing gene expression and cellular processes. This involves the repositioning, restructuring, or removal of nucleosomes, facilitated by various protein complexes, thereby altering the chromatin architecture and its interaction with transcription factors and other regulatory proteins.

Key research themes

1. How do histone modifications regulate chromatin remodeling and transcriptional dynamics?

This research area focuses on the diverse post-translational modifications (PTMs) of histones — such as acetylation, methylation, and their crosstalk — and how they influence chromatin structure and function. Histone modifications serve as molecular signals that recruit or modulate the activities of chromatin remodeling complexes, thereby altering nucleosome positioning, chromatin accessibility, and ultimately gene expression. Understanding the specificity, recruitment mechanisms, and functional consequences of these histone marks is pivotal for connecting epigenetic regulation to transcriptional control and other DNA-templated processes.

Key finding: This foundational paper elucidates how specific histone modifications, such as lysine acetylation mediated by histone acetyltransferases (HATs) and reversed by histone deacetylases (HDACs), modulate chromatin structure and... Read more
Key finding: Using genome-wide approaches in fission yeast, this study links transcriptional activity to histone modifications and nucleosome turnover. It demonstrates that transcription dynamically modulates chromatin structures via... Read more
Key finding: This work reveals that the NuRD complex fine-tunes transcriptional output primarily via its nucleosome remodeling ATPase activity, increasing nucleosome density at regulatory elements and thereby modulating the accessibility... Read more
Key finding: The paper also highlights the role of methylation marks on histones such as H3K4me3 in transcriptional activation, and crosstalk with chromatin remodeler recruitment, providing a molecular basis for how distinct histone PTMs... Read more

2. What are the structural bases and mechanisms of chromatin remodeling complexes in nucleosome manipulation?

This theme encompasses studies elucidating the architecture, molecular components, and mechanistic functions of ATP-dependent chromatin remodeling complexes such as SWI/SNF family members (e.g., BAF), INO80-C, SWR-C, RSC, and CHD family remodelers. These complexes reposition, evict, or restructure nucleosomes to regulate DNA accessibility. Understanding their multidomain organization, nucleosome engagement, ATPase activation, and interactions with histone variants unveils how remodeling activities are precisely targeted and regulated to control chromatin architecture and gene expression.

Key finding: This review consolidates structural and functional insights into remodeler engagement with nucleosomes, detailing how remodelers use ATP hydrolysis to translocate DNA and overcome histone-DNA contacts. It emphasizes the... Read more
Key finding: Recent cryo-EM structures reveal modular architecture of the human BAF complex comprising ATPase, Arp, and body modules, delineating subunit organization and nucleosome engagement sites—especially the ATPase subunit SMARCA4... Read more
Key finding: Electron microscopy and class averaging demonstrate INO80-C and SWR-C share similar dynamic architectures characterized by flexible tail domains and hexameric Rvb1/Rvb2 rings in their head domains. Functional mapping... Read more
Key finding: This innovative approach isolates native yeast mono-nucleosomes for in vitro remodeling assays, demonstrating RSC remodeler preferentially destabilizes H2A.Z-enriched nucleosomes, and this preference is lost in htz1Δ cells.... Read more

3. How does higher-order and dynamic chromatin architecture influence genome function and cellular identity?

This theme explores the spatial organization of chromatin at scales beyond nucleosomes, including loops, topologically associating domains (TADs), and compartments, and how these structures modulate gene expression, genome stability, and cell fate. Integrating genome-wide chromatin conformation capture techniques with live-cell imaging and modeling, this research elucidates chromatin remodeling during differentiation, cell cycle progression, DNA damage response, and transcriptional reprogramming.

Key finding: Genome-wide Hi-C analyses in human ES cells and derived lineages reveal substantial plasticity of A/B compartments affecting 36% of the genome during differentiation. Integration with allele-specific epigenomic data uncovers... Read more
Key finding: Combining live-cell imaging and polymer simulations in fission yeast, this study demonstrates that chromatin loops formed by cohesin and condensin constrain chromatin motion rather than drive it, and identifies the INO80... Read more
Key finding: Reviewing recent 3C-based and imaging approaches, this work conceptualizes chromatin organization in four dimensions—space and time—highlighting hierarchical chromatin structures (loops, TADs, compartments) during interphase... Read more
Key finding: Using two-photon microscopy across multiple yeast species and protists, this study reveals a conserved ~1.5-fold increase in chromatin condensation during mitosis relative to interphase, demonstrating evolutionary... Read more
Key finding: The paper additionally develops a two-photon microscopy method for measuring chromatin condensation in fixed and live cells, expanding tools for assessing genome organization changes in diverse organisms and cellular contexts.

All papers in Chromatin remodeling

Data obtained from cutting-edge research have shown that deregulated epigenetic marks are critical hallmarks of cancer. Rapidly emerging scientific evidence has helped in developing a proper understanding of the mechanisms leading to... more
Chromatin undergoes major remodeling around DNA double-strand breaks (DSB) to promote repair and DNA damage response (DDR) activation. We recently reported a high-resolution map of cH2AX around multiple breaks on the human genome, using a... more
C hromatin structure is regulated by families of proteins that are able to covalently modify the histones and the DNA, as well as to regulate the spacing of nucleosomes along the DNA. Over the years, these chromatin remodeling factors... more
Mango is one of the important perennial fruit crops that exhibits bienniality and results in high economic loss. The molecular mechanisms involved in the bienniality behavior of mango are yet to be fully explored. In this study, an... more
Rsf-1 interacts with human sucrose nonfermenting protein 2 homologue (hSNF2H) to form a chromatin remodeling complex that participates in several biological processes. We have previously shown that Rsf-1 gene amplification was associated... more
A genomewide technology, digital karyotyping, was used to identify subchromosomal alterations in ovarian cancer. Amplification at 11q13.5 was found in three of seven ovarian carcinomas, and amplicon mapping delineated a 1.8-Mb core of... more
Rsf-1 interacts with human sucrose nonfermenting protein 2 homologue (hSNF2H) to form a chromatin remodeling complex that participates in several biological processes. We have previously shown that Rsf-1 gene amplification was associated... more
Our group and others have found that the treatment of embryos with trichostatin A (TSA) after cloning by somatic cell nuclear transfer (SCNT) results in a significant improvement in efficiency. We believe that TSA treatment improves... more
Conserved chromosomal HP1 proteins capable of binding to histone H3 methylated at lysine 9 are believed to provide a dynamic platform for the recruitment and/or spreading of various regulatory proteins involved in diverse chromosomal... more
ABSTRACTThe DNA-binding activities of transcription factors (TFs) are influenced by both intrinsic sequence preferences and extrinsic interactions with cell-specific chromatin landscapes and other regulatory proteins. Disentangling the... more
The long-term storage of memory requires the finely tuned coordination of intracellular signaling with the transcriptional, translational and epigenetic regulations of gene expression. Among the epigenetic mechanisms, however, we know... more
dMi-2, the ATPase subunit of the Drosophila nucleosome remodelling and histone deacetylation (dNuRD) complex, was identified in a two-hybrid screen as an interacting partner of the transcriptional repressor, Tramtrack69 (Ttk69). A short... more
Head and neck squamous cell carcinoma (HNSCC) is a significant global health concern. Though tobacco, alcohol, and betel quid have been previously recognized as the main risk factors for a long time, unique cases of human papillomavirus... more
Human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) have the ability of differentiating into functional cardiomyocytes (CMs) for cell replacement therapy, tissue engineering, drug discovery and toxicity... more
Eukaryotic DNA is wrapped around histone proteins to form a nucleosome, the basic structural unit of chromatin. Multiple levels of chromatin organization are required to compact DNA into chromosomes, to ensure an accurate cell division.... more
The 26S proteasome is a multisubunit enzyme composed of a cylindrical catalytic core (20S) and a regulatory particle (19S) that together perform the essential degradation of cellular proteins tagged by ubiquitin. To date, however,... more
viii to Ribosomal RNA in Species of the Genus Nicotiana 33 II. The Relationship Between Haploid Chromosome Complements and Per Cents of rDNAgo in Nicotiana Species 35 III. Taxonomic and Cytogenetic Data for the Genus Nicotiana 36 IV. The... more
In mammals, histone H1 consists of a family of related proteins, including five replication-dependent (H1.1-H1.5) and two replication-independent (H1.10 and H1.0) subtypes, all expressed in somatic cells. To systematically study the... more
Under the terms of the "nº 2, alínea a, do Art.º 31º do Decreto-lei nº 230/2009", is hereby declared that the author afforded a major contribution to the conceptual design and technical execution of the work, interpretation of the results... more
Prostate cancers (PCas) become resistant to hormone withdrawal through increased androgen receptor (AR) signaling. Here we show increased AR-mediated transcription efficiency in PCa cells that have acquired the ability to grow in low... more
Malignant rhabdoid tumor (MRT) is driven by the loss of the SNF5 subunit of the SWI/SNF chromatin remodeling complex and then thought to be maintained by residual SWI/SNF (rSWI/SNF) complexes that remain present in the absence of SNF5.... more
Cyclin E together with its kinase partner Cdk2 is a critical regulator of entry into S phase. To identify novel genes that regulate the G1- to S-phase transition within a whole animal we made use of a hypomorphic cyclin E mutation,... more
Plant homeodomain (PHD) fingers are frequently present in proteins involved in chromatin remodelling, and some of them bind to histones. The family of proteins inhibitors of growth (ING) contains a PHD finger that bind to histone‐3... more
The effects of genotoxic stress can be mediated by activation of the Ataxia Telangiectasia Mutated (ATM) kinase, under both DNA damage-dependent (including ionizing radiation), and independent (including hypoxic stress) conditions. ATM... more
Background: Dia2 is an F-box protein found in the budding yeast, S. cerevisiae. Together with Skp1 and Cul1, Dia2 forms the substrate-determining part of an E3 ubiquitin ligase complex, otherwise known as the SCF. Dia2 has previously been... more
SummaryPioneer transcription factors direct cell differentiation by deploying new enhancer repertoires through their unique ability to target and initiate remodelling of closed chromatin. The initial steps of their action remain undefined... more
Pioneer transcription factors establish new cell-fate competence by triggering chromatin remodeling. However, many features of pioneer action, such as their kinetics and stability, remain poorly defined. Here, we show that Pax7, by... more
Mediator complex is essential for transcription by RNA polymerase II in eukaryotes. Although chromatin remodeling is an integral part of transcriptional activation at many promoters, whether Mediator is required for this function has not... more
Mediator complex is essential for transcription by RNA polymerase II in eukaryotes. Although chromatin remodeling is an integral part of transcriptional activation at many promoters, whether Mediator is required for this function has not... more
The Polycomb group (PcG) of proteins conveys epigenetic inheritance of repressed transcriptional states. In Drosophila, the Polycomb repressive complex 1 (PRC1) maintains the silent state by inhibiting the transcription machinery and... more
SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) responsive genes during oxidative stress. However, while the mechanism of SIRT6-mediated silencing is well understood, the mechanism of... more
Synthesis of the 45S rRNA by RNA polymerase I limits cell growth. Knowledge of the mechanism of its regulation is therefore key to understanding growth control. rRNA transcription is believed to be regulated solely at initiation/promoter... more
tains multiple tandem homologies to the DNA binding domain of high mobility group 1 (HMG-1), the HMG box (Figure 1C), and loops approximately 140 bp of ribosomal DNA into a single turn, a structure we have called the ribosomal enhancesome... more
Fourier harmonic analysis (FHA) assessed the sperm nuclear shape of 31 buffalo bulls with known fertility to identify the bull with top conception rates of 28-36% and lowest conception rates of 13-19%. The FHA model developed for water... more
Epigenetics refers to the study of heritable changes in gene expression or cellular phenotype without changes in DNA sequence. Epigenetic regulation of gene expression is accomplished by DNA methylation, histone modifications, histone... more
The integrity of the chromatin structure is essential to every process occurring within eukaryotic nuclei. However, there are no reliable tools to decipher the molecular composition of metaphase chromosomes. Here, we have applied infrared... more
Regulator of bithorax (Rg-bx)-, or trithorax (trx)lethal larvae occasionally show a homoeotic transformation of the dorsal prothorax to mesothoracic structures. This transformation suggests a reduced activity of the Sex combs reduced... more
In a dividing eukaryotic cell, proper chromosome segregation requires the dynamic yet persistent attachment of kinetochores to spindle microtubules. In the budding yeast Saccharomyces cerevisiae, this function is especially crucial... more
Human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) have the ability of differentiating into functional cardiomyocytes (CMs) for cell replacement therapy, tissue engineering, drug discovery and toxicity... more
Human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) have the ability of differentiating into functional cardiomyocytes (CMs) for cell replacement therapy, tissue engineering, drug discovery and toxicity... more
Analysis of the relationship between tran- scriptional activators and chromatin organization has focused largely on lower levels of chromatin structure. Here we describe striking remodeling of large-scale chromatin structure induced by a... more
BACKGROUNDProper nuclear organization is critical for cardiomyocyte (CM) function, as global structural remodeling of nuclear morphology and chromatin structure underpins the development and progression of cardiovascular disease. Previous... more
Ubiquitin-dependent molecular chaperone p97, also known as valosin-containing protein (VCP) or Cdc48, is an AAA ATPase involved in protein turnover and degradation. p97 converts its own ATPase hydrolysis into remodeling activity on a... more
It was pleasing to see the careful review of the accuracy of in-hospital falls risk screening tools in your June 2007 issue of the Journal, however, we believe the conclusion that the ''STRATIFY may still be useful in particular... more
The vascular system in plants facilitates long-distance transportation of water and nutrients through the xylem and phloem, while also providing mechanical support for vertical growth. Although many genes that regulate vascular... more
The molecular characterization of mechanisms underlying transcriptional control and epigenetic inheritance since the 1990s has paved the way for the development of targeted therapies that modulate these pathways. In the past two decades,... more
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