aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq

Liu, Wenbin; Yue, Sibiao; Zheng, Xiaobin; Hu, Minjie; Cao, Jia; Zheng, Yixian

doi:10.1080/15592294.2019.1621139

Cited by 3 publications

(1 citation statement)

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“…We show that cTSA-seq can offer high quality mapping of chromatin at or near the NL in as few as 50 000 cells without adding any carriers. We have previously developed a carrier approach to reduce sample loss in low-cell ChIP-seq, and have successfully used this approach to map epigenetic marks and transcription factor binding sites from as few as 100 cells ( 43 , 44 ). Adapting this carrier approach to be compatible with cTSA-seq should enable mapping of chromatin regions at or near the NL in far fewer cells than 50 000, especially considering that these chromatin regions represents 30–50% of the genome.…”

Section: Resultsmentioning

confidence: 99%

High quality mapping of chromatin at or near the nuclear lamina from small numbers of cells reveals cell cycle and developmental changes of chromatin at the nuclear periphery

Tran

Zheng

Adam

et al. 2022

Nucleic Acids Research

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The chromatin associated with the nuclear lamina (NL) is referred to as lamina-associated domains (LADs). Here, we present an adaptation of the tyramide-signal amplification sequencing (TSA-seq) protocol, which we call chromatin pull down-based TSA-seq (cTSA-seq), that can be used to map chromatin regions at or near the NL from as little as 50 000 cells. The cTSA-seq mapped regions are composed of previously defined LADs and smaller chromatin regions that fall within the Hi-C defined B-compartment containing nuclear peripheral heterochromatin. We used cTSA-seq to map chromatin at or near the assembling NL in cultured cells progressing through early G1. cTSA-seq revealed that the distal ends of chromosomes are near or at the reassembling NL during early G1, a feature similar to those found in senescent cells. We expand the use of cTSA-seq to the mapping of chromatin at or near the NL from fixed-frozen mouse cerebellar tissue sections. This mapping reveals a general conservation of NL-associated chromatin and identifies global and local changes during cerebellar development. The cTSA-seq method reported here is useful for analyzing chromatin at or near the NL from small numbers of cells derived from both in vitro and in vivo sources.

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Section: Resultsmentioning

confidence: 99%

High quality mapping of chromatin at or near the nuclear lamina from small numbers of cells reveals cell cycle and developmental changes of chromatin at the nuclear periphery

Tran

Zheng

Adam

et al. 2022

Nucleic Acids Research

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High quality mapping of chromatin at or near the nuclear lamina for small numbers of cells

Tran

Adam

Goldman

et al. 2021

Preprint

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A large fraction of heterochromatin in the metazoan genome is associated with the nuclear lamina (NL) in interphase nuclei. This heterochromatin is often referred to as Lamina-Associated Domains (LADs) and are often mapped from cell populations asynchronously progressing through the cell cycle. We and others have recently reported that LADs are largely stable during G1, S, or G2 phases of the cell cycle, and appear similar to LADs mapped from bulk cell populations. LADs in senescent cells, however, are reported to be quite different from proliferating cells, and it remains unclear how senescent cell LADs are established. As cells finish mitosis and re-enter G1, reassembly of the nuclear envelope and NL appears to precede mitotic chromosome decondensation. Therefore, the initial NL interactions with the decondensing chromatin may be quite different from those reported in asynchronous or FACS isolated G1, S, or G2 populations. By developing a modified version of the Tyramide-Signal Amplification sequencing (TSA-seq), which we call chromatin pull down-based Tyramide Signal Amplification-sequencing (cTSA-seq), we uncover a dynamic NL-chromatin interaction as cells progress through G1. The appearance of stable LADs coincides with sufficient chromatin decondensation and active gene expression in G1. Interestingly, early G1 NL-chromatin interactions, which are found toward the telomeric ends of human chromosomes, are similar to those found in oncogene-induced senescent cells. We find that the assembly of LADs during the formation of the G1 nucleus is gradual and that the arrest of NL-chromatin interactions in early G1 may contribute to genome disorganization of senescence cells.

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Establishment of a Simple, Sensitive, and Specific Salmonella Detection Method Based on Recombinase-Aided Amplification Combined with dsDNA-Specific Nucleases

Zhou,

Zhao,

Guo

et al. 2024

Foods

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Salmonella is a common foodborne pathogen that can cause food poisoning, posing a serious threat to human health. Therefore, quickly, sensitively, and accurately detecting Salmonella is crucial to ensuring food safety. For the Salmonella hilA gene, we designed Recombinase-aided amplification (RAA) primers and dsDNA-specific nuclease (DNase) probes. The ideal primer and probe combination was found when conditions were optimized. Under UV light, a visual Salmonella detection technique (RAA-dsDNase) was developed. Additionally, the RAA-dsDNase was modified to further reduce pollution hazards and simplify operations. One-pot RAA-dsDNase-UV or one-pot RAA-dsDNase-LFD was developed as a Salmonella detection method, using UV or a lateral flow dipstick (LFD) for result observation. Among them, one-pot RAA-dsDNase and one-pot RAA-dsDNase-LFD had detection times of 50 min and 60 min, respectively, for detecting Salmonella genomic DNA. One-pot RAA-dsDNase-UV had a detection limit of 101 copies/μL and 101 CFU/mL, while one-pot RAA-dsDNase-LFD had a sensitivity of 102 copies/μL and 102 CFU/mL. One-pot RAA-dsDNase-UV and one-pot RAA-dsDNase-LFD assays may identify 17 specific Salmonella serovars witho ut causing a cross-reaction with the remaining 8 bacteria, which include E. coli. Furthermore, Salmonella in tissue and milk samples has been reliably detected using both approaches. Overall, the detection method developed in this study can quickly, sensitively, and accurately detect Salmonella, and it is expected to become an important detection tool for the prevention and control of Salmonella in the future.

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aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq

Cited by 3 publications

References 50 publications

High quality mapping of chromatin at or near the nuclear lamina from small numbers of cells reveals cell cycle and developmental changes of chromatin at the nuclear periphery

High quality mapping of chromatin at or near the nuclear lamina from small numbers of cells reveals cell cycle and developmental changes of chromatin at the nuclear periphery

High quality mapping of chromatin at or near the nuclear lamina for small numbers of cells

Establishment of a Simple, Sensitive, and Specific Salmonella Detection Method Based on Recombinase-Aided Amplification Combined with dsDNA-Specific Nucleases

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