Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

Sullivan, Alessandra M.; Arsovski, Andrej A; Lempe, Janne; Bubb, Kerry L.; Weirauch, Matthew T.; Sabo, Peter J.; Sandstrom, Richard; Thurman, Robert E.; Neph, Shane; Reynolds, Alex; Stergachis, Andrew B.; Vernot, Benjamin; Johnson, Audra; Haugen, Eric; Sullivan, Shawn; Thompson, Agnieszka; Neri, Fidencio; Weaver, Molly; Diegel, Morgan; Mnaimneh, Sanié; Yang, Ally; Hughes, Timothy R.; Nemhauser, Jennifer L.; Queitsch, Christine; Stamatoyannopoulos, J

doi:10.1016/j.celrep.2014.08.019

Cited by 263 publications

(394 citation statements)

References 62 publications

(76 reference statements)

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“…DHS is considered to be a hallmark of regulatory DNA elements (Gross and Garrard 1988). In A. thaliana and rice, the DHSs contain the cis-regulatory elements bound by known TFs (Zhang et al 2012;Sullivan et al 2014;Wu et al 2014). Despite the differences in digestion mechanism and cleavage bias between MNase for determining nucleosome occupancy (Chung et al 2010;Vierstra et al 2014) and DNase I for revealing open chromatic regions (Sung et al 2014;Vierstra et al 2014), the positive correlation between motif-specific nucleosome depletion and heightened chromatin accessibility supports the notion that nucleosome-depleted motifs may be bound by TFs.…”

Section: G/c Content and Nucleosome Occupancymentioning

confidence: 68%

“…S3A). In addition, A. thaliana DHSs are located not only in proximal promoter regions but also within the gene body or in intergenic regions more distant from genes (Zhang et al 2012;Sullivan et al 2014). Furthermore, TFBSs located in gene bodies are important for transcriptional regulation (Stergachis et al 2013).…”

Section: Nucleosome Depletion and 6-mer Motif Locationmentioning

confidence: 99%

“…It has also been shown that phased nucleosomes flank known TFBSs and DNase I hypersensitive sites (DHSs) in rice, which are likely bound by regulatory proteins (Wu et al 2014). In addition, studies of DHSs in A. thaliana have revealed the relationships between chromatin accessibility and environmentally sensitive or tissue-specific DNA elements (Zhang et al 2012;Sullivan et al 2014). Nonetheless, there are several questions relevant to the relationships between nucleosome occupancy, cis-regulatory sequences, and gene expression that are yet to be addressed in plants or other model systems.…”

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confidence: 99%

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Determinants of nucleosome positioning and their influence on plant gene expression

et al. 2015

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Nucleosome positioning influences the access of transcription factors (TFs) to their binding sites and gene expression. Studies in plant, animal, and fungal models demonstrate similar nucleosome positioning patterns along genes and correlations between occupancy and expression. However, the relationships among nucleosome positioning, cis-regulatory element accessibility, and gene expression in plants remain undefined. Here we showed that plant nucleosome depletion occurs on specific 6-mer motifs and this sequence-specific nucleosome depletion is predictive of expression levels. Nucleosome-depleted regions in Arabidopsis thaliana tend to have higher G/C content, unlike yeast, and are centered on specific G/C-rich 6-mers, suggesting that intrinsic sequence properties, such as G/C content, cannot fully explain plant nucleosome positioning. These 6-mer motif sites showed higher DNase I hypersensitivity and are flanked by strongly phased nucleosomes, consistent with known TF binding sites. Intriguingly, this 6-mer-specific nucleosome depletion pattern occurs not only in promoter but also in genic regions and is significantly correlated with higher gene expression level, a phenomenon also found in rice but not in yeast. Among the 6-mer motifs enriched in genes responsive to treatment with the defense hormone jasmonate, there are no significant changes in nucleosome occupancy, suggesting that these sites are potentially preconditioned to enable rapid response without changing chromatin state significantly. Our study provides a global assessment of the joint contribution of nucleosome occupancy and motif sequences that are likely cis-elements to the control of gene expression in plants. Our findings pave the way for further understanding the impact of chromatin state on plant transcriptional regulatory circuits.

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Section: G/c Content and Nucleosome Occupancymentioning

confidence: 68%

Section: Nucleosome Depletion and 6-mer Motif Locationmentioning

confidence: 99%

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confidence: 99%

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Determinants of nucleosome positioning and their influence on plant gene expression

et al. 2015

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“…As a result, binding site information is available for relatively few TFs and substantial TFBS coverage is only available for humans and several model organisms. Methods such as DNase hypersensitivity (DHS) assay or ATAC-seq offer more facile approaches for annotating genome-wide regulatory elements across many organisms and cell types (Buenrostro et al, 2015;Sullivan et al, 2014;Thurman et al, 2012). However, without comprehensive knowledge of TF sequence specificity, the targeting TFs of the identified regions cannot be readily verified.…”

Section: Introductionmentioning

confidence: 99%

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

O’Malley¹,

Huang²,

Song³

et al. 2016

Cell

373

482

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SUMMARYThe cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TFspecific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.

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“…To compare replication timing profiles with DNase I hypersensitivity sites (DHSs), we used 809 the dataset (GEO accession PRJNA231710) described by Sullivan et al (2014). The density of 810 DHSs in each RT class ( Fig.…”

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confidence: 99%

Genome-Wide Analysis of the Arabidopsis Replication Timing Program

et al. 2018

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33Eukaryotes use a temporally regulated process, known as the replication timing program, to 34 ensure that their genomes are fully and accurately duplicated during S phase. Replication timing 35 programs are predictive of genomic features and activity, and considered to be functional 36 readouts of chromatin organization. Although replication timing programs have been described 37 for yeast and animal systems, much less is known about the temporal regulation of plant DNA 38 replication or its relationship to genome sequence and chromatin structure. We used the 39 thymidine analog, 5-ethynyl-2'-deoxyuridine, in combination with flow sorting and Repli-Seq to 40 describe, at high-resolution, the genome-wide replication timing program for Arabidopsis 41 thaliana Col-0 suspension cells. We identified genomic regions that replicate predominantly 42 during early, mid and late S phase, and correlated these regions with genomic features and with 43 data for chromatin state, accessibility and long-distance interaction.

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Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

Cited by 263 publications

References 62 publications

Determinants of nucleosome positioning and their influence on plant gene expression

Determinants of nucleosome positioning and their influence on plant gene expression

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

Genome-Wide Analysis of the Arabidopsis Replication Timing Program

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