A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation

Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology

Analisi i valoracio de la implantació de les Superilles a Barcelona

This final work is a summary of all aspects related to creation and making off of the “Superilles” in Barcelona. This allows to understand basic aspects of “Superilles”, such as mobility, quality of public space and the satisfaction of this model in Barcelona. To evaluate the satisfaction, surveys have been developed and carried out for users of the “Superilles”. These surveys have been done face to face and online. The degree of satisfaction and assessment of the model is generally positive, for example the use of public space. On the contrary, there is a negative assessment of private vehicle mobility, because most of the people think that have been getting worse. In addition, people think that they had information about the model but perhaps this did not make the neighbors understand how the transformation would be. Despite the criticism around the “Superilles”, the reality is that the group that is in large numbers is only 30%. Keywords: movility, use of public space, Superilles, Poble Nou.El treball fa un recull d’informacio sobre tots els aspectes relacionats amb la creacio i posada en marxa de les Superilles a Barcelona. Aixo permet entendre aspectes basics d’aquesta, com son la mobilitat, la qualitat d’espai public i la satisfaccio del model. Per valorar la satisfaccio de les Superilles de Barcelona s’ha elaborat i realitzat unes enquestes destinades als usuaris de les Superilles. Aquestes enquestes s’han fet de forma parcial i online. El grau de satisfaccio i la valoracio que es fa del model es en general positiu, tant en termes de satisfaccio com d’us de l’espai public. Per contra hi ha una valoracio negativa de la mobilitat amb vehicle privat, al considerar que ara es pitjor. La gent considera que si que va tenir informacio sobre el model pero potser aquesta no va fer entendre els veins com seria la transformacio. Tot i el soroll que hi ha al voltant de les Superilles, la realitat es que el col•lectiu que s’hi oposa de forma important es nomes del 30%.El trabajo hace una recopilacion de la informacion sobre todos los aspectos relacionados con la creacion y puesta en marcha de las “Superilles” en Barcelona. Esto permite entender aspectos basicos de la misma, como son la movilidad, la calidad de espacio publico y la satisfaccion del modelo. Para valorar la satisfaccion de las “Superilles” de Barcelona se han elaborado y realizado unas encuestas destinadas a los usuarios de las “Superilles”. Las encuestas se han hacho de forma online y en papel. El grado de satisfaccion y la valoracion que se hace del modelo es en general positivo, como sobretodo en el uso del espacio publico. Por el contrario hay una valoracion negativa de la movilidad en vehiculo privado, porque la gran mayoria de los usuarios considera que ha empeorado. Ademas, los vecinos consideran que si tuvieron informacion sobre el modelo pero quizas esta no hizo entender como seria la transformacion. Pese al ruido que hay alrededor de las “Superilles”, la realidad es que el colectivo que se opone de forma importante es solo del 30%. Palabras clave: movilidad, uso espacio publico, Superilles, Poble Nou

Toward a mechanistic understanding of variable chromatin modules

Our genome is a long sequence of DNA that contains all the information to be able to constitute a living organism like us, similarly to what the letters in a book do to create a story. This sequence, which is a stretch of molecules called nucleotides, is almost identical between organisms of the same species (>99.9% in humans), however it varies in a small percentage due to some nucleotides being different at specific positions of the genome. This variation in the DNA will therefore influence our traits and affect our susceptibility to a certain condition. Thus, their study is highly relevant in genetics and biomedicine since they allow not only to predict the predisposition to a disease, such as cancer, but also to understand the molecular and cellular mechanism behind a certain phenotype. The effect of a genetic variant on a phenotype is given by their capacity to modulate the expression of a gene, either by directly impacting its sequence and thus changing the protein, or by regulating its expression levels. Interestingly, more than 88% of the disease-associated genetic variants present in humans are located outside genes, on the so-called non-coding part of the genome. This poses a challenge to identify what gene the genetic variant affects and to understand how it does so. Genetic variants do not only influence gene expression but they also affect the epigenetics state of the DNA (i.e. DNA methylation, histone marks, transcription factor (TF) binding...) and its 3D conformation, consequently modifying the activity of gene regulatory elements like promoters and enhancers. Previously, it has been shown that some of these regulatory regions located in the same locus exhibit a high level of molecular coordination and interindividual variation, mostly affected by genetic variation or environmental effects. These regions were termed variable chromatin modules (VCMs) or cis-regulatory domains (CRDs) and are thought to be the manifestation of fine-grained regulatory units of the genome. Understanding how a VCM is formed and the molecular basis behind the cooperativity between regulatory elements is an outstanding question in the field. In this work, we aim at resolving part of this puzzle by mechanistically dissecting one VCM that is influenced by a non-coding germline variant in B cells. Using a set of tools such as genetic engineering, TF binding assays and chromosome conformation studies, we demonstrate that this variant creates a de novo binding site for the TF MEF2, which acts as a pioneering factor for dozens of other collaborating TFs. In turn, this actuates a cluster of enhancers spanning a region over 150 kilobases (kb) that regulates AXIN2 gene expression, and is associated with a global compaction of the chromatin. In addition, in line with the known tumor-suppressor properties of AXIN2, we found that this variant influences chronic lymphocytic leukemia (CLL) progression and predisposition. Together, the characterization of the AXIN2 VCM provides an unique example to the community of how a germline variant is able to switch on an entire genomic locus with high degree of cooperativity between regulatory elements, since it captures both the formation and transition behavior of a VCM. Furthermore, given the link with CLL, this focal variant could have translational potential by serving as a patient-stratifying or treatment diagnostic

Analisi i valoracio de la implantació de les Superilles a Barcelona

This final work is a summary of all aspects related to creation and making off of the “Superilles” in Barcelona. This allows to understand basic aspects of “Superilles”, such as mobility, quality of public space and the satisfaction of this model in Barcelona. To evaluate the satisfaction, surveys have been developed and carried out for users of the “Superilles”. These surveys have been done face to face and online. The degree of satisfaction and assessment of the model is generally positive, for example the use of public space. On the contrary, there is a negative assessment of private vehicle mobility, because most of the people think that have been getting worse. In addition, people think that they had information about the model but perhaps this did not make the neighbors understand how the transformation would be. Despite the criticism around the “Superilles”, the reality is that the group that is in large numbers is only 30%. Keywords: movility, use of public space, Superilles, Poble Nou.El treball fa un recull d’informacio sobre tots els aspectes relacionats amb la creacio i posada en marxa de les Superilles a Barcelona. Aixo permet entendre aspectes basics d’aquesta, com son la mobilitat, la qualitat d’espai public i la satisfaccio del model. Per valorar la satisfaccio de les Superilles de Barcelona s’ha elaborat i realitzat unes enquestes destinades als usuaris de les Superilles. Aquestes enquestes s’han fet de forma parcial i online. El grau de satisfaccio i la valoracio que es fa del model es en general positiu, tant en termes de satisfaccio com d’us de l’espai public. Per contra hi ha una valoracio negativa de la mobilitat amb vehicle privat, al considerar que ara es pitjor. La gent considera que si que va tenir informacio sobre el model pero potser aquesta no va fer entendre els veins com seria la transformacio. Tot i el soroll que hi ha al voltant de les Superilles, la realitat es que el col•lectiu que s’hi oposa de forma important es nomes del 30%.El trabajo hace una recopilacion de la informacion sobre todos los aspectos relacionados con la creacion y puesta en marcha de las “Superilles” en Barcelona. Esto permite entender aspectos basicos de la misma, como son la movilidad, la calidad de espacio publico y la satisfaccion del modelo. Para valorar la satisfaccion de las “Superilles” de Barcelona se han elaborado y realizado unas encuestas destinadas a los usuarios de las “Superilles”. Las encuestas se han hacho de forma online y en papel. El grado de satisfaccion y la valoracion que se hace del modelo es en general positivo, como sobretodo en el uso del espacio publico. Por el contrario hay una valoracion negativa de la movilidad en vehiculo privado, porque la gran mayoria de los usuarios considera que ha empeorado. Ademas, los vecinos consideran que si tuvieron informacion sobre el modelo pero quizas esta no hizo entender como seria la transformacion. Pese al ruido que hay alrededor de las “Superilles”, la realidad es que el colectivo que se opone de forma importante es solo del 30%. Palabras clave: movilidad, uso espacio publico, Superilles, Poble Nou

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molecular biology to address the major limitations of standard ChIP-seq. The resulting technology, FloChIP, automates and miniaturizes ChIP in a beadless fashion while facilitating the downstream library preparation process through on-chip chromatin tagmentation. FloChIP is fast (<2 h), has a wide dynamic range (from 106 to 500 cells), is scalable and parallelized, and supports antibody- or sample-multiplexed ChIP on both histone marks and transcription factors. In addition, FloChIP's interconnected design allows for straightforward chromatin reimmunoprecipitation, which allows this technology to also act as a microfluidic sequential ChIP-seq system. Finally, we ran FloChIP for the transcription factor MEF2A in 32 distinct human lymphoblastoid cell lines, providing insights into the main factors driving collaborative DNA binding of MEF2A and into its role in B cell-specific gene regulation. Together, our results validate FloChIP as a flexible and reproducible automated solution for individual or sequential ChIP-seq

Reduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer

This study addresses the roles of nuclear receptor corepressor 2 (NCOR2) in prostate cancer (PC) progression in response to androgen deprivation therapy (ADT). Reduced NCOR2 expression significantly associates with shorter disease-free survival in patients with PC receiving adjuvant ADT. Utilizing the CWR22 xenograft model, we demonstrate that stably reduced NCOR2 expression accelerates disease recurrence following ADT, associates with gene expression patterns that include neuroendocrine features, and induces DNA hypermethylation. Stably reduced NCOR2 expression in isogenic LNCaP (androgen-sensitive) and LNCaP-C4-2 (androgen-independent) cells revealed that NCOR2 reduction phenocopies the impact of androgen treatment and induces global DNA hypermethylation patterns. NCOR2 genomic binding is greatest in LNCaP-C4-2 cells and most clearly associates with forkhead box (FOX) transcription factor FOXA1 binding. NCOR2 binding significantly associates with transcriptional regulation most when in active enhancer regions. These studies reveal robust roles for NCOR2 in regulating the PC transcriptome and epigenome and underscore recent mutational studies linking NCOR2 loss of function to PC disease progression