Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq)

Rhie, Suhn Kyong; Schreiner, Shannon; Farnham, P

doi:10.1007/978-1-4939-7768-0_12

Cited by 13 publications

(19 citation statements)

References 32 publications

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“…5a). However, NOMe-seq can identify the NDRs within each enhancer, narrowing the motif search window to ~150 bp regions corresponding to TF landing platforms within the broad H3K27ac ChIP-seq peaks 18 . As an example, an NDR within a large H3K27ac peak (~3 kb) located at chromosome 8q22.3 is identified by NOMe-seq; motif search on this NDR identified a FOXA1 motif (Fig.…”

Section: Resultsmentioning

confidence: 99%

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A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome

et al. 2019

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To better understand the impact of chromatin structure on regulation of the prostate cancer transcriptome, we develop high-resolution chromatin interaction maps in normal and prostate cancer cells using in situ Hi-C. By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and transcriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer-promoter loop anchors. We also find that the chromatin structure surrounding the androgen receptor (AR) locus is altered in the prostate cancer cells with many cancer-specific enhancer-promoter loops. This creation of 3D epigenomic maps enables a better understanding of prostate cancer biology and mechanisms of gene regulation.

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Section: Resultsmentioning

confidence: 99%

“…NOMe-seq was performed following the protocol we have reported in the previous study 18 . Chromatin was treated with the M.CviPI methyltransferase (Cat # M0227B; New England Bio Labs, Ipswich, MA), which methylates GpC dinucleotides that are not protected by nucleosomes or other proteins that are tightly bound to the chromatin.…”

Section: Methodsmentioning

confidence: 99%

A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome

et al. 2019

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“…The prepared DNA is then purified, amplified, and sequenced [ 138 ]. NOMe-seq finds its one drawback in the need for specific DNA fragment sizes to prevent bias towards CpG islands [ 139 ]. There are no published uses of DNase-seq in mosquito disease vectors or in other insects.…”

Section: Indirect Methods For Enhancer Discoverymentioning

confidence: 99%

Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome

Farley

Eggleston

Riehle

2021

Insects

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The portion of the mosquito genome that does not code for proteins contains regulatory elements that likely underlie variation for important phenotypes including resistance and susceptibility to infection with arboviruses and Apicomplexan parasites. Filtering the non-coding genome to uncover these functional elements is an expanding area of research, though identification of non-coding regulatory elements is challenging due to the lack of an amino acid-like code for the non-coding genome and a lack of sequence conservation across species. This review focuses on three types of non-coding regulatory elements: (1) microRNAs (miRNAs), (2) long non-coding RNAs (lncRNAs), and (3) enhancers, and summarizes current advances in technical and analytical approaches for measurement of each of these elements on a genome-wide scale. The review also summarizes and highlights novel findings following application of these techniques in mosquito-borne disease research. Looking beyond the protein-coding genome is essential for understanding the complexities that underlie differential gene expression in response to arboviral or parasite infection in mosquito disease vectors. A comprehensive understanding of the regulation of gene and protein expression will inform transgenic and other vector control methods rooted in naturally segregating genetic variation.

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“…FASTQ files of MCF-7 NOMe-seq data were obtained from GSE57498 (Taberlay et al 2014). Each FASTQ file was aligned to a bisulfite-converted genome (hg19) using BSMAP (Xi and Li 2009) and processed as previously described (Rhie et al 2018). To identify the methylation status of CpG sites (in all HCG trinucleotides) and GpC sites (in all GCH trinucleotides) from the BAM file, the Bis-SNP ) program was used and the Bis-tools was used to visualize DNA methylation and accessibility signals (https://github.com/dnaase/ Bis-tools) (Lay et al 2015).…”

Section: Nome-seqmentioning

confidence: 99%

“…Open chromatin is expected to have high levels of GpC m but low levels of C m pG; thus, each of the two separate methylation analyses serve as independent (but opposite) measures that should provide matching chromatin designations (open versus closed). C4-2B NOMe-seq data were generated as previously described (Rhie et al 2018) and sequenced using an Illumina HiSeq 2000 PE 100 bp to produce FASTQ files. FASTQ files of MCF-7 NOMe-seq data were obtained from GSE57498 (Taberlay et al 2014).…”

Section: Nome-seqmentioning

confidence: 99%

ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters

et al. 2018

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High expression of the transcription factor ZFX is correlated with proliferation, tumorigenesis, and patient survival in multiple types of human cancers. However, the mechanism by which ZFX influences transcriptional regulation has not been determined. We performed ChIP-seq in four cancer cell lines (representing kidney, colon, prostate, and breast cancers) to identify ZFX binding sites throughout the human genome. We identified roughly 9000 ZFX binding sites and found that most of the sites are in CpG island promoters. Moreover, genes with promoters bound by ZFX are expressed at higher levels than genes with promoters not bound by ZFX. To determine if ZFX contributes to regulation of the promoters to which it is bound, we performed RNA-seq analysis after knockdown of ZFX by siRNA in prostate and breast cancer cells. Many genes with promoters bound by ZFX were down-regulated upon ZFX knockdown, supporting the hypothesis that ZFX acts as a transcriptional activator. Surprisingly, ZFX binds at +240 bp downstream from the TSS of the responsive promoters. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds between the open chromatin region at the TSS and the first downstream nucleosome, suggesting that ZFX may play a critical role in promoter architecture. We have also shown that a closely related zinc finger protein ZNF711 has a similar binding pattern at CpG island promoters, but ZNF711 may play a subordinate role to ZFX. This functional characterization of ZFX provides important new insights into transcription, chromatin structure, and the regulation of the cancer transcriptome.

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Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq)

Cited by 13 publications

References 32 publications

A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome

A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome

Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome

ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters

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