Coordinate gene regulation during hematopoiesis is related to genomic organization.

Abstract:

:Gene loci are found in nuclear subcompartments that are related to their expression status. For instance, silent genes are often localized to heterochromatin and the nuclear periphery, whereas active genes tend to be found in the nuclear center. Evidence also suggests that chromosomes may be specifically positioned within the nucleus; however, the nature of this organization and how it is achieved are not yet fully understood. To examine whether gene regulation is related to a discernible pattern of genomic organization, we analyzed the linear arrangement of co-regulated genes along chromosomes and determined the organization of chromosomes during the differentiation of a hematopoietic progenitor to erythroid and neutrophil cell types. Our analysis reveals that there is a significant tendency for co-regulated genes to be proximal, which is related to the association of homologous chromosomes and the spatial juxtaposition of lineage-specific gene domains. We suggest that proximity in the form of chromosomal gene distribution and homolog association may be the basis for organizing the genome for coordinate gene regulation during cellular differentiation.

journal_name

PLoS Biol

journal_title

PLoS biology

authors

Kosak ST,Scalzo D,Alworth SV,Li F,Palmer S,Enver T,Lee JS,Groudine M

doi

10.1371/journal.pbio.0050309

subject

Has Abstract

pub_date

2007-11-01 00:00:00

pages

e309

issue

11

eissn

1544-9173

issn

1545-7885

pii

06-PLBI-RA-1214

journal_volume

5

pub_type

杂志文章
  • Enhancement of SMN2 exon 7 inclusion by antisense oligonucleotides targeting the exon.

    abstract::Several strategies have been pursued to increase the extent of exon 7 inclusion during splicing of SMN2 (survival of motor neuron 2) transcripts, for eventual therapeutic use in spinal muscular atrophy (SMA), a genetic neuromuscular disease. Antisense oligonucleotides (ASOs) that target an exon or its flanking splice ...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.0050073

    authors: Hua Y,Vickers TA,Baker BF,Bennett CF,Krainer AR

    更新日期:2007-04-01 00:00:00

  • Modeling flexible behavior in childhood to adulthood shows age-dependent learning mechanisms and less optimal learning in autism in each age group.

    abstract::Flexible behavior is critical for everyday decision-making and has been implicated in restricted, repetitive behaviors (RRB) in autism spectrum disorder (ASD). However, how flexible behavior changes developmentally in ASD remains largely unknown. Here, we used a developmental approach and examined flexible behavior on...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.3000908

    authors: Crawley D,Zhang L,Jones EJH,Ahmad J,Oakley B,San José Cáceres A,Charman T,Buitelaar JK,Murphy DGM,Chatham C,den Ouden H,Loth E,EU-AIMS LEAP group.

    更新日期:2020-10-27 00:00:00

  • Parallel evolution of the genetic code in arthropod mitochondrial genomes.

    abstract::The genetic code provides the translation table necessary to transform the information contained in DNA into the language of proteins. In this table, a correspondence between each codon and each amino acid is established: tRNA is the main adaptor that links the two. Although the genetic code is nearly universal, sever...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.0040127

    authors: Abascal F,Posada D,Knight RD,Zardoya R

    更新日期:2006-05-01 00:00:00

  • Promoter sequence determines the relationship between expression level and noise.

    abstract::The ability of cells to accurately control gene expression levels in response to extracellular cues is limited by the inherently stochastic nature of transcriptional regulation. A change in transcription factor (TF) activity results in changes in the expression of its targets, but the way in which cell-to-cell variabi...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1001528

    authors: Carey LB,van Dijk D,Sloot PM,Kaandorp JA,Segal E

    更新日期:2013-01-01 00:00:00

  • Distinct mammalian precursors are committed to generate neurons with defined dendritic projection patterns.

    abstract::The mechanisms that regulate how dendrites target different neurons to establish connections with specific cell types remain largely unknown. In particular, the formation of cell-type-specific connectivity during postnatal neurogenesis could be either determined by the local environment of the mature neuronal circuit ...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.0050300

    authors: Kelsch W,Mosley CP,Lin CW,Lois C

    更新日期:2007-11-01 00:00:00

  • A Src-like inactive conformation in the abl tyrosine kinase domain.

    abstract::The improper activation of the Abl tyrosine kinase results in chronic myeloid leukemia (CML). The recognition of an inactive conformation of Abl, in which a catalytically important Asp-Phe-Gly (DFG) motif is flipped by approximately 180 degrees with respect to the active conformation, underlies the specificity of the ...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.0040144

    authors: Levinson NM,Kuchment O,Shen K,Young MA,Koldobskiy M,Karplus M,Cole PA,Kuriyan J

    更新日期:2006-05-01 00:00:00

  • Correction: What do we talk about when we talk about rhythm?

    abstract::[This corrects the article DOI: 10.1371/journal.pbio.2002794.]. ...

    journal_title:PLoS biology

    pub_type: 杂志文章,已发布勘误

    doi:10.1371/journal.pbio.1002615

    authors: Obleser J,Henry MJ,Lakatos P

    更新日期:2017-11-01 00:00:00

  • The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation.

    abstract::DEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed "helicases," their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome ass...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1002480

    authors: Khoshnevis S,Askenasy I,Johnson MC,Dattolo MD,Young-Erdos CL,Stroupe ME,Karbstein K

    更新日期:2016-06-09 00:00:00

  • Self-organizing spots get under your skin.

    abstract::Sixty-five years after Turing first revealed the potential of systems with local activation and long-range inhibition to generate pattern, we have only recently begun to identify the biological elements that operate at many scales to generate periodic patterns in nature. In this Primer, we first review the theoretical...

    journal_title:PLoS biology

    pub_type: 杂志文章,评审

    doi:10.1371/journal.pbio.2004412

    authors: Dalle Nogare D,Chitnis AB

    更新日期:2017-12-20 00:00:00

  • Polarised asymmetric inheritance of accumulated protein damage in higher eukaryotes.

    abstract::Disease-associated misfolded proteins or proteins damaged due to cellular stress are generally disposed via the cellular protein quality-control system. However, under saturating conditions, misfolded proteins will aggregate. In higher eukaryotes, these aggregates can be transported to accumulate in aggresomes at the ...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.0040417

    authors: Rujano MA,Bosveld F,Salomons FA,Dijk F,van Waarde MA,van der Want JJ,de Vos RA,Brunt ER,Sibon OC,Kampinga HH

    更新日期:2006-12-01 00:00:00

  • Evolthon: A community endeavor to evolve lab evolution.

    abstract::In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best to evolve a desired trait? Should the challenge be applied abruptly, gradually, periodically, sporadically? Should one apply chemical mutagenesis, and do strains with high innate m...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.3000182

    authors: Kaminski Strauss S,Schirman D,Jona G,Brooks AN,Kunjapur AM,Nguyen Ba AN,Flint A,Solt A,Mershin A,Dixit A,Yona AH,Csörgő B,Busby BP,Hennig BP,Pál C,Schraivogel D,Schultz D,Wernick DG,Agashe D,Levi D,Zabezhinsky D,

    更新日期:2019-03-29 00:00:00

  • Inhibition of Notch signaling rescues cardiovascular development in Kabuki Syndrome.

    abstract::Kabuki Syndrome patients have a spectrum of congenital disorders, including congenital heart defects, the primary determinant of mortality. Seventy percent of Kabuki Syndrome patients have mutations in the histone methyl-transferase KMT2D. However, the underlying mechanisms that drive these congenital disorders are un...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.3000087

    authors: Serrano MLA,Demarest BL,Tone-Pah-Hote T,Tristani-Firouzi M,Yost HJ

    更新日期:2019-09-03 00:00:00

  • Commensal bacteria and essential amino acids control food choice behavior and reproduction.

    abstract::Choosing the right nutrients to consume is essential to health and wellbeing across species. However, the factors that influence these decisions are poorly understood. This is particularly true for dietary proteins, which are important determinants of lifespan and reproduction. We show that in Drosophila melanogaster,...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.2000862

    authors: Leitão-Gonçalves R,Carvalho-Santos Z,Francisco AP,Fioreze GT,Anjos M,Baltazar C,Elias AP,Itskov PM,Piper MDW,Ribeiro C

    更新日期:2017-04-25 00:00:00

  • Individual metabolomic signatures of circadian misalignment during simulated night shifts in humans.

    abstract::Misalignment of the daily sleep-wake and fasting-feeding cycles with the endogenous circadian timing system is an inevitable consequence of night shift work and is associated with adverse metabolic health effects. However, a detailed characterisation of the effects of night shifts on 24-h rhythms in the metabolome is ...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.3000303

    authors: Kervezee L,Cermakian N,Boivin DB

    更新日期:2019-06-18 00:00:00

  • Effects of resveratrol and SIRT1 on PGC-1α activity and mitochondrial biogenesis: a reevaluation.

    abstract::It has been reported that feeding mice resveratrol activates AMPK and SIRT1 in skeletal muscle leading to deacetylation and activation of PGC-1α, increased mitochondrial biogenesis, and improved running endurance. This study was done to further evaluate the effects of resveratrol, SIRT1, and PGC-1α deacetylation on mi...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1001603

    authors: Higashida K,Kim SH,Jung SR,Asaka M,Holloszy JO,Han DH

    更新日期:2013-07-01 00:00:00

  • Photoperiodic regulation of flowering time through periodic histone deacetylation of the florigen gene FT.

    abstract::The developmental transition from a vegetative to a reproductive phase (i.e., flowering) is timed by the seasonal cue day length or photoperiod in many plant species. Through the photoperiod pathway, inductive day lengths trigger the production of a systemic flowering signal, florigen, to provoke the floral transition...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1001649

    authors: Gu X,Wang Y,He Y

    更新日期:2013-09-01 00:00:00

  • The interaction between a sexually transferred steroid hormone and a female protein regulates oogenesis in the malaria mosquito Anopheles gambiae.

    abstract::Molecular interactions between male and female factors during mating profoundly affect the reproductive behavior and physiology of female insects. In natural populations of the malaria mosquito Anopheles gambiae, blood-fed females direct nutritional resources towards oogenesis only when inseminated. Here we show that ...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1001695

    authors: Baldini F,Gabrieli P,South A,Valim C,Mancini F,Catteruccia F

    更新日期:2013-10-01 00:00:00

  • PiVR: An affordable and versatile closed-loop platform to study unrestrained sensorimotor behavior.

    abstract::Tools enabling closed-loop experiments are crucial to delineate causal relationships between the activity of genetically labeled neurons and specific behaviors. We developed the Raspberry Pi Virtual Reality (PiVR) system to conduct closed-loop optogenetic stimulation of neural functions in unrestrained animals. PiVR i...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.3000712

    authors: Tadres D,Louis M

    更新日期:2020-07-14 00:00:00

  • Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair.

    abstract::Genome editing occurs in the context of chromatin, which is heterogeneous in structure and function across the genome. Chromatin heterogeneity is thought to affect genome editing efficiency, but this has been challenging to quantify due to the presence of confounding variables. Here, we develop a method that exploits ...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.2005595

    authors: Kallimasioti-Pazi EM,Thelakkad Chathoth K,Taylor GC,Meynert A,Ballinger T,Kelder MJE,Lalevée S,Sanli I,Feil R,Wood AJ

    更新日期:2018-12-12 00:00:00

  • Developing international open science collaborations: Funder reflections on the Open Science Prize.

    abstract::The Open Science Prize was established with the following objectives: first, to encourage the crowdsourcing of open data to make breakthroughs that are of biomedical significance; second, to illustrate that funders can indeed work together when scientific interests are aligned; and finally, to encourage international ...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.2002617

    authors: Kittrie E,Atienza AA,Kiley R,Carr D,MacFarlane A,Pai V,Couch J,Bajkowski J,Bonner JF,Mietchen D,Bourne PE

    更新日期:2017-08-01 00:00:00

  • Should a viral genome stay in the host cell or leave? A quantitative dynamics study of how hepatitis C virus deals with this dilemma.

    abstract::Virus proliferation involves gene replication inside infected cells and transmission to new target cells. Once positive-strand RNA virus has infected a cell, the viral genome serves as a template for copying ("stay-strategy") or is packaged into a progeny virion that will be released extracellularly ("leave-strategy")...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.3000562

    authors: Iwanami S,Kitagawa K,Ohashi H,Asai Y,Shionoya K,Saso W,Nishioka K,Inaba H,Nakaoka S,Wakita T,Diekmann O,Iwami S,Watashi K

    更新日期:2020-07-30 00:00:00

  • Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant.

    abstract::Genetically identical cells grown in the same culture display striking cell-to-cell heterogeneity in gene expression and other traits. A crucial challenge is to understand how much of this heterogeneity reflects the noise tolerance of a robust system and how much serves a biological function. In bacteria, stochastic g...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1001325

    authors: Levy SF,Ziv N,Siegal ML

    更新日期:2012-01-01 00:00:00

  • Laboratory mouse housing conditions can be improved using common environmental enrichment without compromising data.

    abstract::Animal welfare requires the adequate housing of animals to ensure health and well-being. The application of environmental enrichment is a way to improve the well-being of laboratory animals. However, it is important to know whether these enrichment items can be incorporated in experimental mouse husbandry without crea...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.2005019

    authors: André V,Gau C,Scheideler A,Aguilar-Pimentel JA,Amarie OV,Becker L,Garrett L,Hans W,Hölter SM,Janik D,Moreth K,Neff F,Östereicher M,Racz I,Rathkolb B,Rozman J,Bekeredjian R,Graw J,Klingenspor M,Klopstock T,Ollert M

    更新日期:2018-04-16 00:00:00

  • A question of fate.

    abstract::Ever since the discovery of neural stem cells in the mammalian brain, the possibility of brain tissue regeneration has captured the minds of scientists, clinicians, and the public. Neural stem cells have been envisioned as a source of donor cells for transplantation and vectors for the delivery of gene therapy. Over t...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.2002329

    authors: Maletic-Savatic M

    更新日期:2017-05-15 00:00:00

  • The velvet family of fungal regulators contains a DNA-binding domain structurally similar to NF-κB.

    abstract::Morphological development of fungi and their combined production of secondary metabolites are both acting in defence and protection. These processes are mainly coordinated by velvet regulators, which contain a yet functionally and structurally uncharacterized velvet domain. Here we demonstrate that the velvet domain o...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1001750

    authors: Ahmed YL,Gerke J,Park HS,Bayram Ö,Neumann P,Ni M,Dickmanns A,Kim SC,Yu JH,Braus GH,Ficner R

    更新日期:2013-12-01 00:00:00

  • Ethoscopes: An open platform for high-throughput ethomics.

    abstract::Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.2003026

    authors: Geissmann Q,Garcia Rodriguez L,Beckwith EJ,French AS,Jamasb AR,Gilestro GF

    更新日期:2017-10-19 00:00:00

  • Opposing activities of LIT-1/NLK and DAF-6/patched-related direct sensory compartment morphogenesis in C. elegans.

    abstract::Glial cells surround neuronal endings to create enclosed compartments required for neuronal function. This architecture is seen at excitatory synapses and at sensory neuron receptive endings. Despite the prevalence and importance of these compartments, how they form is not known. We used the main sensory organ of C. e...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1001121

    authors: Oikonomou G,Perens EA,Lu Y,Watanabe S,Jorgensen EM,Shaham S

    更新日期:2011-08-01 00:00:00

  • Rapid evolution of sex pheromone-producing enzyme expression in Drosophila.

    abstract::A wide range of organisms use sex pheromones to communicate with each other and to identify appropriate mating partners. While the evolution of chemical communication has been suggested to cause sexual isolation and speciation, the mechanisms that govern evolutionary transitions in sex pheromone production are poorly ...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1000168

    authors: Shirangi TR,Dufour HD,Williams TM,Carroll SB

    更新日期:2009-08-01 00:00:00

  • Role of pleiotropy in the evolution of a cryptic developmental variation in Caenorhabditis elegans.

    abstract::Robust biological systems are expected to accumulate cryptic genetic variation that does not affect the system output in standard conditions yet may play an evolutionary role once phenotypically expressed under a strong perturbation. Genetic variation that is cryptic relative to a robust trait may accumulate neutrally...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1001230

    authors: Duveau F,Félix MA

    更新日期:2012-01-01 00:00:00

  • When it is better to regress: dynamics of vascular pruning.

    abstract::Blood vascular networks in vertebrates are essential to tissue survival. Establishment of a fully functional vasculature is complex and requires a number of steps including vasculogenesis and angiogenesis that are followed by differentiation into specialized vascular tissues (i.e., arteries, veins, and lymphatics) and...

    journal_title:PLoS biology

    pub_type: 杂志文章

    doi:10.1371/journal.pbio.1002148

    authors: Ricard N,Simons M

    更新日期:2015-05-15 00:00:00