Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L)

Turpin, Zachary M.; Vera, Daniel; Savadel, Savannah D; Lung, Pei-Yau; Wear, Emily E.; Mickelson-Young, Leigh; Thompson, William F.; Hanley‐Bowdoin, Linda; Dennis, Jane A; Zhang, Jinfeng; Bass, Hank W.

doi:10.1016/j.dib.2018.08.015

Cited by 8 publications

(20 citation statements)

References 6 publications

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“…Many MOA-seq and ATAC peaks were shared in the vicinity of these two genes. However, MOA-seq identified additional peaks, not detected by ATAC, which overlapped with accessible chromatin regions also detected by DNS-seq in earshoot [ 7 ] as well as TF-binding sites such as teosinte branched1 ( tb1 ) and knotted1 ( kn1 ) ( Fig 3D and 3E ). These findings illustrate that MOA-seq and ATAC-seq map ACRs globally with considerable agreement, especially around promoter regions, whereas MOA-seq often further resolves subregions or identifies additional regions ( S5 Fig ), similar to that described for Arabidopsis [ 12 ].…”

Section: Resultsmentioning

confidence: 98%

The native cistrome and sequence motif families of the maize ear

et al. 2021

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Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing these DNA regulatory elements globally remains challenging. Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g. DNAse-seq, ATAC-seq). To address this challenge, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq), a high-resolution (< 30 bp), high-throughput, and genome-wide strategy to globally identify putative TF-binding sites within ACRs. We used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%) of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq. MFs were associated with promoters and significantly enriched for TF-binding and long-range chromatin interaction sites, including for the well-characterized FASCIATED EAR4, KNOTTED1, and TEOSINTE BRANCHED1. Importantly, the MOA-seq strategy improved the spatial resolution of TF-binding prediction and allowed us to identify 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied binding sites across the genome. Our study presents a simple, efficient, and high-resolution approach to identify putative TF footprints and binding motifs genome-wide, to ultimately define a native cistrome atlas.

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Section: Resultsmentioning

confidence: 98%

The native cistrome and sequence motif families of the maize ear

et al. 2021

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“…To determine the regulatory landscape of the maize genome during early inflorescence development, we generated genome-wide, tissue-specific maps of accessible chromatin from immature tassels and ears. We used a method that defines differential sensitivity of chromatin using different concentrations of micrococcal nuclease (MNase), which was previously demonstrated in maize for vegetative tissue types [17,19,34]. Here, maize tassel and ear primordia were precisely staged and hand-dissected from greenhouse-grown, B73 inbred maize plants (Additional file 1: Fig.…”

Section: Mapping Accessible Chromatin In Early Development Of Maize Imentioning

confidence: 99%

“…Intact nuclei were digested with a range of MNase concentrations in order to determine the optimal enzyme concentration for heavy and light digests, as described by [34]. After MNase titration, nuclei were digested by adding MNase to 30 U/ml (light) or 7290 U/ml (heavy), and incubated for 5 min at room temperature.…”

Section: Mnase Digestion Dna Extraction and Library Preparation Andmentioning

confidence: 99%

“…Paired-end reads were trimmed and mapped to the maize B73 AGPv3 reference genome as described in the MNase-seq processing pipeline [34] (Additional File 1: Table S1). Read coverage (in reads per million (RPM)) was calculated in 25 bp windows as described in [34] for input into bedtools. DNS was calculated as the difference of mean normalized depth (RPM) between the light and heavy digests.…”

Section: Mnase-seq Data Mapping and Analysesmentioning

confidence: 99%

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The regulatory landscape of early maize inflorescence development

et al. 2020

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Background: The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. Result: Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen-and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6% of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3′ ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long noncoding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates. Conclusions: These analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

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“…Intact nuclei were digested with a range of MNase concentrations in order to determine the optimal enzyme concentration for heavy and light digests, as described by [110]. After MNase titration, nuclei were digested by adding MNase to 30 U/ml (light) or 7290 U/ml (heavy), and incubated for 5 min at room temperature.…”

Section: Mnase Digestion Dna Extraction and Library Preparation Andmentioning

confidence: 99%

The regulatory landscape of early maize inflorescence development

Parvathaneni

Bertolini

Shamimuzzaman

et al. 2019

Preprint

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The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen-and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profiled accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classified approximately 1.6 percent of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3' ends of maize genes. This approach mapped regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor (TF) occupancy data were used to annotate regulatory factors, such as combinatorial TF binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based only on functional regions delineated by MNase hypersensitivity revealed new SNP-trait associations in known regulators of inflorescence development as well as new candidates. These analyses provide a comprehensive look into the cisregulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

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Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L)

Cited by 8 publications

References 6 publications

The native cistrome and sequence motif families of the maize ear

The native cistrome and sequence motif families of the maize ear

The regulatory landscape of early maize inflorescence development

The regulatory landscape of early maize inflorescence development

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