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Concurrent Mapping of Multiple Epigenetic Marks and Co-enrichment Using ACT2-seq

ABSTRACT: Genome-wide profiling of epigenetic marks is a core technology in molecular genetics. Co-occupancy of different epigenetic marks or protein factors on chromatin is often inferred from their existence at the same genomic locations. However, this strategy does not provide direct evidence whether the epigenetic marks or protein factors occupy the same chromatin loci in the same cell due to the existence of cellular heterogeneity. To address this issue, we report a technique termed ACT2-seq that is capable of concurrently profiling multiple epigenetic marks in a single biological sample. While profiling simultaneously different epigenetic marks or protein factors genome-wide, ACT2 is capable of directly detecting co-occupancy of two different marks or factors on chromatin. This strategy provides direct evidence of co-localization without requiring complex single-molecule, single-cell, or magnetic bead-based approaches. We conclude that ACT2 presents an attractive option for epigenomic profiling due to its ease of use, potential for reducing sample and sequencing costs, and ability to profile co-occupancy of different epigenetic marks and protein factors on chromatin

ORGANISM(S): Homo sapiens

PROVIDER: GSE179047 | GEO | 2021/12/08

REPOSITORIES: GEO

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Project description:Kaposi’s sarcoma-associated herpesvirus (KSHV) is a g-herpesvirus which persists as circular extrachromasomal DNA in the nucleus during latent infection. During latency a limited number of viral proteins are expressed, including LANA (latency-associated nuclear antigen). LANA is a multi-functional protein known to interact with transcriptional regulators and chromatin remodelers, and to regulate the LANA and RTA promoters. We hypothesized that LANA may contribute to the establishment of latency through controlling chromatinization and histone modification of KSHV episomes. We performed ChIP-seq analysis and correlated H3K4me3, H3K27me3, polII, and LANA occupancy of the KSHV genome at nucleotide resolution. Epigenetic marks were analyzed in BCBL-1 lymphoid cells and in telomerase-immortalized vein endothelial TIVE-LTC cells. We found that the transcription active mark H3K4me3, but not silencing mark H3K27me3, was enriched at KSHV regions where LANA is bound. Co-occupancy of LANA and H3K4 was also detected on 167 host genes, of which 89 are actively transcribed. By comparing LANA occupancy with the profiling of 43 transcription factors from ENCODE, a subset of transcription factors was enriched at regions where LANA is bound, including znf143, CTCF, and Stat1. These results indicate that LANA also plays a role in modulating expression of host genes. Co-immunoprecipitation of LANA with the H3K4 methyltransferase hSET1 suggests that LANA recruits hSET1 to specific loci on the viral genome, leading to H3K4 methylation and ensuring transcription of latency-associated genes. Host gene expression may be regulated by the same mechanism. LANA binding was correlated with the distribution in the latent KSHV genome of the transcription active histone modification H3K4me3, the silencing mark H3K27me3, and RNA polymerase II, using cells of lymphoid and endothelial origin. A similar analysis was done for the human genome. Biological replicates (BR) and technical replicates (TR) were included.

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Concurrent Mapping of Multiple Epigenetic Marks and Co-enrichment Using ACT2-seq

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