Nucleo-cytoplasmic environment modulates spatiotemporal p53 phase separation.

Liquid-liquid phase separation of various transcription factors into biomolecular condensates plays an essential role in gene regulation. Here, using cellular models and in vitro studies, we show the spatiotemporal formation and material properties of p53 condensates that might dictate its function. In particular, p53 forms liquid-like condensates in the nucleus of cells, which can bind to DNA and perform transcriptional activity.

UBR7 in concert with EZH2 inhibits the TGF-β signaling leading to extracellular matrix remodeling.

The intricate interplay between resident cells and the extracellular matrix (ECM) profoundly influences cancer progression. In triple-negative breast cancer (TNBC), ECM architecture evolves due to the enrichment of lysyl oxidase, fibronectin, and collagen, promoting distant metastasis. Here we uncover a pivotal transcription regulatory mechanism involving the epigenetic regulator UBR7 and histone methyltransferase EZH2 in regulating transforming growth factor (TGF)-β/Smad signaling, affecting the expression of ECM genes.

Nuclear envelope, chromatin organizers, histones, and DNA: The many achilles heels exploited across cancers.

In eukaryotic cells, the genome is organized in the form of chromatin composed of DNA and histones that organize and regulate gene expression. The dysregulation of chromatin remodeling, including the aberrant incorporation of histone variants and their consequent post-translational modifications, is prevalent across cancers. Additionally, nuclear envelope proteins are often deregulated in cancers, which impacts the 3D organization of the genome.

Nuclear envelope protein lamin B receptor protects the genome from chromosomal instability and tumorigenesis.

Lamin B Receptor (LBR) is an inner nuclear membrane protein that assembles the nuclear envelope post mitosis. Here we show that LBR depletion induces mitotic defects accompanied by recurrent chromosomal losses. In addition, LBR knockdown results in nuclear aberrations such as nuclear blebs and micronuclei, with chromosomes showing higher frequency of losses, being enriched within the micronucleus.

Direct Demonstration of Seed Size-Dependent α-Synuclein Amyloid Amplification.

The size of amyloid seeds is known to modulate their autocatalytic amplification and cellular toxicity. However, the seed size-dependent secondary nucleation mechanism, toxicity, and disease-associated biological processes mediated by α-synuclein (α-Syn) fibrils are largely unknown. Using the cellular model and reconstitution, we showed that the size of α-Syn fibril seeds dictates not only their cellular internalization and associated cell death but also the distinct mechanisms of fibril amplification pathways involved in the pathological conformational change of α-Syn.

Nup93 and CTCF modulate spatiotemporal dynamics and function of the HOXA gene locus during differentiation.

Nucleoporins regulate nuclear transport and are also involved in DNA damage, repair, cell cycle, chromatin organization and gene expression. Here, we studied the role of nucleoporin Nup93 and the chromatin organizer CTCF in regulating expression of the HOXA gene locus during differentiation. ChIP sequencing revealed a significant overlap between Nup93 and CTCF peaks.

Studying the Role of Chromosomal Instability (CIN) in GI Cancers Using Patient-derived Organoids.

Chromosomal instability (CIN) is associated with the initiation and progression of gastrointestinal (GI) tract cancers. Cancers of the GI tract are typically characterized by altered chromosome numbers. While the dynamics of CIN have been extensively characterized in 2D monolayer cell cultures derived from GI tumors, the tumor microenvironment and 3D tumor architecture also contribute to the progression of CIN, which is not captured in 2D cell culture systems.

A Novel Regulatory Element Regulates Human in a CTCF-Dependent Manner.

The long noncoding RNA XIST is the master regulator for the process of X chromosome inactivation (XCI) in mammalian females. Here, we report the existence of a hitherto-uncharacterized regulatory element (cRE) within the first exon of human , which determines the transcriptional status of during the initiation and maintenance phases of XCI. In the initiation phase, pluripotency factors bind to this cRE and keep repressed.

Role of A- and B-type lamins in nuclear structure-function relationships.

Nuclear lamins are type V intermediate filament proteins that form a filamentous meshwork beneath the inner nuclear membrane. Additionally, a sub-population of A- and B-type lamins localizes in the nuclear interior. The nuclear lamina protects the nucleus from mechanical stress and mediates nucleo-cytoskeletal coupling.

Twist1 induces chromosomal instability (CIN) in colorectal cancer cells.

Twist1 is a basic helix-loop-helix transcription factor, essential during early development in mammals. While Twist1 induces epithelial-to-mesenchymal transition (EMT), here we show that Twist1 overexpression enhances nuclear and mitotic aberrations. This is accompanied by an increase in whole chromosomal copy number gains and losses, underscoring the role of Twist1 in inducing chromosomal instability (CIN) in colorectal cancer cells.

Lamin A/C modulates spatial organization and function of the Hsp70 gene locus via nuclear myosin I.

The structure-function relationship of the nucleus is tightly regulated, especially during heat shock. Typically, heat shock activates molecular chaperones that prevent protein misfolding and preserve genome integrity. However, the molecular mechanisms that regulate nuclear structure-function relationships during heat shock remain unclear.

Imaging Chromosome Territory and Gene Loci Positions in Cells Grown on Soft Matrices.

It is well established that the genome is non-randomly organized in the interphase nucleus with gene rich chromosome territories toward the nuclear interior, while gene poor chromosome territories are proximal to the nuclear periphery. In vivo tissue stiffness and architecture modulates cell type-specific genome organization and gene expression programs. However, the impact of external mechanical forces on the non-random organization of the genome is not completely understood.

Lamin A/C and Emerin depletion impacts chromatin organization and dynamics in the interphase nucleus.

Background: Nuclear lamins are type V intermediate filament proteins that maintain nuclear structure and function. Furthermore, Emerin - an interactor of Lamin A/C, facilitates crosstalk between the cytoskeleton and the nucleus as it also interacts with actin and Nuclear Myosin 1 (NM1).

Results: Here we show that the depletion of Lamin A/C or Emerin, alters the localization of the nuclear motor protein - Nuclear Myosin 1 (NM1) that manifests as an increase in NM1 foci in the nucleus and are rescued to basal levels upon the combined knockdown of Lamin A/C and Emerin.

Nucleolin modulates compartmentalization and dynamics of histone 2B-ECFP in the nucleolus.

Eukaryotic cells have 2 to ​3 discrete nucleoli required for ribosome synthesis. Nucleoli are phase separated nuclear sub-organelles. Here we examined the role of nuclear Lamins and nucleolar factors in modulating the compartmentalization and dynamics of histone 2B (H2B-ECFP) in the nucleolus.

Genome 3D-architecture: Its plasticity in relation to function.

The genome of higher eukaryotes is non-randomly organized in the interphase nucleus. However, notwithstanding the absence of membrane bound sub-compartments, the nucleus coordinates a number of functions largely by organizing chromatin in a non-random but dynamic manner. The plasticity of chromatin structure and function relies on epigenetic modifications as well as its association with nuclear landmarks such as the nuclear envelope, nuclear lamina, nuclear pore complex and nuclear bodies such as the nucleolus among others.

Emerin modulates spatial organization of chromosome territories in cells on softer matrices.

Cells perceive and relay external mechanical forces into the nucleus through the nuclear envelope. Here we examined the effect of lowering substrate stiffness as a paradigm to address the impact of altered mechanical forces on nuclear structure-function relationships. RNA sequencing of cells on softer matrices revealed significant transcriptional imbalances, predominantly in chromatin associated processes and transcriptional deregulation of human Chromosome 1.

Lamin B2 Modulates Nucleolar Morphology, Dynamics, and Function.

The nucleolus is required for ribosome biogenesis. Human cells have 2 or 3 nucleoli associated with nucleolar organizer region (NOR)-bearing chromosomes. An increase in number and altered nucleolar morphology define cancer cells.

HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205.

Background: The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associated with human chromosomes 5, 7 and 16 and with the promoters of the HOXA gene as revealed by ChIP-on-chip studies using tiling microarrays for these chromosomes.

A Small Molecule for Controlled Generation of Peroxynitrite.

2-Methyl-3-[1-(N,N-dimethylamino)diazen-1-ium-1,2-diol-2-ato-methyl]-naphthalene-1,4-dione 1 (HyPR-1), a small molecule containing a superoxide generator strategically linked to a diazeniumdiolate-based nitric oxide donor, is reported. Evidence for HyPR-1's ability to generate peroxynitrite in the presence of an enzyme as well as enhance peroxynitrite within cells is provided. The utility of this tool in generating peroxynitrite for cellular studies is demonstrated.

Chromosomal aneuploidies induced upon Lamin B2 depletion are mislocalized in the interphase nucleus.

Chromosome territories assume non-random positions in the interphase nucleus with gene-rich chromosomes localized toward the nuclear interior and gene-poor chromosome territories toward the nuclear periphery. Lamins are intermediate filament proteins of the inner nuclear membrane required for the maintenance of nuclear structure and function. Here, we show using whole-genome expression profiling that Lamin A/C or Lamin B2 depletion in an otherwise diploid colorectal cancer cell line (DLD1) deregulates transcript levels from specific chromosomes.

A highly selective sulfinate ester probe for thiol bioimaging.

We describe here hitherto unexplored chemistry of the sulfinate ester functional group as being highly selective towards nucleophilic substitution by thiols at physiological pH. Using this cleavable trigger, an optical thiol probe that is suitable for thiol bioimaging has been developed.

Nitroreductase-activated nitric oxide (NO) prodrugs.

Due to the involvement of nitric oxide (NO) in numerous and diverse physiological processes, site-directed delivery of therapeutic NO in order to minimize unwanted side-effects is necessary. O(2)-(4-Nitrobenzyl) diazeniumdiolates are designed as substrates for Escherichia coli nitroreductase (NTR), an enzyme that is frequently used to facilitate directed delivery of cytotoxic species to cancers. O(2)-(4-Nitrobenzyl) diazeniumdiolates are found to be stable in aqueous buffer but are metabolized by NTR to produce NO.

INDQ/NO, a bioreductively activated nitric oxide prodrug.

The design, synthesis, and development of INDQ/NO, a novel nitric oxide (NO) prodrug targeted by a bioreductive trigger, are described. INDQ/NO, an indolequinone-diazeniumdiolate is found to be metabolized to produce NO by DT-diaphorase, a bioreductive enzyme that is overexpressed in certain cancers and hypoxic tumors. Cell-based assays revealed that INDQ/NO induces DNA damage and is a potent inhibitor of cancer cell proliferation.

Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted.

Background: While attempting to reanalyze published data from Agilent 4 x 44 human expression chips, we found that some of the 60-mer olignucleotide features could not be interpreted as representing single human genes. For example, some of the oligonucleotides align with the transcripts of more than one gene. We decided to check the annotations for all autosomes and the X chromosome systematically using bioinformatics methods.

Impaired DNA damage response, genome instability, and tumorigenesis in SIRT1 mutant mice.

In lower eukaryotes, Sir2 serves as a histone deacetylase and is implicated in chromatin silencing, longevity, and genome stability. Here we mutated the Sirt1 gene, a homolog of yeast Sir2, in mice to study its function. We show that a majority of SIRT1 null embryos die between E9.