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Elucidating transcription factor binding dynamics in Salmonella Typhimurium under macrophages in vivo conditions using a low-Input ChIP-exo approach [ChIP-mini]

ABSTRACT: Elucidating transcription factor binding dynamics in Salmonella Typhimurium under macrophages in vivo conditions using a low-Input ChIP-exo approach [ChIP-mini]

PROVIDER: PRJNA1061106 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27429467.fastq.gz	Fastqsanger.gz
	SRR27429468.fastq.gz	Fastqsanger.gz
	SRR27429469.fastq.gz	Fastqsanger.gz
	SRR27429470.fastq.gz	Fastqsanger.gz
	SRR27429471.fastq.gz	Fastqsanger.gz

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Elucidating transcription factor binding dynamics in Salmonella Typhimurium under macrophages in vivo conditions using a low-Input ChIP-exo approach [ChIP-mini]

Project description:We present the low-input ChIP-exo minimization (ChIP-mini) method, which is suitable for processing small bacterial cell numbers, as few as 4.8x10⁶ (bacterial culture volume: 10 µl). This method faithfully maintains the relevant binding profiles of Escherichia coli K-12 MG1655 RpoD, as generated by the traditional ChIP-exo method (bacterial culture volume: 50 ml). Additionally, ChIP-mini was applied in the conventional infection process of mouse macrophages-like cells (J774A.1, RAW264.7) and human epithelial cells (HeLa, INT407) with Salmonella Typhimurium 14028s to directly capture both host extracellular and intracellular bacteria (extracellular and intracellular ChIP-mini). These applications of ChIP-mini in infectious S. Typhimurium provided near-base pair resolution to measure the impact of environmental changes on the binding profiles of H-NS and RpoD.

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ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.

Project description:Genome-wide identification of binding profiles for DNA-binding proteins from the limited number of intracellular pathogens in infection studies is crucial for understanding virulence and cellular processes but remains challenging, as the current ChIP-exo is designed for high-input bacterial cells (>1010). Here, we developed an optimized ChIP-mini method, a low-input ChIP-exo utilizing a 5,000-fold reduced number of initial bacterial cells and an analysis pipeline, to identify genome-wide binding dynamics of DNA-binding proteins in host-infected pathogens. Applying ChIP-mini to intracellular Salmonella Typhimurium, we identified 642 and 1,837 binding sites of H-NS and RpoD, respectively, elucidating changes in their binding position and binding intensity during infection. Post-infection, we observed 21 significant reductions in H-NS binding at intergenic regions, exposing the promoter region of virulence genes, such as those in Salmonella pathogenicity islands-2, 3 and effectors. Furthermore, we revealed the crucial phenomenon that novel and significantly increased RpoD bindings were found within regions exhibiting diminished H-NS binding, thereby facilitating substantial upregulation of virulence genes. These findings markedly enhance our understanding of how H-NS and RpoD simultaneously coordinate the transcription initiation of virulence genes within macrophages. Collectively, this work demonstrates a broadly adaptable tool that will enable the elucidation of DNA-binding protein dynamics in diverse intracellular pathogens during infection.

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Project description:Several recently emerging ChIP-seq (chromatin immunoprecipitation followed by sequencing) based methods perform chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for bioinformatics and data quality analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. Application of this method allowed for discovery of a novel CTCF binding motif from ChIP-exo data.

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Project description:Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.

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Project description:Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and its ultra-high resolution cousin ChIP-exo are methods that identify where proteins bind along any genome in vivo. ChIP-exo achieves near-base pair resolution by creating exonuclease stop sites just 5’ to where formaldehyde-induced protein-DNA cross-links occur. Whereas construction of ChIP genomic libraries is straightforward and widely adopted for ChIP-seq, ChIP-exo is technically more involved which has resulted in limited adoption. Here we describe multiple ChIP-exo protocols, each with use-specific advantages and limitations. The new versions are greatly simplified through removal of multiple enzymatic steps. This is achieved in part through the use of Tn5 tagmentation and/or single-stranded DNA ligation. The result is greater library yields, lower processing time, and lower cost. A similar streamlined approach was developed for ChIP-seq, called ChIP-seq 1-step, where library construction is achieved in one-step.

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