162 results found
Al-Jibury E, King JWD, Guo Y, et al., 2023, A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks, Nature Communications, Vol: 14, ISSN: 2041-1723
The organisation of the genome in nuclear space is an important frontier of biology. Chromosome conformation capture methods such as Hi-C and Micro-C produce genome-wide chromatin contact maps that provide rich data containing quantitative and qualitative information about genome architecture. Most conventional approaches to genome-wide chromosome conformation capture data are limited to the analysis of pre-defined features, and may therefore miss important biological information. One constraint is that biologically important features can be masked by high levels of technical noise in the data. Here we introduce a replicate-based method for deep learning from chromatin conformation contact maps. Using a Siamese network configuration our approach learns to distinguish technical noise from biological variation and outperforms image similarity metrics across a range of biological systems. The features extracted from Hi-C maps after perturbation of cohesin and CTCF reflect the distinct biological functions of cohesin and CTCF in the formation of domains and boundaries, respectively. The learnt distance metrics are biologically meaningful, as they mirror the density of cohesin and CTCF binding. These properties make our method a powerful tool for the exploration of chromosome conformation capture data, such as Hi-C capture Hi-C, and Micro-C.
Dimond A, 2023, Drug-induced loss of imprinting revealed using bioluminescent reporters of Cdkn1c, Scientific Reports, Vol: 13, Pages: 1-14, ISSN: 2045-2322
Genomic imprinting is an epigenetically mediated mechanism that regulates allelic expression of genes based upon parent-of-origin and provides a paradigm for studying epigenetic silencing and release. Here, bioluminescent reporters for the maternally-expressed imprinted gene Cdkn1c are used to examine the capacity of chromatin-modifying drugs to reverse paternal Cdkn1c silencing. Exposure of reporter mouse embryonic stem cells (mESCs) to 5-Azacytidine, HDAC inhibitors, BET inhibitors or GSK-J4 (KDM6A/B inhibitor) relieved repression of paternal Cdkn1c, either selectively or by inducing biallelic effects. Treatment of reporter fibroblasts with HDAC inhibitors or GSK-J4 resulted in similar paternal Cdkn1c activation, whereas BET inhibitor-induced loss of imprinting was specific to mESCs. Changes in allelic expression were generally not sustained in dividing cultures upon drug removal, indicating that the underlying epigenetic memory of silencing was maintained. In contrast, Cdkn1c de-repression by GSK-J4 was retained in both mESCs and fibroblasts following inhibitor removal, although this impact may be linked to cellular stress and DNA damage. Taken together, these data introduce bioluminescent reporter cells as tools for studying epigenetic silencing and disruption, and demonstrate that Cdkn1c imprinting requires distinct and cell-type specific chromatin features and modifying enzymes to enact and propagate a memory of silencing.
Fisher AGG, Merkenschlager M, 2023, Avrion Mitchison (1928-2022), NATURE IMMUNOLOGY, Vol: 24, Pages: 559-559, ISSN: 1529-2908
Djeghloul D, Dimond A, Cheriyamkunnel S, et al., 2023, Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis, NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 30, Pages: 489-+, ISSN: 1545-9993
Gleneadie HJJ, Fernandez-Ruiz B, Sardini A, et al., 2023, Endogenous bioluminescent reporters reveal a sustained increase in utrophin gene expression upon EZH2 and ERK1/2 inhibition, COMMUNICATIONS BIOLOGY, Vol: 6
Guo Y, Al-Jibury E, Garcia-Millan R, et al., 2022, Chromatin jets define the properties of cohesin-driven in vivo loop extrusion, Molecular Cell, Vol: 82, Pages: 3769-3780.e5, ISSN: 1097-2765
Complex genomes show intricate organization in three-dimensional (3D) nuclear space. Current models posit that cohesin extrudes loops to form self-interacting domains delimited by the DNA binding protein CTCF. Here, we describe and quantitatively characterize cohesin-propelled, jet-like chromatin contacts as landmarks of loop extrusion in quiescent mammalian lymphocytes. Experimental observations and polymer simulations indicate that narrow origins of loop extrusion favor jet formation. Unless constrained by CTCF, jets propagate symmetrically for 1-2 Mb, providing an estimate for the range of in vivo loop extrusion. Asymmetric CTCF binding deflects the angle of jet propagation as experimental evidence that cohesin-mediated loop extrusion can switch from bi- to unidirectional and is controlled independently in both directions. These data offer new insights into the physiological behavior of in vivo cohesin-mediated loop extrusion and further our understanding of the principles that underlie genome organization.
Robles-Rebollo I, Cuartero S, Canellas-Socias A, et al., 2022, Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters, Nature Communications, Vol: 13, ISSN: 2041-1723
Innate immune responses rely on inducible gene expression programmes which, in contrast to steady-state transcription, are highly dependent on cohesin. Here we address transcriptional parameters underlying this cohesin-dependence by single-molecule RNA-FISH and single-cell RNA-sequencing. We show that inducible innate immune genes are regulated predominantly by an increase in the probability of active transcription, and that probabilities of enhancer and promoter transcription are coordinated. Cohesin has no major impact on the fraction of transcribed inducible enhancers, or the number of mature mRNAs produced per transcribing cell. Cohesin is, however, required for coupling the probabilities of enhancer and promoter transcription. Enhancer-promoter coupling may not be explained by spatial proximity alone, and at the model locus Il12b can be disrupted by selective inhibition of the cohesinopathy-associated BET bromodomain BD2. Our data identify discrete steps in enhancer-mediated inducible gene expression that differ in cohesin-dependence, and suggest that cohesin and BD2 may act on shared pathways.
Dsouza KB, Maslova A, Al-Jibury E, et al., 2022, Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of conformation, NATURE COMMUNICATIONS, Vol: 13
Van de Pette M, Dimond A, Galvao AM, et al., 2022, Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice, Nature Communications, Vol: 13, ISSN: 2041-1723
Transmission of epigenetic information between generations occurs in nematodes, flies and plants, mediated by specialised small RNA pathways, modified histones and DNA methylation. Similar processes in mammals can also affect phenotype through intergenerational or trans-generational mechanisms. Here we generate a luciferase knock-in reporter mouse for the imprinted Dlk1 locus to visualise and track epigenetic fidelity across generations. Exposure to high-fat diet in pregnancy provokes sustained re-expression of the normally silent maternal Dlk1 in offspring (loss of imprinting) and increased DNA methylation at the somatic differentially methylated region (sDMR). In the next generation heterogeneous Dlk1 mis-expression is seen exclusively among animals born to F1-exposed females. Oocytes from these females show altered gene and microRNA expression without changes in DNA methylation, and correct imprinting is restored in subsequent generations. Our results illustrate how diet impacts the foetal epigenome, disturbing canonical and non-canonical imprinting mechanisms to modulate the properties of successive generations of offspring.
Calderon L, Weiss FD, Beagan JA, et al., 2022, Cohesin-dependence of neuronal gene expression relates to chromatin loop length, eLife, Vol: 11, ISSN: 2050-084X
Cohesin and CTCF are major drivers of 3D genome organization, but their role in neurons is still emerging. Here, we show a prominent role for cohesin in the expression of genes that facilitate neuronal maturation and homeostasis. Unexpectedly, we observed two major classes of activity-regulated genes with distinct reliance on cohesin in mouse primary cortical neurons. Immediate early genes (IEGs) remained fully inducible by KCl and BDNF, and short-range enhancer-promoter contacts at the IEGs Fos formed robustly in the absence of cohesin. In contrast, cohesin was required for full expression of a subset of secondary response genes characterized by long-range chromatin contacts. Cohesin-dependence of constitutive neuronal genes with key functions in synaptic transmission and neurotransmitter signaling also scaled with chromatin loop length. Our data demonstrate that key genes required for the maturation and activation of primary cortical neurons depend on cohesin for their full expression, and that the degree to which these genes rely on cohesin scales with the genomic distance traversed by their chromatin contacts.Editor's
Weiss FD, Calderon L, Wang Y-F, et al., 2021, Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and reexpression of cohesin, Nature Communications, Vol: 12, ISSN: 2041-1723
Cornelia de Lange Syndrome (CdLS) is a human developmental disorder caused by mutations that compromise the function of cohesin, a major regulator of 3D genome organization. Cognitive impairment is a universal and as yet unexplained feature of CdLS. We characterize the transcriptional profile of cortical neurons from CdLS patients and find deregulation of hundreds of genes enriched for neuronal functions related to synaptic transmission, signalling processes, learning and behaviour. Inducible proteolytic cleavage of cohesin disrupts 3D genome organization and transcriptional control in post-mitotic cortical mouse neurons, demonstrating that cohesin is continuously required for neuronal gene expression. The genes affected by acute depletion of cohesin belong to similar gene ontology classes and show significant numerical overlap with genes deregulated in CdLS. Interestingly, reconstitution of cohesin function largely rescues altered gene expression, including the expression of genes deregulated in CdLS.
Calderon L, Weiss FD, Beagan JA, et al., 2021, Reliance of neuronal gene expression on cohesin scales with chromatin loop length
<jats:title>Abstract</jats:title><jats:p>Cohesin and CTCF are major drivers of 3D genome organization, but their role in neurons is still emerging. Here we show a prominent role for cohesin in the expression of genes that facilitate neuronal maturation and homeostasis. Unexpectedly, we observed two major classes of activity-regulated genes with distinct reliance on cohesin in primary cortical neurons. Immediate early genes remained fully inducible by KCl and BDNF, and short-range enhancer-promoter contacts at the Immediate early gene <jats:italic>Fos</jats:italic> formed robustly in the absence of cohesin. In contrast, cohesin was required for full expression of a subset of secondary response genes characterised by long-range chromatin contacts. Cohesin-dependence of constitutive neuronal genes with key functions in synaptic transmission and neurotransmitter signaling also scaled with chromatin loop length. Our data demonstrate that key genes required for the maturation and activation of primary cortical neurons depend cohesin for their full expression, and that the degree to which these genes rely on cohesin scales with the genomic distance traversed by their chromatin contacts.</jats:p>
Karimi MM, Guo Y, Cui X, et al., 2021, The order and logic of CD4 CD8 lineage choice and differentiation in mouse thymus, Nature Communications, Vol: 12, ISSN: 2041-1723
CD4 and CD8 mark helper and cytotoxic T cell lineages, respectively, and serve as coreceptors for MHC-restricted TCR recognition. How coreceptor expression is matched with TCR specificity is central to understanding CD4/CD8 lineage choice, but visualising coreceptor gene activity in individual selection intermediates has been technically challenging. It therefore remains unclear whether the sequence of coreceptor gene expression in selection intermediates follows a stereotypic pattern, or is responsive to signaling. Here we use single cell RNA sequencing (scRNA-seq) to classify mouse thymocyte selection intermediates by coreceptor gene expression. In the unperturbed thymus, Cd4+Cd8a- selection intermediates appear before Cd4-Cd8a+ selection intermediates, but the timing of these subsets is flexible according to the strength of TCR signals. Our data show that selection intermediates discriminate MHC class prior to the loss of coreceptor expression and suggest a model where signal strength informs the timing of coreceptor gene activity and ultimately CD4/CD8 lineage choice.
Djeghloul D, Patel B, Kramer H, et al., 2020, Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction, Nature Communications, Vol: 11, Pages: 1-15, ISSN: 2041-1723
Epigenetic information is transmitted from mother to daughter cells through mitosis. Here, to identify factors that might play a role in conveying epigenetic memory through cell division, we report on the isolation of unfixed, native chromosomes from metaphase-arrested cells using flow cytometry and perform LC-MS/MS to identify chromosome-bound proteins. A quantitative proteomic comparison between metaphase-arrested cell lysates and chromosome-sorted samples reveals a cohort of proteins that were significantly enriched on mitotic ESC chromosomes. These include pluripotency-associated transcription factors, repressive chromatin-modifiers such as PRC2 and DNA methyl-transferases, and proteins governing chromosome architecture. Deletion of PRC2, Dnmt1/3a/3b or Mecp2 in ESCs leads to an increase in the size of individual mitotic chromosomes, consistent with de-condensation. Similar results were obtained by the experimental cleavage of cohesin. Thus, we identify chromosome-bound factors in pluripotent stem cells during mitosis and reveal that PRC2, DNA methylation and Mecp2 are required to maintain chromosome compaction.
Weiss FD, Calderon L, Wang Y-F, et al., 2020, Partial rescue of neuronal genes deregulated in Cornelia de Lange Syndrome by cohesin
<jats:title>Abstract</jats:title><jats:p>Cornelia de Lange Syndrome (CdLS) is a human developmental disorder caused by mutations that compromise the function of cohesin, a major regulator of 3D genome organization. Cognitive impairment is a universal and as yet unexplained feature of CdLS. We characterized the transcriptional profile of cortical neurons from CdLS patients and found deregulation of hundreds of genes enriched for neuronal functions related to synaptic transmission, signalling processes, learning and behaviour. Inducible proteolytic cleavage of cohesin disrupted 3-D genome organization and transcriptional control in post-mitotic cortical mouse neurons. The genes affected belonged to similar gene ontology classes and showed significant numerical overlap with those deregulated in CdLS. Interestingly, gene expression was largely rescued by subsequent reconstitution of cohesin function. These experiments show that cohesin is continuously required for neuronal gene expression and provide a tractable approach for addressing mechanisms of neuronal dysfunction in CdLS.</jats:p>
Bystricky K, Merkenschlager M, 2020, Editorial overview: Genome architecture and expression, CURRENT OPINION IN GENETICS & DEVELOPMENT, Vol: 61, Pages: III-VI, ISSN: 0959-437X
Rojec M, Hocher A, Stevens KM, et al., 2019, Chromatinization of Escherichia coli with archaeal histones, eLife, Vol: 8, Pages: 1-23, ISSN: 2050-084X
Nucleosomes restrict DNA accessibility throughout eukaryotic genomes, withrepercussions for replication, transcription, and other DNA-templated processes. How this globallyrestrictive organization emerged during evolution remains poorly understood. Here, to betterunderstand the challenges associated with establishing globally restrictive chromatin, we expresshistones in a naive system that has not evolved to deal with nucleosomal structures: Escherichiacoli. We find that histone proteins from the archaeon Methanothermus fervidus assemble on the E.coli chromosome in vivo and protect DNA from micrococcal nuclease digestion, allowing us to mapbinding footprints genome-wide. We show that higher nucleosome occupancy at promoters isassociated with lower transcript levels, consistent with local repressive effects. Surprisingly,however, this sudden enforced chromatinization has only mild repercussions for growth unless cellsexperience topological stress. Our results suggest that histones can become established asubiquitous chromatin proteins without interfering critically with key DNA-templated processes.
Jansen C, Ramirez RN, El-Ali NC, et al., 2019, Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps, PLOS COMPUTATIONAL BIOLOGY, Vol: 15, ISSN: 1553-734X
Gomez-Cabrero D, Tarazona S, Ferreiros-Vidal I, et al., 2019, STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse, Scientific Data, Vol: 6, Pages: 1-15, ISSN: 2052-4463
Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemented with single-cell data. To our knowledge, the STATegra collection is the most diverse multi-omics dataset describing a dynamic biological system.
Palmisano I, Danzi MC, Hutson TH, et al., 2019, Epigenomic signatures underpin the axonal regenerative ability of dorsal root ganglia sensory neurons, Nature Neuroscience, Vol: 22, Pages: 1913-1924, ISSN: 1097-6256
Axonal injury results in regenerative success or failure, depending on whether the axon lies in the peripheral or the CNS, respectively. The present study addresses whether epigenetic signatures in dorsal root ganglia discriminate between regenerative and non-regenerative axonal injury. Chromatin immunoprecipitation for the histone 3 (H3) post-translational modifications H3K9ac, H3K27ac and H3K27me3; an assay for transposase-accessible chromatin; and RNA sequencing were performed in dorsal root ganglia after sciatic nerve or dorsal column axotomy. Distinct histone acetylation and chromatin accessibility signatures correlated with gene expression after peripheral, but not central, axonal injury. DNA-footprinting analyses revealed new transcriptional regulators associated with regenerative ability. Machine-learning algorithms inferred the direction of most of the gene expression changes. Neuronal conditional deletion of the chromatin remodeler CCCTC-binding factor impaired nerve regeneration, implicating chromatin organization in the regenerative competence. Altogether, the present study offers the first epigenomic map providing insight into the transcriptional response to injury and the differential regenerative ability of sensory neurons.
Cuartero S, Innes AJ, Merkenschlager M, 2019, Towards a better understanding of cohesin mutations in AML, Frontiers in Oncology, Vol: 9, ISSN: 2234-943X
Classical driver mutations in acute myeloid leukemia (AML) typically affect regulatorsof cell proliferation, differentiation, and survival. The selective advantage of increasedproliferation, improved survival, and reduced differentiation on leukemia progression isimmediately obvious. Recent large-scale sequencing efforts have uncovered numerousnovel AML-associated mutations. Interestingly, a substantial fraction of the mostfrequently mutated genes encode general regulators of transcription and chromatinstate. Understanding the selective advantage conferred by these mutations remains amajor challenge. A striking example are mutations in genes of the cohesin complex,a major regulator of three-dimensional genome organization. Several landmark studieshave shown that cohesin mutations perturb the balance between self-renewal anddifferentiation of hematopoietic stem and progenitor cells (HSPC). Emerging data nowbegin to uncover the molecular mechanisms that underpin this phenotype. Amongthese mechanisms is a role for cohesin in the control of inflammatory responses inHSPCs and myeloid cells. Inflammatory signals limit HSPC self-renewal and driveHSPC differentiation. Consistent with this, cohesin mutations promote resistance toinflammatory signals, and may provide a selective advantage for AML progression.In this review, we discuss recent progress in understanding cohesin mutations inAML, and speculate whether vulnerabilities associated with these mutations could beexploited therapeutically
Bruno L, Ramlall V, Studer RA, et al., 2019, Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system, Nature Immunology, Vol: 20, Pages: 1372-1380, ISSN: 1529-2908
In multicellular organisms, duplicated genes can diverge through tissue-specific gene expression patterns, as exemplified by highly regulated expression of Runx transcription factor paralogs with apparent functional redundancy. Here we asked what cell type-specific biologies might be supported by the selective expression of Runx paralogs during Langerhans cell and inducible regulatory T cell differentiation. We uncovered functional non-equivalence between Runx paralogs. Selective expression of native paralogs allowed integration of transcription factor activity with extrinsic signals, while non-native paralogs enforced differentiation even in the absence of exogenous inducers. DNA-binding affinity was controlled by divergent amino acids within the otherwise highly conserved RUNT domain, and evolutionary reconstruction suggested convergence of RUNT domain residues towards sub-maximal strength. Hence, the selective expression of gene duplicates in specialized cell types can synergize with the acquisition of functional differences to enable appropriate gene expression, lineage choice and differentiation in the mammalian immune system.
Ferreirós-Vidal I, Carroll T, Zhang T, et al., 2019, Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation, PLoS Biology, Vol: 17, ISSN: 1544-9173
The differentiation of self-renewingprogenitor cells requires not only the regulation of lineage-and developmental stage-specific genes, but also the coordinated adaptation of housekeeping functionsfrom a metabolically active, proliferative state towards quiescence. How metabolic and cell cycle states are coordinated with the regulation of cell type-specific genes is an important question, as dissociation between differentiation, cell cycle, and metabolic states is a hallmark of cancer. Here we use a model system to systematically identify key transcriptional regulators of Ikaros-dependent B cell progenitor differentiation. We find that the coordinated regulation of housekeeping functions and tissue-specific gene expressionrequires afeedforward circuit whereby Ikarosdownregulates the expression of Myc. Our findings show how coordination between differentiation and housekeeping statescan be achieved by interconnected regulators. Similar principles likely coordinate differentiation and housekeeping functions during progenitor cell differentiation in other cell lineages.
Calderon L, Weiss FD, Carroll T, et al., 2019, Cohesin is continuously required to sustain neuronal gene expression, 29th Mammalian Genetics and Development Workshop of the Genetics-Society, Publisher: HINDAWI LTD, ISSN: 0016-6723
Jansen C, Ramirez RN, El-Ali NC, et al., 2018, Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self-Organizing Maps
<jats:title>Abstract</jats:title><jats:p>Rapid advances in single-cell assays have outpaced methods for analysis of those data types. Different single-cell assays show extensive variation in sensitivity and signal to noise levels. In particular, scATAC-seq generates extremely sparse and noisy datasets. Existing methods developed to analyze this data require cells amenable to pseudo-time analysis or require datasets with drastically different cell-types. We describe a novel approach using self-organizing maps (SOM) to link scATAC-seq and scRNA-seq data that overcomes these challenges and can generate draft regulatory networks. Our SOMatic package generates chromatin and gene expression SOMs separately and combines them using a linking function. We applied SOMatic on a mouse pre-B cell differentiation time-course using controlled Ikaros over-expression to recover gene ontology enrichments, identify motifs in genomic regions showing similar single-cell profiles, and generate a gene regulatory network that both recovers known interactions and predicts new Ikaros targets during the differentiation process. The ability of linked SOMs to detect emergent properties from multiple types of highly-dimensional genomic data with very different signal properties opens new avenues for integrative analysis of single-cells.</jats:p>
Merkenschlager M, Cuartero S, Weiss F, et al., 2018, Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation, Nature Immunology, Vol: 19, Pages: 932-941, ISSN: 1529-2908
Cohesin is important for 3D genome organization. Nevertheless, even the complete removal of cohesin has surprisingly little impact on steady-state gene transcription and enhancer activity. Here we show that cohesin is required for the core transcriptional response of primary macrophages to microbial signals, and for inducible enhancer activity that underpins inflammatory gene expression. Consistent with a role for inflammatory signals in promoting myeloid differentiation of hematopoietic stem and progenitor cells (HPSCs), cohesin mutations in HSPCs led to reduced inflammatory gene expression and increased resistance to differentiation-inducing inflammatory stimuli. These findings uncover an unexpected dependence of inducible gene expression on cohesin, link cohesin with myeloid differentiation, and may help explain the prevalence of cohesin mutations in human acute myeloid leukemia.
Cuartero S, Merkenschlager M, 2018, Three-dimensional genome organization in normal and malignant haematopoiesis., Current Opinion in Hematology, Vol: 25, Pages: 323-328, ISSN: 1065-6251
PURPOSE OF REVIEW: The three-dimensional organization of the genome inside the nucleus impacts on key aspects of genome function, including transcription, DNA replication and repair. The chromosome maintenance complex cohesin and the DNA binding protein CTCF cooperate to drive the formation of self-interacting topological domains. This facilitates transcriptional regulation via enhancer-promoter interactions, controls the distribution and release of torsional strain, and affects the frequency with which particular translocations arise, based on the spatial proximity of translocation partners. Here we discuss recent insights into the mechanisms of three-dimensional genome organization, their relationship to haematopoietic differentiation and malignant transformation. RECENT FINDINGS: Cohesin mutations are frequently found in myeloid malignancies. Significantly, cohesin mutations can drive increased self-renewal of haematopoietic stem and progenitor cells, which may facilitate the accumulation of genetic lesions and leukaemic transformation. It is therefore important to elucidate the mechanisms that link cohesin to pathways that regulate the balance between self-renewal and differentiation. Chromosomal translocations are key to lymphoid malignancies, and recent findings link three-dimensional genome organization to the frequency and the genomic position of DNA double strand breaks. SUMMARY: Three-dimensional genome organization can help explain genome function in normal and malignant haematopoiesis.
Harmston N, Ing-Simmons E, Tan G, et al., 2017, Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation, Nature Communications, Vol: 8, ISSN: 2041-1723
Developmental genes in metazoan genomes are surrounded by dense clusters of conserved noncoding elements (CNEs). CNEs exhibit unexplained extreme levels of sequence conservation, with many acting as developmental long-range enhancers. Clusters of CNEs define the span of regulatory inputs for many important developmental regulators and have been described previously as genomic regulatory blocks (GRBs). Their function and distribution around important regulatory genes raises the question of how they relate to 3D conformation of these loci. Here, we show that clusters of CNEs strongly coincide with topological organisation, predicting the boundaries of hundreds of topologically associating domains (TADs) in human and Drosophila. The set of TADs that are associated with high levels of noncoding conservation exhibit distinct properties compared to TADs devoid of extreme noncoding conservation. The close correspondence between extreme noncoding conservation and TADs suggests that these TADs are ancient, revealing a regulatory architecture conserved over hundreds of millions of years.Metazoan genomes contain many clusters of conserved noncoding elements. Here, the authors provide evidence that these clusters coincide with distinct topologically associating domains in humans and Drosophila, revealing a conserved regulatory genomic architecture.
Perez MEF, Bloznelyte K, Merkenschlager M, et al., 2017, Visualizing CTCF-mediated DNA looping at the single-molecule level, 19th IUPAB Congress / 11th EBSA Congress, Publisher: SPRINGER, Pages: S141-S141, ISSN: 0175-7571
Fisher AG, Stumpf MPH, Merkenschlager M, 2017, Reconciling Epigenetic Memory and Transcriptional Responsiveness, CELL SYSTEMS, Vol: 4, Pages: 373-374, ISSN: 2405-4712
The molecular basis of cellular memory is important but poorly understood. Using estimates of histone dynamics, Martin Howard and colleagues construct a mathematical model that helps to explain both the stability and flexibility of Polycomb-mediated gene regulation in cellular memory.
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.