Purification and enrichment of specific chromatin loci.

Abstract:

:Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then describe the published strategies and discuss their advantages and limitations. We conclude by discussing why significant technology developments are required to unambiguously describe the composition of small single loci.

journal_name

Nat Methods

journal_title

Nature methods

authors

Gauchier M,van Mierlo G,Vermeulen M,Déjardin J

doi

10.1038/s41592-020-0765-4

subject

Has Abstract

pub_date

2020-04-01 00:00:00

pages

380-389

issue

4

eissn

1548-7091

issn

1548-7105

pii

10.1038/s41592-020-0765-4

journal_volume

17

pub_type

杂志文章,评审
  • Harnessing fungal bioluminescence.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-019-0311-4

    authors: Strack R

    更新日期:2019-02-01 00:00:00

  • Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.

    abstract::Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been cha...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2558

    authors: Gisselbrecht SS,Barrera LA,Porsch M,Aboukhalil A,Estep PW 3rd,Vedenko A,Palagi A,Kim Y,Zhu X,Busser BW,Gamble CE,Iagovitina A,Singhania A,Michelson AM,Bulyk ML

    更新日期:2013-08-01 00:00:00

  • Long-term expansion of alveolar stem cells derived from human iPS cells in organoids.

    abstract::The stable expansion of tissue-specific stem cells in vitro has contributed to research on several organs. Alveolar epithelial type II (AT2) cells function as tissue stem cells in the lung, but robust models for studying human AT2 cells are lacking. Here we report a method for the efficient generation and long-term ex...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4448

    authors: Yamamoto Y,Gotoh S,Korogi Y,Seki M,Konishi S,Ikeo S,Sone N,Nagasaki T,Matsumoto H,Muro S,Ito I,Hirai T,Kohno T,Suzuki Y,Mishima M

    更新日期:2017-11-01 00:00:00

  • Glycomics: an integrated systems approach to structure-function relationships of glycans.

    abstract::In comparison with genomics and proteomics, the advancement of glycomics has faced unique challenges in the pursuit of developing analytical and biochemical tools and biological readouts to investigate glycan structure-function relationships. Glycans are more diverse in terms of chemical structure and information dens...

    journal_title:Nature methods

    pub_type: 杂志文章,评审

    doi:10.1038/nmeth807

    authors: Raman R,Raguram S,Venkataraman G,Paulson JC,Sasisekharan R

    更新日期:2005-11-01 00:00:00

  • An FDR metric for top-down proteomics.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 评论,杂志文章

    doi:10.1038/s41592-019-0343-9

    authors: Doerr A

    更新日期:2019-03-01 00:00:00

  • Induction of linear tracks of DNA double-strand breaks by alpha-particle irradiation of cells.

    abstract::Understanding how cells maintain genome integrity when challenged with DNA double-strand breaks (DSBs) is of major importance, particularly since the discovery of multiple links of DSBs with genome instability and cancer-predisposition disorders. Ionizing radiation is the agent of choice to produce DSBs in cells; howe...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.f.206

    authors: Stap J,Krawczyk PM,Van Oven CH,Barendsen GW,Essers J,Kanaar R,Aten JA

    更新日期:2008-03-01 00:00:00

  • Deciphering laminar-specific neural inputs with line-scanning fMRI.

    abstract::Using a line-scanning method during functional magnetic resonance imaging (fMRI), we obtained high temporal (50-ms) and spatial (50-μm) resolution information along the cortical thickness and showed that the laminar position of fMRI onset coincides with distinct neural inputs in rat somatosensory and motor cortices. T...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2730

    authors: Yu X,Qian C,Chen DY,Dodd SJ,Koretsky AP

    更新日期:2014-01-01 00:00:00

  • Detection of minor drug-resistant populations by parallel allele-specific sequencing.

    abstract::We developed a highly sensitive parallel allele-specific sequencing (PASS) assay to simultaneously analyze a large number of viral genomes and detect minor drug-resistant populations at approximately 0.1-0.01% levels. Using this assay on samples from individuals infected with human immunodeficiency viruses (HIV), we s...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth995

    authors: Cai F,Chen H,Hicks CB,Bartlett JA,Zhu J,Gao F

    更新日期:2007-02-01 00:00:00

  • Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis.

    abstract::Generation of complex libraries of defined nucleic acid sequences can greatly aid the functional analysis of protein and gene function. Previously, such studies relied either on individually synthesized oligonucleotides or on cellular nucleic acids as the starting material. As each method has disadvantages, we have de...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth724

    authors: Cleary MA,Kilian K,Wang Y,Bradshaw J,Cavet G,Ge W,Kulkarni A,Paddison PJ,Chang K,Sheth N,Leproust E,Coffey EM,Burchard J,McCombie WR,Linsley P,Hannon GJ

    更新日期:2004-12-01 00:00:00

  • Measurement of atom resolvability in cryo-EM maps with Q-scores.

    abstract::Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-020-0731-1

    authors: Pintilie G,Zhang K,Su Z,Li S,Schmid MF,Chiu W

    更新日期:2020-03-01 00:00:00

  • Pulse proteolysis: a simple method for quantitative determination of protein stability and ligand binding.

    abstract::Thermodynamic stability is fundamental to the biology of proteins. Information on protein stability is essential for studying protein structure and folding and can also be used indirectly to monitor protein-ligand or protein-protein interactions. While clearly valuable, the experimental determination of a protein's st...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth740

    authors: Park C,Marqusee S

    更新日期:2005-03-01 00:00:00

  • Engineering of human brain organoids with a functional vascular-like system.

    abstract::Human cortical organoids (hCOs), derived from human embryonic stem cells (hESCs), provide a platform to study human brain development and diseases in complex three-dimensional tissue. However, current hCOs lack microvasculature, resulting in limited oxygen and nutrient delivery to the inner-most parts of hCOs. We engi...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-019-0586-5

    authors: Cakir B,Xiang Y,Tanaka Y,Kural MH,Parent M,Kang YJ,Chapeton K,Patterson B,Yuan Y,He CS,Raredon MSB,Dengelegi J,Kim KY,Sun P,Zhong M,Lee S,Patra P,Hyder F,Niklason LE,Lee SH,Yoon YS,Park IH

    更新日期:2019-11-01 00:00:00

  • Cell-type specific sequencing of microRNAs from complex animal tissues.

    abstract::MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular r...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4610

    authors: Alberti C,Manzenreither RA,Sowemimo I,Burkard TR,Wang J,Mahofsky K,Ameres SL,Cochella L

    更新日期:2018-04-01 00:00:00

  • Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction.

    abstract::Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability ne...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-020-00990-8

    authors: Punjani A,Zhang H,Fleet DJ

    更新日期:2020-12-01 00:00:00

  • Evaluating measures of association for single-cell transcriptomics.

    abstract::Single-cell transcriptomics provides an opportunity to characterize cell-type-specific transcriptional networks, intercellular signaling pathways and cellular diversity with unprecedented resolution by profiling thousands of cells in a single experiment. However, owing to the unique statistical properties of scRNA-seq...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-019-0372-4

    authors: Skinnider MA,Squair JW,Foster LJ

    更新日期:2019-05-01 00:00:00

  • A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates.

    abstract::New methods to quantify protein kinase activities directly from complex cellular mixtures are critical for understanding biological regulatory pathways. Herein, a fluorescence-based chemosensor strategy for the direct measurement of kinase activities in crude mammalian cell lysates is described. We first designed a ne...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth747

    authors: Shults MD,Janes KA,Lauffenburger DA,Imperiali B

    更新日期:2005-04-01 00:00:00

  • Multicolor two-photon tissue imaging by wavelength mixing.

    abstract::We achieve simultaneous two-photon excitation of three chromophores with distinct absorption spectra using synchronized pulses from a femtosecond laser and an optical parametric oscillator. The two beams generate separate multiphoton processes, and their spatiotemporal overlap provides an additional two-photon excitat...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2098

    authors: Mahou P,Zimmerley M,Loulier K,Matho KS,Labroille G,Morin X,Supatto W,Livet J,Débarre D,Beaurepaire E

    更新日期:2012-07-08 00:00:00

  • De novo assembly and analysis of RNA-seq data.

    abstract::We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads f...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1517

    authors: Robertson G,Schein J,Chiu R,Corbett R,Field M,Jackman SD,Mungall K,Lee S,Okada HM,Qian JQ,Griffith M,Raymond A,Thiessen N,Cezard T,Butterfield YS,Newsome R,Chan SK,She R,Varhol R,Kamoh B,Prabhu AL,Tam A,Zhao Y

    更新日期:2010-11-01 00:00:00

  • Author Correction: Genome-wide high-throughput screening of T cell epitopes.

    abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title:Nature methods

    pub_type: 已发布勘误

    doi:10.1038/s41592-019-0660-z

    authors: Singh A

    更新日期:2019-12-01 00:00:00

  • High-speed nanoscopic tracking of the position and orientation of a single virus.

    abstract::Optical studies have revealed that, after binding, virions move laterally on the plasma membrane, but the complexity of the cellular environment and the drawbacks of fluorescence microscopy have prevented access to the molecular dynamics of early virus-host couplings, which are important for cell infection. Here we pr...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1395

    authors: Kukura P,Ewers H,Müller C,Renn A,Helenius A,Sandoghdar V

    更新日期:2009-12-01 00:00:00

  • A bright and photostable photoconvertible fluorescent protein.

    abstract::Photoconvertible fluorescent proteins are potential tools for investigating dynamic processes in living cells and for emerging super-resolution microscopy techniques. Unfortunately, most probes in this class are hampered by oligomerization, small photon budgets or poor photostability. Here we report an EosFP variant t...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1296

    authors: McKinney SA,Murphy CS,Hazelwood KL,Davidson MW,Looger LL

    更新日期:2009-02-01 00:00:00

  • Fluorogenic DNA sequencing in PDMS microreactors.

    abstract::We developed a multiplex sequencing-by-synthesis method combining terminal phosphate-labeled fluorogenic nucleotides (TPLFNs) and resealable polydimethylsiloxane (PDMS) microreactors. In the presence of phosphatase, primer extension by DNA polymerase using nonfluorescent TPLFNs generates fluorophores, which are confin...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1629

    authors: Sims PA,Greenleaf WJ,Duan H,Xie XS

    更新日期:2011-06-12 00:00:00

  • Post-translational selective intracellular silencing of acetylated proteins with de novo selected intrabodies.

    abstract::The ability to selectively interfere with post-translationally modified proteins would have many biological and therapeutic applications. However, post-translational modifications cannot be selectively targeted by nucleic-acid-based interference approaches. Here we describe post-translational intracellular silencing a...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4144

    authors: Chirichella M,Lisi S,Fantini M,Goracci M,Calvello M,Brandi R,Arisi I,D'Onofrio M,Di Primio C,Cattaneo A

    更新日期:2017-03-01 00:00:00

  • Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane.

    abstract::Numerous drugs and endogenous ligands bind to cell surface receptors leading to modulation of downstream signaling cascades and frequently to adaptation of the plasma membrane proteome. In-depth analysis of dynamic processes at the cell surface is challenging due to biochemical properties and low abundances of plasma ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-020-01022-1

    authors: Kalxdorf M,Günthner I,Becher I,Kurzawa N,Knecht S,Savitski MM,Eberl HC,Bantscheff M

    更新日期:2021-01-01 00:00:00

  • Chemically defined generation of human cardiomyocytes.

    abstract::Existing methods for human induced pluripotent stem cell (hiPSC) cardiac differentiation are efficient but require complex, undefined medium constituents that hinder further elucidation of the molecular mechanisms of cardiomyogenesis. Using hiPSCs derived under chemically defined conditions on synthetic matrices, we s...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2999

    authors: Burridge PW,Matsa E,Shukla P,Lin ZC,Churko JM,Ebert AD,Lan F,Diecke S,Huber B,Mordwinkin NM,Plews JR,Abilez OJ,Cui B,Gold JD,Wu JC

    更新日期:2014-08-01 00:00:00

  • In vivo cell-cycle profiling in xenograft tumors by quantitative intravital microscopy.

    abstract::Quantification of cell-cycle state at a single-cell level is essential to understand fundamental three-dimensional (3D) biological processes such as tissue development and cancer. Analysis of 3D in vivo images, however, is very challenging. Today's best practice, manual annotation of select image events, generates arb...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3363

    authors: Chittajallu DR,Florian S,Kohler RH,Iwamoto Y,Orth JD,Weissleder R,Danuser G,Mitchison TJ

    更新日期:2015-06-01 00:00:00

  • Analysis of the Human Protein Atlas Image Classification competition.

    abstract::Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and pr...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-019-0658-6

    authors: Ouyang W,Winsnes CF,Hjelmare M,Cesnik AJ,Åkesson L,Xu H,Sullivan DP,Dai S,Lan J,Jinmo P,Galib SM,Henkel C,Hwang K,Poplavskiy D,Tunguz B,Wolfinger RD,Gu Y,Li C,Xie J,Buslov D,Fironov S,Kiselev A,Panchenko D,C

    更新日期:2019-12-01 00:00:00

  • Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq.

    abstract::Massively parallel single-cell and single-nucleus RNA sequencing has opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so is the need for computational pipelines for scaled analysis. Here we developed Cumulus-a cloud-based framework for analyzing large-s...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-020-0905-x

    authors: Li B,Gould J,Yang Y,Sarkizova S,Tabaka M,Ashenberg O,Rosen Y,Slyper M,Kowalczyk MS,Villani AC,Tickle T,Hacohen N,Rozenblatt-Rosen O,Regev A

    更新日期:2020-08-01 00:00:00

  • Molecular engineering: Unnatural design.

    abstract::Researchers designed an enzyme to carry out the Diels-Alder reaction, an activity not found in nature. ...

    journal_title:Nature methods

    pub_type: 评论,杂志文章

    doi:10.1038/nmeth0910-671

    authors: Doerr A

    更新日期:2010-09-01 00:00:00

  • Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.

    abstract::Database searching is an essential element of large-scale proteomics. Because these methods are widely used, it is important to understand the rationale of the algorithms. Most algorithms are based on concepts first developed in SEQUEST and PeptideSearch. Four basic approaches are used to determine a match between a s...

    journal_title:Nature methods

    pub_type: 杂志文章,评审

    doi:10.1038/nmeth725

    authors: Sadygov RG,Cociorva D,Yates JR 3rd

    更新日期:2004-12-01 00:00:00