Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques.

Abstract:

:Little is known about how chromatin folds in its native state. Using optimized in situ hybridization and live imaging techniques have determined compaction ratios and fiber flexibility for interphase chromatin in budding yeast. Unlike previous studies, ours examines nonrepetitive chromatin at intervals short enough to be meaningful for yeast chromosomes and functional domains in higher eukaryotes. We reconcile high-resolution fluorescence in situ hybridization data from intervals of 14-100 kb along single chromatids with measurements of whole chromosome arms (122-623 kb in length), monitored in intact cells through the targeted binding of bacterial repressors fused to GFP derivatives. The results are interpreted with a flexible polymer model and suggest that interphase chromatin exists in a compact higher-order conformation with a persistence length of 170-220 nm and a mass density of approximately 110-150 bp/nm. These values are equivalent to 7-10 nucleosomes per 11-nm turn within a 30-nm-like fiber structure. Comparison of long and short chromatid arm measurements demonstrates that chromatin fiber extension is also influenced by nuclear geometry. The observation of this surprisingly compact chromatin structure for transcriptionally competent chromatin in living yeast cells suggests that the passage of RNA polymerase II requires a very transient unfolding of higher-order chromatin structure.

authors

Bystricky K,Heun P,Gehlen L,Langowski J,Gasser SM

doi

10.1073/pnas.0402766101

keywords:

subject

Has Abstract

pub_date

2004-11-23 00:00:00

pages

16495-500

issue

47

eissn

0027-8424

issn

1091-6490

pii

0402766101

journal_volume

101

pub_type

杂志文章
  • An alternative pathway for signal flow from rod photoreceptors to ganglion cells in mammalian retina.

    abstract::Rod signals in the mammalian retina are thought to reach ganglion cells over the circuit rod-->rod depolarizing bipolar cell-->AII amacrine cell-->cone bipolar cells-->ganglion cells. A possible alternative pathway involves gap junctions linking the rods and cones, the circuit being rod-->cone-->cone bipolar cells-->g...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.23.10658

    authors: DeVries SH,Baylor DA

    更新日期:1995-11-07 00:00:00

  • Synthesis of bacteriophage lambda DNA in vitro: requirement for O and P gene products.

    abstract::We have developed a cell-free system to study bacteriophage lambda DNA replication. Maximal DNA synthesis in vitro requires the four deoxynucleoside triphosphates, ATP, and exogenous lambda DNA. DNA synthesis requires the products of the phage O and P genes but is not inhibited by lambda repressor. The kinetics of syn...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.71.5.1758

    authors: Shizuya H,Richardson CC

    更新日期:1974-05-01 00:00:00

  • Identification of a new subset of lymph node stromal cells involved in regulating plasma cell homeostasis.

    abstract::Antibody-secreting plasma cells (PCs) arise rapidly during adaptive immunity to control infections. The early PCs are retained within the reactive lymphoid organ where their localization and homeostasis rely on extrinsic factors, presumably produced by local niche cells. While myeloid cells have been proposed to form ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1712628115

    authors: Huang HY,Rivas-Caicedo A,Renevey F,Cannelle H,Peranzoni E,Scarpellino L,Hardie DL,Pommier A,Schaeuble K,Favre S,Vogt TK,Arenzana-Seisdedos F,Schneider P,Buckley CD,Donnadieu E,Luther SA

    更新日期:2018-07-17 00:00:00

  • GABA uptake into astrocytes is not associated with significant metabolic cost: implications for brain imaging of inhibitory transmission.

    abstract::Synaptically released glutamate has been identified as a signal coupling excitatory neuronal activity to increased glucose utilization. The proposed mechanism of this coupling involves glutamate uptake into astrocytes resulting in increased intracellular Na+ (Nai+) and activation of the Na+/K+-ATPase. Increased metabo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2132096100

    authors: Chatton JY,Pellerin L,Magistretti PJ

    更新日期:2003-10-14 00:00:00

  • Squid Pax-6 and eye development.

    abstract::Pax-6 in vertebrates and its homolog eyeless in Drosophila are known to be essential for eye development. Here we investigate the role of Pax-6 in eye development in another major systematic group, molluscs. We demonstrate that alternatively spliced RNAs derived from a single Pax-6 gene in the squid (Loligo opalescens...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.6.2421

    authors: Tomarev SI,Callaerts P,Kos L,Zinovieva R,Halder G,Gehring W,Piatigorsky J

    更新日期:1997-03-18 00:00:00

  • Skint-1 is a highly specific, unique selecting component for epidermal T cells.

    abstract::αβ T-cell repertoire selection is mediated by peptide-MHC complexes presented by thymic epithelial or myeloid cells, and by lipid-CD1 complexes expressed by thymocytes. γδ T-cell repertoire selection, by contrast, is largely unresolved. Mice mutant for Skint-1, a unique Ig superfamily gene, do not develop canonical Vγ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1010890108

    authors: Barbee SD,Woodward MJ,Turchinovich G,Mention JJ,Lewis JM,Boyden LM,Lifton RP,Tigelaar R,Hayday AC

    更新日期:2011-02-22 00:00:00

  • Condition and fate of logged forests in the Brazilian Amazon.

    abstract::The long-term viability of a forest industry in the Amazon region of Brazil depends on the maintenance of adequate timber volume and growth in healthy forests. Using extensive high-resolution satellite analyses, we studied the forest damage caused by recent logging operations and the likelihood that logged forests wou...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0604093103

    authors: Asner GP,Broadbent EN,Oliveira PJ,Keller M,Knapp DE,Silva JN

    更新日期:2006-08-22 00:00:00

  • EPSIN1 and MTV1 define functionally overlapping but molecularly distinct trans-Golgi network subdomains in Arabidopsis.

    abstract::The plant trans-Golgi network (TGN) is a central trafficking hub where secretory, vacuolar, recycling, and endocytic pathways merge. Among currently known molecular players involved in TGN transport, three different adaptor protein (AP) complexes promote vesicle generation at the TGN with different cargo specificity a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2004822117

    authors: Heinze L,Freimuth N,Rößling AK,Hahnke R,Riebschläger S,Fröhlich A,Sampathkumar A,McFarlane HE,Sauer M

    更新日期:2020-10-13 00:00:00

  • Identification of a natural soluble neuropilin-1 that binds vascular endothelial growth factor: In vivo expression and antitumor activity.

    abstract::Neuropilin-1 (NRP1) is a 130-kDa transmembrane receptor for semaphorins, mediators of neuronal guidance, and for vascular endothelial growth factor 165 (VEGF(165)), an angiogenesis factor. A 2.2-kb truncated NRP1 cDNA was cloned that encodes a 644-aa soluble NRP1 (sNRP1) isoform containing just the a/CUB and b/coagula...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.040337597

    authors: Gagnon ML,Bielenberg DR,Gechtman Z,Miao HQ,Takashima S,Soker S,Klagsbrun M

    更新日期:2000-03-14 00:00:00

  • Computation of mutual fitness by competing bacteria.

    abstract::Competing populations in shared spaces with nonrenewable resources do not necessarily wage a battle for dominance at the cost of extinction of the less-fit strain if there are fitness advantages to the presence of the other strain. We report on the use of nanofabricated habitat landscapes to study the population dynam...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0810792105

    authors: Keymer JE,Galajda P,Lambert G,Liao D,Austin RH

    更新日期:2008-12-23 00:00:00

  • Regulation of T-cell antigen receptor (TCR) alpha-chain expression by TCR beta-chain transcripts.

    abstract::The TCR is an alpha beta heterodimer, a part of the multimeric structure through which physiological T-cell activation occurs. The expression of TCR alpha chain is greatly diminished in a beta-chain-deficient mutant Jurkat cell line (J.RT3-T3.5). The relationship between the expression of the TCR alpha and beta chains...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.9.3712

    authors: Chung S,Strominger JL

    更新日期:1995-04-25 00:00:00

  • Discovery of a free-living chlorophyll d-producing cyanobacterium with a hybrid proteobacterial/cyanobacterial small-subunit rRNA gene.

    abstract::Chlorophyll d-producing cyanobacteria are a recently described group of phototrophic bacteria that is a major focus of photosynthesis research, previously known only from marine environments in symbiosis with eukaryotes. We have discovered a free-living member of this group from a eutrophic hypersaline lake. Phylogene...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0405667102

    authors: Miller SR,Augustine S,Olson TL,Blankenship RE,Selker J,Wood AM

    更新日期:2005-01-18 00:00:00

  • Observing the 1H NMR signal of the myoglobin Val-E11 in myocardium: an index of cellular oxygenation.

    abstract::The 1H NMR signal from oxymyoglobin, a low-concentration diamagnetic protein, is visible in myocardial tissue. The methyl group of the Val-E11 resonates in a clear spectral region at -2.76 ppm and responds to dynamic changes in cellular oxygenation. With CO, the signal shifts to -2.4 ppm. The Val-E11 peak assignment a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.10.4731

    authors: Kreutzer U,Wang DS,Jue T

    更新日期:1992-05-15 00:00:00

  • Role of the regulatory subunit of bovine pyruvate dehydrogenase phosphatase.

    abstract::Bovine pyruvate dehydrogenase phosphatase (PDP) is a Mg2+-dependent and Ca2+-stimulated heterodimer that is a member of the protein phosphatase 2C family and is localized to mitochondria. Insight into the function of the regulatory subunit of PDP (PDPr) has been gained. It decreases the sensitivity of the catalytic su...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.10.4953

    authors: Yan J,Lawson JE,Reed LJ

    更新日期:1996-05-14 00:00:00

  • Neural-inspired sensors enable sparse, efficient classification of spatiotemporal data.

    abstract::Sparse sensor placement is a central challenge in the efficient characterization of complex systems when the cost of acquiring and processing data is high. Leading sparse sensing methods typically exploit either spatial or temporal correlations, but rarely both. This work introduces a sparse sensor optimization that i...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1808909115

    authors: Mohren TL,Daniel TL,Brunton SL,Brunton BW

    更新日期:2018-10-16 00:00:00

  • Expression of cellular homologues of retroviral onc genes in human hematopoietic cells.

    abstract::Total cellular poly(A)-enriched RNA from a variety of fresh human leukemic blood cells and hematopoietic cell lines was analyzed for homology with molecularly cloned DNA probes containing the onc sequence of Abelson murine leukemia virus (Ab-MuLV), Harvey murine sarcoma virus (Ha-MuSV), simian sarcoma virus (SSV), and...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.8.2490

    authors: Westin EH,Wong-Staal F,Gelmann EP,Dalla-Favera R,Papas TS,Lautenberger JA,Eva A,Reddy EP,Tronick SR,Aaronson SA,Gallo RC

    更新日期:1982-04-01 00:00:00

  • Transverse fields to tune an Ising-nematic quantum phase transition.

    abstract::The paradigmatic example of a continuous quantum phase transition is the transverse field Ising ferromagnet. In contrast to classical critical systems, whose properties depend only on symmetry and the dimension of space, the nature of a quantum phase transition also depends on the dynamics. In the transverse field Isi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1712533114

    authors: Maharaj AV,Rosenberg EW,Hristov AT,Berg E,Fernandes RM,Fisher IR,Kivelson SA

    更新日期:2017-12-19 00:00:00

  • From the Cover: Osmotrophy in modular Ediacara organisms.

    abstract::The Ediacara biota include macroscopic, morphologically complex soft-bodied organisms that appear globally in the late Ediacaran Period (575-542 Ma). The physiology, feeding strategies, and functional morphology of the modular Ediacara organisms (rangeomorphs and erniettomorphs) remain debated but are critical for und...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0904836106

    authors: Laflamme M,Xiao S,Kowalewski M

    更新日期:2009-08-25 00:00:00

  • Molecular cloning of the pheromone biosynthesis-activating neuropeptide in Helicoverpa zea.

    abstract::Pheromone biosynthesis-activating neuropeptide (PBAN) regulates sex pheromone biosynthesis in female Helicoverpa (Heliothis) zea. Two oligonucleotide probes representing two overlapping amino acid regions of PBAN were used to screen 2.5 x 10(5) recombinant plaques, and a positive recombinant clone was isolated. Sequen...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.1.142

    authors: Davis MT,Vakharia VN,Henry J,Kempe TG,Raina AK

    更新日期:1992-01-01 00:00:00

  • Insect immune response to bacterial infection is mediated by eicosanoids.

    abstract::Inhibition of eicosanoid formation in larvae of the tobacco hornworm Manduca sexta, using specific inhibitors of phospholipase A2, cyclooxygenase, and lipoxygenase, severely weakened the ability of larvae to clear the bacterium Serratia marscescens from their hemolymph. The reduced capability to remove bacteria is ass...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.3.1064

    authors: Stanley-Samuelson DW,Jensen E,Nickerson KW,Tiebel K,Ogg CL,Howard RW

    更新日期:1991-02-01 00:00:00

  • A unifying framework for the transient parasite dynamics of migratory hosts.

    abstract::Migrations allow animals to track seasonal changes in resources, find mates, and avoid harsh climates, but these regular, long-distance movements also have implications for parasite dynamics and animal health. Migratory animals have been dubbed "superspreaders" of infection, but migration can also reduce parasite burd...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1908777117

    authors: Peacock SJ,Krkošek M,Lewis MA,Molnár PK

    更新日期:2020-05-19 00:00:00

  • A DNA fragment with an alpha-phosphorothioate nucleotide at one end is asymmetrically blocked from digestion by exonuclease III and can be replicated in vivo.

    abstract::2'-Deoxyadenosine 5'-O-(1-thiotriphosphate) (dATP[alpha S]) was introduced into the 3' ends of DNA restriction fragments with Escherichia coli DNA polymerase I to give phosphorothioate internucleotide linkages. Such "capped" 3' ends were found to be resistant to exonuclease III digestion. Moreover, the resistance to d...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.78.12.7350

    authors: Putney SD,Benkovic SJ,Schimmel PR

    更新日期:1981-12-01 00:00:00

  • Unliganded gating of acetylcholine receptor channels.

    abstract::We estimated the unliganded opening and closing rate constants of neuromuscular acetylcholine receptor-channels (AChRs) having mutations that increased the gating equilibrium constant. For some mutant combinations, spontaneous openings occurred in clusters. For 25 different constructs, the unliganded gating equilibriu...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0809272106

    authors: Purohit P,Auerbach A

    更新日期:2009-01-06 00:00:00

  • MiR-2 family regulates insect metamorphosis by controlling the juvenile hormone signaling pathway.

    abstract::In 2009 we reported that depletion of Dicer-1, the enzyme that catalyzes the final step of miRNA biosynthesis, prevents metamorphosis in Blattella germanica. However, the precise regulatory roles of miRNAs in the process have remained elusive. In the present work, we have observed that Dicer-1 depletion results in an ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1418522112

    authors: Lozano J,Montañez R,Belles X

    更新日期:2015-03-24 00:00:00

  • The Wingless homolog Wnt5a stimulates phagocytosis but not bacterial killing.

    abstract::Phagocytosis is a primary defense program orchestrated by monocytes/macrophages. Unregulated phagocytosis can lead to pathological conditions. In the current study we have demonstrated that Wnt5a stimulates phagocytosis through PI3 kinase-Rac1 and lipid-raft-dependent processes. Wnt5a-mediated augmentation in phagocyt...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1207789109

    authors: Maiti G,Naskar D,Sen M

    更新日期:2012-10-09 00:00:00

  • Reduced production of B-1-specified common lymphoid progenitors results in diminished potential of adult marrow to generate B-1 cells.

    abstract::B-1 B cells have been proposed to be preferentially generated from fetal progenitors, but this view is challenged by studies concluding that B-1 production is sustained throughout adult life. To address this controversy, we compared the efficiency with which hematopoietic stem cells (HSCs) and common lymphoid progenit...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1107172108

    authors: Barber CL,Montecino-Rodriguez E,Dorshkind K

    更新日期:2011-08-16 00:00:00

  • Several mRNAs with variable 3' untranslated regions and different stability encode the human PR264/SC35 splicing factor.

    abstract::We have recently established that several mRNAs encode the PR264/SC35 splicing factor and that their expression is related to that of c-Myb in human hematopoietic cells. We now report that the various PR264 mRNAs whose expression is transactivated by c-Myb proteins encode an identical PR264/SC35 polypeptide. These mRN...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.3.932

    authors: Sureau A,Perbal B

    更新日期:1994-02-01 00:00:00

  • Imaging the Holon string of the Hubbard model.

    abstract::It has been a long-sought goal of quantum simulation to find answers to outstanding questions in condensed-matter physics. A famous example is finding the ground state and the excitations of the two-dimensional (2D) Hubbard model with strong repulsion below half-filling. This system is a doped antiferromagnet and is o...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2004268117

    authors: Ho TL

    更新日期:2020-10-20 00:00:00

  • The final acylation step in taxol biosynthesis: cloning of the taxoid C13-side-chain N-benzoyltransferase from Taxus.

    abstract::The formation of several acyl groups and an amide group of Taxol is catalyzed by regioselective CoA thioester-dependent acyltransferases. Several full-length acyltransferase sequences, obtained from a cDNA library constructed from mRNA isolated from Taxus cuspidata cells induced for Taxol production with methyl jasmon...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.082115799

    authors: Walker K,Long R,Croteau R

    更新日期:2002-07-09 00:00:00

  • Chronicling changes in the somatosensory neurons after peripheral nerve injury.

    abstract::Current drug discovery efforts focus on identifying lead compounds acting on a molecular target associated with an established pathological state. Concerted molecular changes that occur in specific cell types during disease progression have generally not been identified. Here, we used constellation pharmacology to inv...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1922618117

    authors: Raghuraman S,Xie JY,Giacobassi MJ,Tun JO,Chase K,Lu D,Teichert RW,Porreca F,Olivera BM

    更新日期:2020-10-20 00:00:00