Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.


:Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around nucleosomes in Saccharomyces cerevisiae, and use this distinctive two-dimensional nucleosomal "fingerprint" as the basis for a new nucleosome-positioning algorithm called NucleoATAC. We show that NucleoATAC can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy in S. cerevisiae, Schizosaccharomyces pombe, and human cells. We demonstrate the application of NucleoATAC to a number of outstanding problems in chromatin biology, including analysis of sequence features underlying nucleosome positioning, promoter chromatin architecture across species, identification of transient changes in nucleosome occupancy and positioning during a dynamic cellular response, and integrated analysis of nucleosome occupancy and transcription factor binding.


Genome Res


Genome research


Schep AN,Buenrostro JD,Denny SK,Schwartz K,Sherlock G,Greenleaf WJ




Has Abstract


2015-11-01 00:00:00














  • Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements.

    abstract::The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to approximately 1% of euchromatic regions of the human genome. Gap filling is a lab...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Leem SH,Kouprina N,Grimwood J,Kim JH,Mullokandov M,Yoon YH,Chae JY,Morgan J,Lucas S,Richardson P,Detter C,Glavina T,Rubin E,Barrett JC,Larionov V

    更新日期:2004-02-01 00:00:00

  • Systematic identification of novel protein domain families associated with nuclear functions.

    abstract::A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic l...

    journal_title:Genome research

    pub_type: 信件


    authors: Doerks T,Copley RR,Schultz J,Ponting CP,Bork P

    更新日期:2002-01-01 00:00:00

  • Prioritizing candidate disease genes by network-based boosting of genome-wide association data.

    abstract::Network "guilt by association" (GBA) is a proven approach for identifying novel disease genes based on the observation that similar mutational phenotypes arise from functionally related genes. In principle, this approach could account even for nonadditive genetic interactions, which underlie the synergistic combinatio...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Lee I,Blom UM,Wang PI,Shim JE,Marcotte EM

    更新日期:2011-07-01 00:00:00

  • A general approach for identifying distant regulatory elements applied to the Gdf6 gene.

    abstract::Regulatory sequences in higher genomes can map large distances from gene coding regions, and cannot yet be identified by simple inspection of primary DNA sequence information. Here we describe an efficient method of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distan...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Mortlock DP,Guenther C,Kingsley DM

    更新日期:2003-09-01 00:00:00

  • Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.

    abstract::Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm that integrates e...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Roy S,Wapinski I,Pfiffner J,French C,Socha A,Konieczka J,Habib N,Kellis M,Thompson D,Regev A

    更新日期:2013-06-01 00:00:00

  • Prokaryotic phylogenies inferred from protein structural domains.

    abstract::The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Deeds EJ,Hennessey H,Shakhnovich EI

    更新日期:2005-03-01 00:00:00

  • Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication.

    abstract::Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced th...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Heidel AJ,Lawal HM,Felder M,Schilde C,Helps NR,Tunggal B,Rivero F,John U,Schleicher M,Eichinger L,Platzer M,Noegel AA,Schaap P,Glöckner G

    更新日期:2011-11-01 00:00:00

  • Global survey of escape from X inactivation by RNA-sequencing in mouse.

    abstract::X inactivation equalizes the dosage of gene expression between the sexes, but some genes escape silencing and are thus expressed from both alleles in females. To survey X inactivation and escape in mouse, we performed RNA sequencing in Mus musculus x Mus spretus cells with complete skewing of X inactivation, relying o...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Yang F,Babak T,Shendure J,Disteche CM

    更新日期:2010-05-01 00:00:00

  • Construction of a linkage map of the medaka (Oryzias latipes) and mapping of the Da mutant locus defective in dorsoventral patterning.

    abstract::Double anal fin (Da) is a medaka with an autosomal semidominant mutation that causes mirror image duplication of the ventral region concentrating on the caudal region. The chromosomal location of the Da gene and its sequence have remained unknown. We constructed a medaka linkage map as a first step to approach positio...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Ohtsuka M,Makino S,Yoda K,Wada H,Naruse K,Mitani H,Shima A,Ozato K,Kimura M,Inoko H

    更新日期:1999-12-01 00:00:00

  • Pattern of sequence variation across 213 environmental response genes.

    abstract::To promote the clinical and epidemiological studies that improve our understanding of human genetic susceptibility to environmental exposure, the Environmental Genome Project (EGP) has scanned 213 environmental response genes involved in DNA repair, cell cycle regulation, apoptosis, and metabolism for single nucleotid...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Livingston RJ,von Niederhausern A,Jegga AG,Crawford DC,Carlson CS,Rieder MJ,Gowrisankar S,Aronow BJ,Weiss RB,Nickerson DA

    更新日期:2004-10-01 00:00:00

  • An abundance of bidirectional promoters in the human genome.

    abstract::The alignment of full-length human cDNA sequences to the finished sequence of the human genome provides a unique opportunity to study the distribution of genes throughout the genome. By analyzing the distances between 23,752 genes, we identified a class of divergently transcribed gene pairs, representing more than 10%...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Trinklein ND,Aldred SF,Hartman SJ,Schroeder DI,Otillar RP,Myers RM

    更新日期:2004-01-01 00:00:00

  • Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors.

    abstract::Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Robbins CM,Tembe WA,Baker A,Sinari S,Moses TY,Beckstrom-Sternberg S,Beckstrom-Sternberg J,Barrett M,Long J,Chinnaiyan A,Lowey J,Suh E,Pearson JV,Craig DW,Agus DB,Pienta KJ,Carpten JD

    更新日期:2011-01-01 00:00:00

  • A non-EST-based method for exon-skipping prediction.

    abstract::It is estimated that between 35% and 74% of all human genes can undergo alternative splicing. Currently, the most efficient methods for large-scale detection of alternative splicing use expressed sequence tags (ESTs) or microarray analysis. As these methods merely sample the transcriptome, splice variants that do not ...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Sorek R,Shemesh R,Cohen Y,Basechess O,Ast G,Shamir R

    更新日期:2004-08-01 00:00:00

  • Gene regulation and speciation in house mice.

    abstract::One approach to understanding the process of speciation is to characterize the genetic architecture of post-zygotic isolation. As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproduct...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Mack KL,Campbell P,Nachman MW

    更新日期:2016-04-01 00:00:00

  • Evolution and multilevel optimization of the genetic code.

    abstract::The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show t...

    journal_title:Genome research

    pub_type: 评论,杂志文章,评审


    authors: Bollenbach T,Vetsigian K,Kishony R

    更新日期:2007-04-01 00:00:00

  • Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes.

    abstract::Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Rasmussen MD,Kellis M

    更新日期:2007-12-01 00:00:00

  • Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure.

    abstract::Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Storlazzi CT,Lonoce A,Guastadisegni MC,Trombetta D,D'Addabbo P,Daniele G,L'Abbate A,Macchia G,Surace C,Kok K,Ullmann R,Purgato S,Palumbo O,Carella M,Ambros PF,Rocchi M

    更新日期:2010-09-01 00:00:00

  • The effect of translocation-induced nuclear reorganization on gene expression.

    abstract::Translocations are known to affect the expression of genes at the breakpoints and, in the case of unbalanced translocations, alter the gene copy number. However, a comprehensive understanding of the functional impact of this class of variation is lacking. Here, we have studied the effect of balanced chromosomal rearra...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Harewood L,Schütz F,Boyle S,Perry P,Delorenzi M,Bickmore WA,Reymond A

    更新日期:2010-05-01 00:00:00

  • Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera).

    abstract::The remarkable olfactory power of insect species is thought to be generated by a combinatorial action of two large protein families, G protein-coupled olfactory receptors (ORs) and odorant binding proteins (OBPs). In olfactory sensilla, OBPs deliver hydrophobic airborne molecules to ORs, but their expression in nonolf...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Forêt S,Maleszka R

    更新日期:2006-11-01 00:00:00

  • Genomic evolution, patterns of global dissemination, and interspecies transmission of human and simian T-cell leukemia/lymphotropic viruses.

    abstract::Using both env and long terminal repeat (LTR) sequences, with maximal representation of genetic diversity within primate strains, we revise and expand the unique evolutionary history of human and simian T-cell leukemia/lymphotropic viruses (HTLV/STLV). Based on the robust application of three different phylogenetic al...

    journal_title:Genome research

    pub_type: 杂志文章,评审


    authors: Slattery JP,Franchini G,Gessain A

    更新日期:1999-06-01 00:00:00

  • A matter of life or death: how microsatellites emerge in and vanish from the human genome.

    abstract::Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypot...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Kelkar YD,Eckert KA,Chiaromonte F,Makova KD

    更新日期:2011-12-01 00:00:00

  • Sequence diversity and genomic organization of vomeronasal receptor genes in the mouse.

    abstract::The vomeronasal system of mice is thought to be specialized in the detection of pheromones. Two multigene families have been identified that encode proteins with seven putative transmembrane domains and that are expressed selectively in subsets of neurons of the vomeronasal organ. The products of these vomeronasal rec...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Del Punta K,Rothman A,Rodriguez I,Mombaerts P

    更新日期:2000-12-01 00:00:00

  • 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis.

    abstract::Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, widespread utilizati...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Greshock J,Naylor TL,Margolin A,Diskin S,Cleaver SH,Futreal PA,deJong PJ,Zhao S,Liebman M,Weber BL

    更新日期:2004-01-01 00:00:00

  • HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

    abstract::Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessin...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Yang T,Zhang F,Yardımcı GG,Song F,Hardison RC,Noble WS,Yue F,Li Q

    更新日期:2017-11-01 00:00:00

  • Core promoter T-blocks correlate with gene expression levels in C. elegans.

    abstract::Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulator...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Grishkevich V,Hashimshony T,Yanai I

    更新日期:2011-05-01 00:00:00

  • Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster.

    abstract::Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy u...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: He B,Caudy A,Parsons L,Rosebrock A,Pane A,Raj S,Wieschaus E

    更新日期:2012-12-01 00:00:00

  • Predicting deleterious amino acid substitutions.

    abstract::Many missense substitutions are identified in single nucleotide polymorphism (SNP) data and large-scale random mutagenesis projects. Each amino acid substitution potentially affects protein function. We have constructed a tool that uses sequence homology to predict whether a substitution affects protein function. SIFT...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Ng PC,Henikoff S

    更新日期:2001-05-01 00:00:00

  • Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis.

    abstract::The draft genome ( approximately 160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromoso...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Shoguchi E,Kawashima T,Satou Y,Hamaguchi M,Sin-I T,Kohara Y,Putnam N,Rokhsar DS,Satoh N

    更新日期:2006-02-01 00:00:00

  • Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions.

    abstract::Recent studies have revealed that insertions and deletions (indels) are more different in their formation than previously assumed. What remains enigmatic is how the local DNA sequence context contributes to these differences. To investigate the relative impact of various molecular mechanisms to indel formation, we ana...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Kvikstad EM,Chiaromonte F,Makova KD

    更新日期:2009-07-01 00:00:00

  • Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data.

    abstract::A rigorous analysis of the Merck-sponsored EST data with respect to known gene sequences increases the utility of the data set and helps refine methods for building a gene index. A highly curated human transcript data base was used as a reference data set of known genes. A detailed analysis of EST sequences derived fr...

    journal_title:Genome research

    pub_type: 杂志文章


    authors: Aaronson JS,Eckman B,Blevins RA,Borkowski JA,Myerson J,Imran S,Elliston KO

    更新日期:1996-09-01 00:00:00