Abstract：
:Genomes exist in vivo as complex physical structures, and their functional output (i.e. the gene expression profile of a cell) is related to their spatial organization inside the nucleus as well as to local chromatin status. Chromatin modifications and chromosome conformation are distinct in different tissues and cell types, which corresponds closely with the diversity in gene-expression patterns found in different tissues of the body. The biological processes and mechanisms driving these general correlations are currently the topic of intense study. An emerging theme is that genome compartmentalization - both along the linear length of chromosomes, and in three dimensions by the spatial colocalization of chromatin domains and genomic loci from across the genome - is a crucial parameter in regulating genome expression. In this Commentary, we propose that a full understanding of genome regulation requires integrating three different types of data: first, one-dimensional data regarding the state of local chromatin - such as patterns of protein binding along chromosomes; second, three-dimensional data that describe the population-averaged folding of chromatin inside cells and; third, single-cell observations of three-dimensional spatial colocalization of genetic loci and trans factors that reveal information about their dynamics and frequency of colocalization.
journal_name
J Cell Scijournal_title
Journal of cell scienceauthors
Naumova N,Dekker Jdoi
10.1242/jcs.051631subject
Has Abstractpub_date
2010-06-15 00:00:00pages
1979-88issue
Pt 12eissn
0021-9533issn
1477-9137pii
123/12/1979journal_volume
123pub_type
杂志文章abstract：:Sequence similarity between the Drosophila segment polarity protein Armadillo and the vertebrate adherens junction protein beta-catenin raised the possibility that adherens junctions function in transduction of intercellular signals like that mediated by Wingless/Wnt-1. To substantiate the sequence similarity, propert...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1993-08-01 00:00:00
abstract：:Genetic analysis in the yeast Schizosaccharomyces pombe has shown that three genes cdc18, cut5, and cdt1, are essential for DNA synthesis and also for the checkpoint control that couples completion of DNA replication to the onset of mitosis. To test whether assembly of the replication initiation complex is an importan...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1995-09-01 00:00:00
abstract：:During spermatogenesis in mammals, the transcripts of transition protein 1 (TP 1) and protamine 1 (Prm 1) are under translational regulation. Following their transcription in round spermatids, the mRNAs for TP 1 and Prm 1 are stored in the cytoplasm from 3-7 days before being translated towards the end of spermatogene...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1991-09-01 00:00:00
abstract：:An analysis of the concanavalinA binding polypeptide components of bovine tongue epithelial desmosomes reveals that in addition to the known desmosomal glycoproteins of 100/115K (the 'desmocollins'), 140K and 160/165K ('desmoglein 1') there is an uncharacterized glycoprotein of 125K (K = Mr x 10(-3). This latter polyp...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1988-02-01 00:00:00
abstract：:The C terminus of the tubulin alpha-subunit of most eukaryotic cells undergoes a cycle of tyrosination and detyrosination using two specific enzymes, a tubulin tyrosine ligase (TTL) and a tubulin carboxypeptidase. Although this enzyme cycle is conserved in evolution and exhibits rapid turnover, the meaning of this mod...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1998-01-01 00:00:00
abstract：:Plectin, a cytolinker protein greater than 500 kDa in size, has an important role as a mechanical stabiliser of cells. It interlinks the various cytoskeletal filament systems and anchors intermediate filaments to peripheral junctional complexes. In addition, there is increasing evidence that plectin acts as a scaffold...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.02891
更新日期：2006-05-01 00:00:00
abstract：:Nearly all intermediate filament (IF) proteins share two sequence motifs located at the N- and the C-terminal ends of their helical rod domain ('coil 1a' and 'coil 2b', respectively). To examine the structural role of the coil 2b motif, we have performed in vitro assembly studies and in vivo microinjection experiments...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1992-05-01 00:00:00
abstract：:Regulation of the localization of mRNAs and local translation are universal features in eukaryotes and contribute to cellular asymmetry and differentiation. In Saccharomyces cerevisiae, localization of mRNAs that encode membrane proteins requires the She protein machinery, including the RNA-binding protein She2p, as w...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.149799
更新日期：2014-08-01 00:00:00
abstract：:The vacuolar H(+)-ATPase (V-ATPase) establishes pH gradients along secretory and endocytic pathways. Progressive acidification is essential for proteolytic processing of prohormones and aggregation of soluble content proteins. The V-ATPase V(0) subunit is thought to have a separate role in budding and fusion events. P...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.034298
更新日期：2009-10-01 00:00:00
abstract：:Integrin and receptor tyrosine kinase signalling networks cooperate to regulate various biological functions. The molecular details underlying the integration of both signalling networks remain largely uncharacterized. Here we identify a signalling module composed of a fibronectin-α5β1-integrin-integrin-linked-kinase ...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.091652
更新日期：2012-01-15 00:00:00
abstract：:Although endocytosis and exocytosis have been extensively studied in budding yeast, there have been relatively few investigations of these complex processes in the fission yeast Schizosaccharomyces pombe. Here we identify and characterize fission yeast Mug33, a novel Tea1-interacting protein, and show that Mug33 is in...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.084038
更新日期：2011-07-01 00:00:00
abstract：:5'AMP nucleotidase activity was localized by electron microscopy in Dictyostelium discoideum during cell differentiation. In addition, the activity was assayed by micro enzymic methods in sections dissected from specific cellular regions of lyophilized individuals. The results of the 2 procedures were in agreement, de...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1980-10-01 00:00:00
abstract：:The atomic force microscope (AFM) was used to directly image hippocampal neurons and glia. Using chemically fixed and living cells it was possible to reconstruct three-dimensional cell structure and detect sub-cellular features such as the nucleus, mitochondria and filaments. By repeatedly scanning a single living cel...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1993-02-01 00:00:00
abstract：:The working mechanism of the eukaryotic flagellar axoneme remains one of nature's most enduring puzzles. The basic mechanical operation of the axoneme is now a story that is fairly complete; however, the mechanism for coordinating the action of the dynein motor proteins to produce beating is still controversial. Altho...
journal_title：Journal of cell science
pub_type： 杂志文章,评审
doi：10.1242/jcs.051326
更新日期：2010-02-15 00:00:00
abstract：:Sonic hedgehog (Shh) and its patched-smoothened receptor complex control a variety of functions in the developing central nervous system, such as neural cell proliferation and differentiation. Recently, Shh signaling components have been found to be expressed at the synaptic level in the postnatal brain, suggesting a ...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.247700
更新日期：2020-10-23 00:00:00
abstract：:In primary cultures of rat cerebellar granule cells with a functional network of glutamatergic neurons, the expression pattern of the different subunits of nitric-oxide (NO)-sensitive guanylyl cyclase changes during cell differentiation. These cells express the alpha1, alpha2 and beta1 subunits of NO-sensitive guanyly...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.00620
更新日期：2003-08-01 00:00:00
abstract：:A major challenge in biology is to understand how genetic information is interpreted to direct the formation of specialized tissues within a multicellular organism. During differentiation, changes in chromatin structure and nuclear organization establish heritable patterns of gene expression in response to signals. Ep...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.01390
更新日期：2004-09-01 00:00:00
abstract：:Several lines of evidence indicate that increases in nuclear Ca(2+) have specific biological effects that differ from those of cytosolic Ca(2+), suggesting that they occur independently. The mechanisms involved in controlling nuclear Ca(2+) signaling are both controversial and still poorly understood. Using hypotonic ...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.02446
更新日期：2005-07-15 00:00:00
abstract：:Recently, several 3D images of kinesin-family motor domains interacting with microtubules have been obtained by analysis of electron microscope images of frozen hydrated complexes at much higher resolutions (9-12 A) than in previous reports (15-30 A). The high-resolution maps show a complex interaction interface betwe...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.016931
更新日期：2007-11-15 00:00:00
abstract：:The early adhesive interaction of living cells with substrates was examined. L1210 cells were allowed to interact with collagen or glass in serum-containing medium (time of cell-substrate interaction, tint, under stationary conditions, was within 2-25 min) or in serum-free medium (tint was 5 s-15 min). The relative nu...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1984-03-01 00:00:00
abstract：:Rab GTPases regulate various membrane trafficking pathways but the mechanisms by which GTPase-activating proteins recognise specific Rabs are not clear. Rab8 is involved in controlling several trafficking processes, including the trafficking of transferrin receptor from the early endosome to the recycling endosome. He...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.102327
更新日期：2012-11-01 00:00:00
abstract：:In this paper we examine DNA repair in the mouse. Using stringently applied inhibitors of DNA synthesis (hydroxyurea and 1-beta-D-arabinofuranosylcytosine) after ultraviolet irradiation we have quantitated an early step in the repair process - the frequency of single-strand DNA breaks, products of enzymic incision--in...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1983-03-01 00:00:00
abstract：:The adaptive immune response depends on the interaction of T cells and antigen-presenting cells at the immune synapse. Formation of the immune synapse and the subsequent T-cell activation are highly dependent on the actin cytoskeleton. In this work, we describe that T cells express drebrin, a neuronal actin-binding pr...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.064238
更新日期：2010-04-01 00:00:00
abstract：:The effects of isolated plasma membranes on cohesion of Dictyostelium discoideum Ax-2 cells have been studied. Membranes isolated from cells in the log phase of growth gave complete inhibition of log-phase cell cohesion. This effect was specific for the cohesion log-phase cells mediated by contact sites B, since the c...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1979-12-01 00:00:00
abstract：:Expression of actin was examined in a cultured rat embryonic cell line 3Y1 and transformed cell lines that originated from 3Y1. An alpha-actin in addition to cytoplasmic beta- and gamma-actins was detected in 3Y1 by two-dimensional gel electrophoresis. This alpha-actin was hardly detected at all in the transformants i...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1990-08-01 00:00:00
abstract：:The proteasome is the major degradation machinery of the cell that regulates multiple cellular processes as diverse as cell cycle, signal transduction and gene expression. Recognition and unfolding of target proteins involves the regulatory cap whose base contains six AAA-ATPases that display reverse chaperone activit...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.02743
更新日期：2006-01-15 00:00:00
abstract：:The lipid phosphate phosphatase-related proteins (LPPRs), also known as plasticity-related genes (PRGs), are classified as a new brain-enriched subclass of the lipid phosphate phosphatase (LPP) superfamily. They induce membrane protrusions, neurite outgrowth or dendritic spine formation in cell lines and primary neuro...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.169789
更新日期：2015-09-01 00:00:00
abstract：:Activator of G-protein signaling 3 (AGS3, also known as GPSM1) regulates the trans-Golgi network. The AGS3 GoLoco motif binds to Gαi and thereby regulates the transport of proteins to the plasma membrane. Compaction of early embryos is based on the accumulation of E-cadherin (Cdh1) at cell-contacted membranes. However...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.243238
更新日期：2020-12-07 00:00:00
abstract：:Cartilage oligomeric matrix protein (COMP) is an abundant component in the extracellular matrix (ECM) of load-bearing tissues such as tendons and cartilage. It provides adaptor functions by bridging different ECM structures. We have previously shown that COMP is also a constitutive component of healthy human skin and ...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：10.1242/jcs.180216
更新日期：2016-02-15 00:00:00
abstract：:High endothelial cells lining the post capillary venules in the paracortical areas of rat lymph nodes were found by autoradiography to incorporate [35S]sulphate, whether it was injected into the footpad to reach the draining popliteal lymph node or added to short-term cultures of cervical lymph node slices. The early ...
journal_title：Journal of cell science
pub_type： 杂志文章
doi：
更新日期：1982-10-01 00:00:00
