Surveying the epigenomic landscape, one base at a time

Zentner, Gabriel E.; Henikoff, Steven

doi:10.1186/gb-2012-13-10-250

Cited by 27 publications

(14 citation statements)

References 49 publications

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“…However, in the independently sorted untreated control and 40 min post-HSKT samples we do not observe this coupling of TSS-flanking nucleosome sensitivity and regulatory factor occupancy, which further suggests that the chromatin signature at the 20 min post-HKST indicates an early genomic response to HKST ( Figure 3B). The presence of sensitive nucleosomes flanking TF binding sites (TFBS) is concordant with similar results from plants and yeast (Zentner and Henikoff 2012;Vera et al, 2014;Pass et al, 2017). These results are consistent with a model in which nucleosomes that provide access to regulatory factor binding sites necessary for a specific genomic response will be more mobile and this will be reflected in greater sensitivity to digestion by MNase.…”

Section: Sensitivity Of Tss-flanking Nucleosomes Is Associated With Tsupporting

confidence: 83%

MNase Profiling of Promoter Chromatin in Salmonella typhimurium-Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture

Cole

Dennis

2020

G3 Genes|Genomes|Genetics

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The nucleosome is the primary unit of chromatin structure and commonly imputed as a regulator of nuclear events, although the exact mechanisms remain unclear. Recent studies have shown that certain nucleosomes can have different sensitivities to micrococcal nuclease (MNase) digestion, resulting in the release of populations of nucleosomes dependent on the concentration of MNase. Mapping MNase sensitivity of nucleosomes at transcription start sites genome-wide reveals an important functional nucleosome organization that correlates with gene expression levels and transcription factor binding. In order to understand nucleosome distribution and sensitivity dynamics during a robust genome response, we mapped nucleosome position and sensitivity using multiple concentrations of MNase. We used the innate immune response as a model system to understand chromatin-mediated regulation. Herein we demonstrate that stimulation of a human lymphoblastoid cell line (GM12878) with heat-killed Salmonella typhimurium (HKST) results in changes in nucleosome sensitivity to MNase. We show that the HKST response alters the sensitivity of -1 nucleosomes at highly expressed promoters. Finally, we correlate the increased sensitivity with response-specific transcription factor binding. These results indicate that nucleosome sensitivity dynamics reflect the cellular response to HKST and pave the way for further studies that will deepen our understanding of the specificity of genome response.

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Section: Sensitivity Of Tss-flanking Nucleosomes Is Associated With Tsupporting

confidence: 83%

MNase Profiling of Promoter Chromatin in Salmonella typhimurium-Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture

Cole

Dennis

2020

G3 Genes|Genomes|Genetics

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“…In this way, plotting the fragment sizes over genomic position relative to a binding site reveals a characteristic V shape if the binding site is occupied (for further description of V-plots, see Supplemental Fig. S6; Henikoff et al, 2011;Zentner and Henikoff, 2012). For both G-boxes in binding pattern 1 and binding pattern 2, we see a strong V pattern suggestive of in vivo occupancy (Fig.…”

Section: Results Bzip Homodimers Only Bind To a Subset Of Perfect G-bmentioning

confidence: 85%

The G-Box Transcriptional Regulatory Code in Arabidopsis

et al. 2017

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Plants have significantly more transcription factor (TF) families than animals and fungi, and plant TF families tend to contain more genes; these expansions are linked to adaptation to environmental stressors. Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG), so it is difficult to predict regulatory relationships. We determined that the flanking sequences near G-boxes help determine in vitro specificity but that this is insufficient to predict the transcription pattern of genes near G-boxes. Therefore, we constructed a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of the expression of genes downstream of perfect G-boxes. This network accurately predicts transcriptional patterns and reconstructs known regulatory subnetworks. Finally, we present Ara-BOX-cis (araboxcis.org), a Web site that provides interactive visualizations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations.

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“…Differential MNase-seq revealed a number of genomic regions detectable only under light digest conditions [3,4] and occupied by either transcription factors or nucleosomes with conformations making linker DNA more accessible. We detected an abundance of MSFs in the proximal regulatory regions, where the levels of chromatin accessibility showed a positive correlation with gene expression [1,3,54,55] and were predictive of the unbalanced expression levels among the duplicated homoeologs, supporting the results of chromatin accessibility studies conducted using the DNaseseq and ATAC-seq approaches in wheat [18,29]. However, the majority of MSF (67%) identified in our study were located in the TE-rich intergenic regions, with an average distance of 137 kb from the closest gene, and overlapped with annotated TEs.…”

Section: Discussionmentioning

confidence: 93%

Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes

Jordan

Soto

et al. 2020

Genome Biol

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Background: Our understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome. Results: Although open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs' chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin. Conclusions: Chromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.

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Surveying the epigenomic landscape, one base at a time

Abstract: Epigenomics, the determination of epigenetic landscapes on a genome-wide scale, has progressed at an astounding rate over the past decade. Recent technological developments have enabled base-pair resolution of various epigenomic features, leading to new insights into epigenetic regulation.

Cited by 27 publications

References 49 publications

MNase Profiling of Promoter Chromatin in Salmonella typhimurium-Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture

MNase Profiling of Promoter Chromatin in Salmonella typhimurium-Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture

The G-Box Transcriptional Regulatory Code in Arabidopsis

Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes

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