Chromosome Compaction by Active Loop Extrusion

During cell division, chromosomes are compacted in length by more than a 100-fold. A wide range of experiments demonstrated that in their compacted state, mammalian chromosomes form arrays of closely stacked consecutive ∼100 kb loops. The mechanism underlying the active process of chromosome compaction into a stack of loops is unknown. Here we test the hypothesis that chromosomes are compacted by enzymatic machines that actively extrude chromatin loops. When such loop-extruding factors (LEF) bind to chromosomes, they p rogressively bridge sites that are further away along the chromosome, thus extruding a loop. We demonstrate that collective action of LEFs leads to formation of a dynamic array of consecutive loops. Simulations and an analytically solved model identify two distinct steady states: a sparse state, where loops are highly dynamic but provide little compaction; and a dense state, where there are more stable loops and dramatic chromosome compaction. We find that human chromosomes operate at the border of the dense steady state. Our analysis also shows how the macroscopic characteristics of the loop array are determined by the microscopic properties of LEFs and their abundance. When the number of LEFs are used that match experimentally based estimates, the model can quantitatively reproduce the average loop length, the degree of compaction, and the general loop-array morphology of compact human chromosomes. Our study demonstrates that efficient chromosome compaction can be achieved solely by an active loop-extrusion process.National Institutes of Health (U.S.) (Grant GM114190)National Institutes of Health (U.S.) (Grant R01HG003143

Práticas formais, informais e de poder sombra no espaço político contemporâneo

The present paper considers various forms and practices of power-related interaction in the political system of modern society. It is noted that the institutional-normative and structural-functional aspects do not reflect the variety of forms and types of communication between public and power. The authors substantiate the methodological position according to which the activity of political subjects should not be considered in traditional theoretical and methodological coordinates, where attention is paid only to "positive phenomena", and power communication is not analyzed from the standpoint of "negative structures", i. e. those aspects which are not recognized as being fit into the dominant type of political and legal activity, into the framework of the emerging social order as a whole. The formal, informal, shadow and other power practices that exist in today's political space are considered in the work from this position.El presente trabajo considera diversas formas y prácticas de interacción relacionada con el poder en el sistema político de la sociedad moderna. Se observa que los aspectos institucional-normativos y estructural-funcionales no reflejan la variedad de formas y tipos de comunicación entre el público y el poder. Los autores corroboran la posición metodológica según la cual la actividad de los sujetos políticos no debe considerarse en las coordenadas teóricas y metodológicas tradicionales, donde la atención se centra únicamente en los "fenómenos positivos" y la comunicación de poder no se analiza desde el punto de vista de las "estructuras negativas", aquellos aspectos que no se reconocen como adecuados para el tipo dominante de actividad política y legal, en el marco del orden social emergente como un todo. Las prácticas formales, informales, de sombra y otras prácticas de poder que existen en el espacio político actual se consideran en el trabajo desde esta posición.O presente trabalho considera diversas formas e práticas de interação relacionadas ao poder no sistema político da sociedade moderna. Observa-se que os aspectos institucionais-normativos e estruturais-funcionais não refletem a variedade de formas e tipos de comunicação entre o público e o poder. Os autores confirmam a posição metodológica que a atividade de sujeitos políticos não deve ser considerada em coordenadas teóricas e metodológicas tradicionais, onde o foco é apenas sobre os "desenvolvimentos positivos" e comunicação de poder não é analisado do ponto de vista das "estruturas negativas", aqueles aspectos que não são reconhecidos como adequados ao tipo dominante de atividade política e legal, no contexto da ordem social emergente como um todo. As práticas formais, informais, sombra e outras práticas de poder que existem no espaço político atual são consideradas no trabalho a partir desta posição

C3G mediated suppression of malignant transformation involves activation of PP2A phosphatases at the subcortical actin cytoskeleton

In previous work, we demonstrated that C3G suppresses Ras oncogenic transformation by a mechanism involving inhibition of ERK phosphorylation. Here we present evidences indicating that this suppression mechanism is mediated, at least in part, by serine/threonine phosphatases of the PP2A family. Thus: (i) ectopic expression of C3G or C3GΔCat (mutant lacking the GEF activity) increases specific ERK-associated PP2A phosphatase activities; (ii) C3G and PP2A interact, as demonstrated by immunofluorescence and co-immunoprecipitation experiments; (iii) association between PP2A and MEK or ERK increases in C3G overexpressing cells; (iv) phosphorylated-inactive PP2A level decreases in C3G expressing clones and, most importantly, (v) okadaic acid reverts the inhibitory effect of C3G on ERK phosphorylation. Moreover, C3G interacts with Ksr-1, a scaffold protein of the Ras-ERK pathway that also associates with PP2A. The fraction of C3G involved in transformation suppression is restricted to the subcortical actin cytoskeleton where it interacts with actin. Furthermore, the association between C3G and PP2A remains stable even after cytoskeleton disruption with cytochalasin D, suggesting that the three proteins form a complex at this subcellular compartment. Finally, C3G- and C3GΔCat-mediated inhibition of ERK phosphorylation is reverted by incubation with cytochalasin D. We hypothesize that C3G triggers PP2A activation and binding to MEK and ERK at the subcortical actin cytoskeleton, thus favouring ERK dephosphorylation. © 2007 Elsevier Inc. All rights reserved.This work was supported by grants SAF2003-04177 andGEN2003- 20239-C06-02 from MEC, Spain, FIS-FEDERPI030651, PI041324 and PI061274 from ISCIII,MSC, Spain, as well as institutional support from Redes Temáticas (C03/10 and RD06/0020/0000) de investigación en cáncer from ISCIII, MSC, Spain. S. M-E is a postodoctoral fellow supported by grant GEN2003-20239-C06-02. C.G. was supported by the Ramón y Cajal Program from the Spanish Ministry of Education.Peer Reviewe

Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization

Extracting biologically meaningful information from chromosomal interactions obtained with genome-wide chromosome conformation capture (3C) analyses requires elimination of systematic biases. We present a pipeline that integrates a strategy for mapping of sequencing reads and a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities. We validate ICE (Iterative Correction and Eigenvector decomposition) on published Hi-C data, and demonstrate that eigenvector decomposition of the obtained maps provides insights into local chromatin states, global patterns of chromosomal interactions, and the conserved organization of human and mouse chromosomes

Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization [preprint]

The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and segmental organization into topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding, and CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Further, our data supports that CTCF mediates transcriptional insulator function through enhancer-blocking but not direct chromatin barrier activity. These results define the functions of CTCF in chromosome folding, and provide new fundamental insights into the rules governing mammalian genome organization

Treatment costs of chronic diseases of small bronchi in children

The aim of the present study was to determine the prevalence of chronic non-allergic diseases of small bronchi in children, and to estimate direct costs of outpatient management for this category of patients. Materials and methods: 3024 subjects 0-18 years old, living in St. Petersburg and its suburb (Vsevolozhsk), were randomly selected, and a questionnaire for every subject was filled. Calculation of direct costs was based on medical economy standards for one patient, and for pediatric population of 1000, taking into account the prevalence. Results: total prevalence of chronic non-allergic diseases of small bronchi in children was 0.33% in St. Petersburg and 0.46% in the suburb. Yearly costs of adequate outpatient observation were 8282.92 roubles for bronchopulmonary dysplasia and 7298.37 roubles for obliterating bronchiolitis obliterans. Treatment costs for bronchopulmonary dysplasia come to 35352.74 roubles per year and are similar to that for bronchiolitis obliterans.Цель: Определить распространенность хронических болезней мелких бронхов неаллергической этиологии у детей и рассчитать прямые финансовые затраты на амбулаторный этап ведения данной группы больных. Методы: Использовался метод случайной выборки с заполнением опросника на 3024 ребенка, в возрасте от 0 до 18 лет, компактно проживающих на территории г. Санкт-Петербурга (СПб) и г. Всеволожска Ленинградской области (ЛО). Расчет прямых затрат проводился по медико-экономическим стандартам на одного пациента и, с учетом распространенности, на 1000 детского населения. Результаты: Распространенность хронических болезней мелких бронхов неаллергического генеза в сумме составила 0,33% в СПб, и 0,46% в ЛО. Стоимость адекватного диспансерного наблюдения в течение года детей с бронхолегочной дисплазией составляет 8282,92 руб., облитерирующего бронхиолита 7298,37руб. Затраты на медикаментозное лечение детей с БЛД составляет 35352,74 руб. в год и практически не отличается от стоимости лечения облитерирующего бронхиолита

Clinical picture of community-acquired pneumonia onset in young children

In the following paper there is a comparative analysis of clinical and hematological parameters in the group of young children with community-acquired pneumonia in the early period of the disease. 60 children are divided into two age groups: children of the first year of life (n = 30) and children under 3 years old(n = 30). In all patients the diagnosis of pneumonia was confirmed radiologicaly. The evident differences in the incidence of clinical symptoms of CAP in the two groups have been detected. The early period of CAP in infants is characterized by the development of bronchial obstruction, general signs of intoxication and inflammatory hematological changes. For patients from 1 up to 3 years of age typical characteristic of the disease is high fever and inflammatory changes in the haemogram. Characteristic spptoms for the clinical diagnosis of community-acquired pneumonia in young children are not established.В работе проведен сравнительный анализ клинических и гематологических показателей в группе детей раннего возраста с внебольничной пневмонией в раннем периоде болезни. 60 детей разделены на две возрастные группы: дети первого года жизни (n=30) и дети с года до 3-х лет (n=30). У всех пациентов диагноз пневмонии был подтвержден рентгенологически. Установлены достоверные различия в частоте встречаемости клинических симптомов ВП в сравниваемых группах. Для раннего периода ВП у детей первого года жизни характерно развитие бронхообструктивного синдрома, на фоне симптомов общей интоксикации и воспалительных гематологических изменений. Для пациентов с года до 3-х лет характерно типичное течение болезни с высоким уровнем лихорадки и воспалительными изменениями в гемограмме. Патогномоничных симптомов для клинической диагностики внебольничной пневмонии у детей раннего возраста не установлено

A pathway for mitotic chromosome formation

Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C analysis of synchronous DT40 cell cultures with polymer simulations. Here we show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner, and arrays of consecutive 60-kilobase (kb) loops are formed. During prometaphase, ~80-kb inner loops are nested within ~400-kb outer loops. The loop array acquires a helical arrangement with consecutive loops emanating from a central spiral staircase condensin scaffold. The size of helical turns progressively increases to ~12 megabases during prometaphase. Acute depletion of condensin I or II shows that nested loops form by differential action of the two condensins, whereas condensin II is required for helical winding

Hematopoietic Stem Cells Are the Major Source of Multilineage Hematopoiesis in Adult Animals

Hematopoietic stem cells (HSCs) sustain long-term reconstitution of hematopoiesis in transplantation recipients, yet their role in the endogenous steady-state hematopoiesis remains unclear. In particular, recent studies suggested that HSCs provide a relatively minor contribution to immune cell development in adults. We directed transgene expression in a fraction of HSCs that maintained reconstituting activity during serial transplantations. Inducible genetic labeling showed that transgene-expressing HSCs gave rise to other phenotypic HSCs, confirming their top position in the differentiation hierarchy. The labeled HSCs rapidly contributed to committed progenitors of all lineages and to mature myeloid cells and lymphocytes, but not to B-1a cells or tissue macrophages. Importantly, labeled HSCs gave rise to more than two-thirds of all myeloid cells and platelets in adult mice, and this contribution could be accelerated by an induced interferon response. Thus, classically defined HSCs maintain immune cell development in the steady state and during systemic cytokine responses