scholarly journals Characterizing higher order structures of chromatin in human cells

2018 ◽  
Author(s):  
Uwe Schwartz ◽  
Attila Németh ◽  
Sarah Diermeier ◽  
Josef Exler ◽  
Stefan Hansch ◽  
...  
Keyword(s):  
Large Scale ◽  
Structural Changes ◽  
Computer Modelling ◽  
Regulatory Elements ◽  
Higher Order ◽  
Chromatin Organization ◽  
Transcription Start Sites ◽  
Irregular Structure ◽  
Genomic Regions ◽  
Order Structures

AbstractPackaging of DNA into chromatin regulates DNA accessibility and, consequently, all DNA-dependent processes, such as transcription, recombination, repair, and replication. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This defined organization of chromatin has been recently questioned using microscopy techniques, proposing a rather irregular structure. To gain more insight into the principles of chromatin organization, we applied an in situ differential MNase-seq strategy and analyzed in silico the results of complete and partial digestions of human chromatin. We investigated whether different levels of chromatin packaging exist in the cell. Thus, we assessed the accessibility of chromatin within distinct domains of kb to Mb genomic regions by utilizing statistical data analyses and computer modelling. We found no difference in the degree of compaction between domains of euchromatin and heterochromatin or between other sequence and epigenomic features of chromatin. Thus, our data suggests the absence of differentially compacted domains of higher-order structures of chromatin. Moreover, we identified only local structural changes, with individual hyper-accessible nucleosomes surrounding regulatory elements, such as enhancers and transcription start sites. The regulatory sites per se are occupied with structurally altered nucleosomes, exhibiting increased MNase sensitivity. Our findings provide biochemical evidence that supports an irregular model of large-scale chromatin organization.

scholarly journals Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Elissavet Kentepozidou ◽  
Sarah J. Aitken ◽  
Christine Feig ◽  
Klara Stefflova ◽  
Ximena Ibarra-Soria ◽  
...  
Keyword(s):  
Large Scale ◽  
Evolutionary Dynamics ◽  
Computational Study ◽  
Genome Structure ◽  
Higher Order ◽  
Ctcf Binding ◽  
Natural Genetic Variation ◽  
Transcription Start Sites ◽  
Topologically Associating Domains ◽  
Species Specific

Abstract Background CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. Results We carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. Conclusions Dynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure.

Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei

2000 ◽  
Vol 113 (9) ◽  
pp. 1565-1576 ◽  
Author(s):  
E.V. Volpi ◽  
E. Chevret ◽  
T. Jones ◽  
R. Vatcheva ◽  
J. Williamson ◽  
...  
Keyword(s):  
Major Histocompatibility Complex ◽  
Large Scale ◽  
Gene Clusters ◽  
Cell Types ◽  
Chromatin Organization ◽  
Chromosome 6 ◽  
Chromatin Loop ◽  
Major Histocompatibility ◽  
Histocompatibility Complex ◽  
Genomic Regions

The large-scale chromatin organization of the major histocompatibility complex and other regions of chromosome 6 was studied by three-dimensional image analysis in human cell types with major differences in transcriptional activity. Entire gene clusters were visualized by fluorescence in situ hybridization with multiple locus-specific probes. Individual genomic regions showed distinct configurations in relation to the chromosome 6 terrritory. Large chromatin loops containing several megabases of DNA were observed extending outwards from the surface of the domain defined by the specific chromosome 6 paint. The frequency with which a genomic region was observed on an external chromatin loop was cell type dependent and appeared to be related to the number of active genes in that region. Transcriptional up-regulation of genes in the major histocompatibility complex by interferon-gamma led to an increase in the frequency with which this large gene cluster was found on an external chromatin loop. Our data are consistent with an association between large-scale chromatin organization of specific genomic regions and their transcriptional status.

The role of Bni5 in the regulation of septin higher-order structure formation

2015 ◽  
Vol 396 (12) ◽  
pp. 1325-1337 ◽  
Author(s):  
Csilla Patasi ◽  
Jana Godočíková ◽  
Soňa Michlíková ◽  
Yan Nie ◽  
Radka Káčeriková ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Structural Changes ◽  
Higher Order ◽  
Cytoskeletal Proteins ◽  
Order Structure ◽  
Division Plane ◽  
Cellular Processes ◽  
Order Structures

Abstract Septins are a family of conserved cytoskeletal proteins playing an essential role in cytokinesis and in many other cellular processes in fungi and animals. In budding yeast Saccharomyces cerevisiae, septins form filaments and higher-order structures at the mother-bud neck depending on the particular stage of the cell cycle. Septin structures at the division plane serve as a scaffold to recruit the proteins required for particular cellular processes. The formation and localization of septin structures at particular stages of the cell cycle also determine functionality of these proteins. Many different proteins participate in regulating septin assembly. Despite recent developments, we are only beginning to understand how specific protein-protein interactions lead to changes in the polymerization of septin filaments or assembly of higher-order structures. Here, using fluorescence and electron microscopy, we found that Bni5 crosslinks septin filaments into networks by bridging pairs or multiple filaments, forming structures that resemble railways. Furthermore, Bni5 appears to be a substrate of the Elm1 protein kinase in vitro. Moreover, Elm1 induces in the presence of Bni5 disassembly of long septin filaments, suggesting that these proteins may participate in the hourglass to double ring transition. This work gives new insight into the regulatory role of Bni5 in the structural changes of septins.

scholarly journals CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

2016 ◽  
Author(s):  
David J. Arenillas ◽  
Alistair R.R. Forrest ◽  
Hideya Kawaji ◽  
Timo Lassman ◽  
Wyeth W. Wasserman ◽  
...  
Keyword(s):  
Large Scale ◽  
Enrichment Analysis ◽  
Cell Types ◽  
Specific Cell ◽  
Data Sets ◽  
Transcription Start Sites ◽  
Supplementary Material ◽  
Supplementary Text ◽  
Cap Analysis ◽  
Genomic Regions

AbstractSummaryWith the emergence of large-scale Cap Analysis of Gene Expression (CAGE) data sets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived genomic regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The webtool allows for the analysis of CAGE-derived transcription start sites (TSSs) either provided by the user or selected from ~1,300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool helps power insights into the regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions.Availability and implementationThe CAGEd-oPOSUM web tool is implemented in Perl, MySQL, and Apache and is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM.Supporting InformationSupplementary Text, Figures, and Data are available online at bioRxiv.

scholarly journals The Evolutionary History of Common Genetic Variants Influencing Human Cortical Surface Area

2020 ◽  
Author(s):  
Amanda K Tilot ◽  
Ekaterina A Khramtsova ◽  
Dan Liang ◽  
Katrina L Grasby ◽  
Neda Jahanshad ◽  
...  
Keyword(s):  
Human Brain ◽  
Surface Area ◽  
Brain Structure ◽  
Visual Processing ◽  
Large Scale ◽  
Structural Changes ◽  
Homo Sapiens ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Common Genetic Variants

Abstract Structural brain changes along the lineage leading to modern Homo sapiens contributed to our distinctive cognitive and social abilities. However, the evolutionarily relevant molecular variants impacting key aspects of neuroanatomy are largely unknown. Here, we integrate evolutionary annotations of the genome at diverse timescales with common variant associations from large-scale neuroimaging genetic screens. We find that alleles with evidence of recent positive polygenic selection over the past 2000–3000 years are associated with increased surface area (SA) of the entire cortex, as well as specific regions, including those involved in spoken language and visual processing. Therefore, polygenic selective pressures impact the structure of specific cortical areas even over relatively recent timescales. Moreover, common sequence variation within human gained enhancers active in the prenatal cortex is associated with postnatal global SA. We show that such variation modulates the function of a regulatory element of the developmentally relevant transcription factor HEY2 in human neural progenitor cells and is associated with structural changes in the inferior frontal cortex. These results indicate that non-coding genomic regions active during prenatal cortical development are involved in the evolution of human brain structure and identify novel regulatory elements and genes impacting modern human brain structure.

scholarly journals Spectacle: Faster and more accurate chromatin state annotation using spectral learning

2014 ◽  
Author(s):  
Jimin Song ◽  
Kevin C Chen
Keyword(s):  
Histone Modifications ◽  
Large Scale ◽  
Markov Models ◽  
State Of The Art ◽  
Estimation Algorithm ◽  
Regulatory Elements ◽  
Transcription Start Sites ◽  
Spectral Learning ◽  
Parameter Estimation Algorithm ◽  
A Cell

Recently, a wealth of epigenomic data has been generated by biochemical assays and next-generation sequencing (NGS) technologies. In particular, histone modification data generated by the ENCODE project and other large-scale projects show specific patterns associated with regulatory elements in the human genome.It is important to build a unified statistical model to decipher the patterns of multiple histone modifications in a cell type to annotate chromatin states such as transcription start sites, enhancers and transcribed regions rather than to map histone modifications individually to regulatory elements. Several genome-wide statistical models have been developed based on hidden Markov models (HMMs). These methods typically use the Expectation-Maximization (EM) algorithm to estimate the parameters of the model.Here we used spectral learning, a state-of-the-art parameter estimation algorithm in machine learning.We found that spectral learning plus a few (up to five) iterations of local optimization of the likelihood outperforms the standard EM algorithm.We also evaluated our software implementation called Spectacle on independent biological datasets and found that Spectacle annotated experimentally defined functional elements such as enhancers significantly better than a previous state-of-the-art method. Spectacle can be downloaded from https://github.com/jiminsong/Spectacle .

scholarly journals Systematic comparison of experimental assays and analytical pipelines for identification of active enhancers genome-wide

2021 ◽  
Author(s):  
Li Yao ◽  
Jin Liang ◽  
Abdullah Ozer ◽  
Alden King-Yung Leung ◽  
John T. Lis ◽  
...  
Keyword(s):  
Large Scale ◽  
K562 Cells ◽  
Cost Effective ◽  
Regulatory Elements ◽  
Nascent Transcript ◽  
Transcription Start Sites ◽  
The Road ◽  
Genome Wide ◽  
Active Enhancer ◽  
Effective Manner

Mounting evidence supports the idea that transcriptional patterns serve as more specific identifiers of active enhancers than histone marks; however, the optimal strategy to identify active enhancers both experimentally and computationally has not been determined. In this study, we compared 13 genome-wide RNA sequencing assays in K562 cells and showed that the nuclear run-on followed by cap-selection assay (namely, GRO/PRO-cap) has significant advantages in eRNA detection and active enhancer identification. We also introduced a new analytical tool, Peak Identifier for Nascent-Transcript Sequencing (PINTS), to identify active promoters and enhancers genome-wide and pinpoint the precise location of the 5′ transcription start sites (TSSs) within these regulatory elements. Finally, we compiled a comprehensive enhancer candidate compendium based on the detected eRNA TSSs available in 120 cell and tissue types. To facilitate the exploration and prioritization of these enhancer candidates, we also built a user-friendly web server (https://pints.yulab.org) for the compendium with various additional genomic and epigenomic annotations. With the knowledge of the best available assays and pipelines, this large-scale annotation of candidate enhancers will pave the road for selection and characterization of their functions in a time-, labor-, and cost-effective manner in future.

scholarly journals Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

2019 ◽  
Author(s):  
Elissavet Kentepozidou ◽  
Sarah J Aitken ◽  
Christine Feig ◽  
Klara Stefflova ◽  
Ximena Ibarra-Soria ◽  
...  
Keyword(s):  
Large Scale ◽  
Evolutionary Dynamics ◽  
Computational Study ◽  
Genome Structure ◽  
Higher Order ◽  
Ctcf Binding ◽  
Natural Genetic Variation ◽  
Transcription Start Sites ◽  
Topologically Associating Domains ◽  
Species Specific

ABSTRACTCTCF binding contributes to the establishment of higher order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). We have carried out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We performed CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associated them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by an equilibrium of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor rapidly evolving clusters containing both evolutionary old and young CTCF sites as a result of repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. Overall, CTCF site clusters are an apparently important feature of CTCF binding evolution that are critical the functional stability of higher order chromatin structure.

scholarly journals Characterizing Promoter and Enhancer Sequences by a Deep Learning Method

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Zeng ◽  
Sung-Joon Park ◽  
Kenta Nakai
Keyword(s):  
Deep Learning ◽  
High Throughput Sequencing ◽  
Rna Stability ◽  
Predictive Performance ◽  
Regulatory Elements ◽  
Critical Determinant ◽  
Transcription Start Sites ◽  
Sequencing Technologies ◽  
Genomic Regions ◽  
Order Sequence

Promoters and enhancers are well-known regulatory elements modulating gene expression. As confirmed by high-throughput sequencing technologies, these regulatory elements are bidirectionally transcribed. That is, promoters produce stable mRNA in the sense direction and unstable RNA in the antisense direction, while enhancers transcribe unstable RNA in both directions. Although it is thought that enhancers and promoters share a similar architecture of transcription start sites (TSSs), how the transcriptional machinery distinctly uses these genomic regions as promoters or enhancers remains unclear. To address this issue, we developed a deep learning (DL) method by utilizing a convolutional neural network (CNN) and the saliency algorithm. In comparison with other classifiers, our CNN presented higher predictive performance, suggesting the overarching importance of the high-order sequence features, captured by the CNN. Moreover, our method revealed that there are substantial sequence differences between the enhancers and promoters. Remarkably, the 20–120 bp downstream regions from the center of bidirectional TSSs seemed to contribute to the RNA stability. These regions in promoters tend to have a larger number of guanines and cytosines compared to those in enhancers, and this feature contributed to the classification of the regulatory elements. Our CNN-based method can capture the complex TSS architectures. We found that the genomic regions around TSSs for promoters and enhancers contribute to RNA stability and show GC-biased characteristics as a critical determinant for promoter TSSs.

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