scholarly journals NucleoMap: a computational tool for identifying nucleosomes in ultra-high resolution contact maps

2021 ◽  
Author(s):  
Yuanhao Huang ◽  
Bingjiang Wang ◽  
Jie Liu
Keyword(s):  
High Resolution ◽  
Spatial Organization ◽  
Embryonic Stem ◽  
Identification Methods ◽  
Contact Maps ◽  
Functional Regions ◽  
Contact Distance ◽  
Genome Wide ◽  
Capture Techniques ◽  
Nucleosome Binding

Although poorly positioned nucleosomes are ubiquitous in the prokaryote genome, they are difficult to identify with existing nucleosome identification methods. Recently available enhanced high-throughput chromatin conformation capture techniques such as Micro-C, DNase Hi-C, and Hi-CO characterize nucleosome-level chromatin proximity, probing the positions of mono-nucleosomes and the spacing between nucleosome pairs at the same time, enabling profiling of nucleosomes in poorly positioned regions. Here we develop a novel computational approach, NucleoMap, to identify nucleosome positioning from ultra-high resolution chromatin contact maps. By integrating nucleosome binding preferences, read density, and pairing information, NucleoMap precisely locates nucleosomes in both eukaryotic and prokaryotic genomes and outperforms existing nucleosome identification methods in sensitivity and specificity. We rigorously characterize genome-wide association in eukaryotes between the spatial organization of mono-nucleosomes and their corresponding histone modifications, protein binding activities, and higher-order chromatin functions. We also predict two tetra-nucleosome folding structures in human embryonic stem cells using machine learning methods and analysis their distribution at different structural and functional regions. Based on the identified nucleosomes, nucleosome contact maps are constructed, reflecting the inter-nucleosome distances and preserving the original data's contact distance profile.

scholarly journals Human exonization through differential nucleosome occupancy

2018 ◽  
Vol 115 (35) ◽  
pp. 8817-8822 ◽  
Author(s):  
Yumei Li ◽  
Chen Li ◽  
Shuxian Li ◽  
Qi Peng ◽  
Ni A. An ◽  
...  
Keyword(s):  
High Resolution ◽  
Epigenetic Regulation ◽  
Nucleosome Occupancy ◽  
Tree Shrew ◽  
Gc Content ◽  
Comparative Approach ◽  
Local Difference ◽  
Genome Wide ◽  
Pig Genome ◽  
Nucleosome Binding

Nucleosomal modifications have been implicated in fundamental epigenetic regulation, but the roles of nucleosome occupancy in shaping changes through evolution remain to be addressed. Here we present high-resolution nucleosome occupancy profiles for multiple tissues derived from human, macaque, tree shrew, mouse, and pig. Genome-wide comparison reveals conserved nucleosome occupancy profiles across both different species and tissue types. Notably, we found significantly higher levels of nucleosome occupancy in exons than in introns, a pattern correlated with the different exon–intron GC content. We then determined whether this biased occupancy may play roles in the origination of new exons through evolution, rather than being a downstream effect of exonization, through a comparative approach to sequentially trace the order of the exonization and biased nucleosome binding. By identifying recently evolved exons in human but not in macaque using matched RNA sequencing, we found that higher exonic nucleosome occupancy also existed in macaque regions orthologous to these exons. Presumably, such biased nucleosome occupancy facilitates the origination of new exons by increasing the splice strength of the ancestral nonexonic regions through driving a local difference in GC content. These data thus support a model that sites bound by nucleosomes are more likely to evolve into exons, which we term the “nucleosome-first” model.

scholarly journals HiC-ACT: Improved Detection of Chromatin Interactions from Hi-C Data via Aggregated Cauchy Test

2020 ◽  
Author(s):  
Taylor M. Lagler ◽  
Yuchen Yang ◽  
Armen Abnousi ◽  
Ming Hu ◽  
Yun Li
Keyword(s):  
High Resolution ◽  
Cell Line ◽  
Spatial Organization ◽  
Embryonic Stem Cell Line ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Type I ◽  
Spatial Dependency ◽  
Computationally Efficient ◽  
Chromatin Interactions

AbstractGenome-wide chromatin conformation capture technologies such as Hi-C are commonly employed to study chromatin spatial organization. In particular, to identify statistically significant long-range chromatin interactions from Hi-C data, most existing methods such as Fit-Hi-C/FitHiC2 and HiCCUPS assume that all chromatin interactions are statistically independent. Such an independence assumption is reasonable at low resolution (e.g., 40Kb bin), but is invalid at high resolution (e.g., 5 or 10Kb bins) since spatial dependency of neighboring chromatin interactions is non-negligible at high resolution. Our previous hidden Markov random field based methods accommodate spatial dependency but are computationally intensive. It is urgent to develop approaches that can model spatial dependence, in a computationally efficient and scalable manner. Here, we develop HiC-ACT, an aggregated Cauchy test (ACT) based approach, to improve the detection of chromatin interactions by post-processing results from methods assuming independence. To benchmark the performance of HiC-ACT, we re-analyzed deeply sequenced Hi-C data from a human lymphoblastoid cell line GM12878 and mouse embryonic stem cell line (mESC). Our results demonstrate advantages of HiC-ACT in improving sensitivity with controlled type-I error. By leveraging information from neighboring chromatin interactions, HiC-ACT enhances the power to detect interactions with lower signal to noise ratio and similar (if not stronger) epigenetic signatures that suggest regulatory roles. We further demonstrate that HiC-ACT peaks show higher overlap with known enhancers than Fit-Hi-C/FitHiC2 peaks, in both GM12878 and mESC. HiC-ACT, effectively a summary statistic based approach, is computationally efficient (~6 minutes and ~2GB memory to process 25,000 pairwise interactions).

scholarly journals Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 706
Author(s):  
Antonio J. Moreno-Pérez ◽  
Raquel Martins-Noguerol ◽  
Cristina DeAndrés-Gil ◽  
Mónica Venegas-Calerón ◽  
Rosario Sánchez ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Chromatin Remodeling ◽  
Molecular Mechanisms ◽  
Acid Metabolism ◽  
Fatty Acid Biosynthesis ◽  
Acid Synthesis ◽  
Sunflower Seeds ◽  
Acid Biosynthesis ◽  
Functional Regions ◽  
Genome Wide

Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism and facilitates the identification of new functional regions in oil crop genomes. The present study characterizes the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid-related genes and transcription factors in developing sunflower seeds. Two master transcriptional regulators identified in this analysis, VIV1 (homologous to Arabidopsis ABI3) and FUS3, cooperate in the regulation of WRINKLED 1, a transcriptional factor regulating glycolysis, and fatty acid synthesis in developing oilseeds.

scholarly journals Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression

2021 ◽  
Vol 9 (1) ◽  
pp. 6
Author(s):  
Narendra Pratap Singh ◽  
Bony De Kumar ◽  
Ariel Paulson ◽  
Mark E. Parrish ◽  
Carrie Scott ◽  
...  
Keyword(s):  
Dna Binding ◽  
Target Genes ◽  
Embryonic Stem ◽  
Binding Motif ◽  
Binding Assays ◽  
Histone Marks ◽  
Genome Wide ◽  
Hox Cofactors

Knowledge of the diverse DNA binding specificities of transcription factors is important for understanding their specific regulatory functions in animal development and evolution. We have examined the genome-wide binding properties of the mouse HOXB1 protein in embryonic stem cells differentiated into neural fates. Unexpectedly, only a small number of HOXB1 bound regions (7%) correlate with binding of the known HOX cofactors PBX and MEIS. In contrast, 22% of the HOXB1 binding peaks display co-occupancy with the transcriptional repressor REST. Analyses revealed that co-binding of HOXB1 with PBX correlates with active histone marks and high levels of expression, while co-occupancy with REST correlates with repressive histone marks and repression of the target genes. Analysis of HOXB1 bound regions uncovered enrichment of a novel 15 base pair HOXB1 binding motif HB1RE (HOXB1 response element). In vitro template binding assays showed that HOXB1, PBX1, and MEIS can bind to this motif. In vivo, this motif is sufficient for direct expression of a reporter gene and over-expression of HOXB1 selectively represses this activity. Our analyses suggest that HOXB1 has evolved an association with REST in gene regulation and the novel HB1RE motif contributes to HOXB1 function in part through a repressive role in gene expression.

scholarly journals Chromatin loop anchors contain core structural components of the gene expression machinery in maize

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Stéphane Deschamps ◽  
John A. Crow ◽  
Nadia Chaidir ◽  
Brooke Peterson-Burch ◽  
Sunil Kumar ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Transcriptional Activity ◽  
Spatial Organization ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Maize Genome ◽  
Chromatin Loop ◽  
Structural Components ◽  
Chromatin Loops

Abstract Background Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome.

scholarly journals Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

Methods ◽  
2017 ◽  
Vol 123 ◽  
pp. 56-65 ◽  
Author(s):  
Houda Belaghzal ◽  
Job Dekker ◽  
Johan H. Gibcus
Keyword(s):  
High Resolution ◽  
Chromosome Conformation ◽  
Genome Wide
Sign in / Sign up

Export Citation Format

Share Document