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Bridge Linker-Hi-C (BL-Hi-C) analysis after YY1 knockdown in glioblastoma stem cells

ABSTRACT: Bridge Linker-Hi-C (BL-Hi-C) analysis after YY1 knockdown in glioblastoma stem cells

PROVIDER: PRJNA655726 | ENA |

REPOSITORIES: ENA

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Bridge Linker-Hi-C (BL-Hi-C) analysis after YY1 knockdown in glioblastoma stem cells

Project description:Bridge Linker-Hi-C (BL-Hi-C) analysis after YY1 knockdown in glioblastoma stem cells

2022-06-01 | GSE155835 | GEO

BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions

Project description:We propose a novel in situ Hi-C method named Bridge-Linker-Hi-C (BL-Hi-C) for structural and regulatory chromatin interactions capture by restriction enzyme targeting and two-step proximity ligation. It improves the sensitivity and specificity for active chromatin loop detection and can reveal a better enhancer-promoter regulatory architecture than conventional method at a lower sequencing depth and with a simpler protocol.

2018-01-23 | GSE93921 | GEO

Hi-C in Drosophila embryos at NC14 depleted of Beaf-32, CP190 or CTCF using the Bridge Adaptor Protocol

Project description:Hi-C was performed using the Bridge Adaptor Protocol in 2 biological replicates of Drosophila embryos at NC14 depleted of the maternal deposition of Beaf-32, CP190 or CTCF mRNA and protein. Embryos were collected at 2-3h AEL and were derived from mothers expressing RNAi against Beaf-32 or CP190 in the germline, or were genetic null for the maternal and zygotic contribution of CTCF.

2022-12-17 | E-MTAB-9158 | biostudies-arrayexpress

BAT Hi-C maps global chromatin interactions in an efficient and economical way

Project description:We describe the Bridge linker-Alul-Tn5 Hi-C (BAT Hi-C) method, which is a simple and efficient method for delineating chromatin conformational features of mouse embryonic stem (mES) cells and uncover DNA loops. This protocol combines Alul fragmentation and biotinylated linker-mediated proximity ligation to obtain kilobase (kb) resolution with a marked increase in the amount of unique read pairs. The protocol also includes chromatin isolation to reduce background noise and Tn5 tagmentation to cut down on preparation time.

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H3K27ac BL HiChIP and GRID-seq data of LW and MS

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Assessing the dynamics and macromolecular interactions of the intrinsically disordered protein YY1

Project description:YY1 is a ubiquitously expressed, intrinsically disordered transcription factor involved in neural development. The oligomeric state of YY1 varies depending on the environment. These changes may alter its DNA binding ability and hence its transcriptional activity. In addition to its oligomeric state, the interaction of YY1 with proteins such as FOXP2 can impact its role in transcription. The aim of this work is to study the structure and dynamics of YY1 binding to DNA and to determine the influence of oligomerisation and associations with FOXP2 on its DNA binding mechanism. Size exclusion chromatography, fluorescence anisotropy and electrophoretic mobility shift assays were used to study YY1 oligomerisation and interaction with FOXP2. To better understand potential structural changes to YY1 upon DNA binding, hydrogen deuterium exchange mass spectrometry was used. The results indicate that YY1 consists of specific structured regions, while most of the sequence remains disordered. Furthermore, the oligomeric nature of the protein is dependent on ionic strength. DNA affects oligomerisation and the protein undergoes changes in structure and dynamics upon DNA binding. YY1 and FOXP2 were found to interact with each other both in isolation and in the presence of YY1-specific DNA. The heterogeneous, dynamic multimerisation of YY1 identified in this work is, therefore, likely to be important for its ability to make heterologous associations with other proteins such as FOXP2. The interactions that YY1 forms with itself, FOXP2 and DNA form part of an intricate mechanism of transcriptional regulation by YY1, which is vital for appropriate neural development.

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RNA seq analysis of BL/6C57 or BL/6NZB mice

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Fusobacterium necrophorum BL strain:BL

Project description:Fusobacterium necrophorum BL strain:BL Genome sequencing and assembly

| PRJNA232676 | ENA

Dissecting developmental disorders caused by CTCF mutation at R567 [Hi-C]

Project description:In this study, we performed BL-Hi-C experiments to investigate the influence of CTCF mutation on higher-order chromatin structures.

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Single cell Hi-C reveals cell-to-cell variability in chromosome structure

Project description:Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes, to show that individual chromosomes maintain domain organisation at the megabase scale, but show variable cell-to-cell chromosome territory structures at larger scales. Despite this structural stochasticity, localisation of active gene domains to boundaries of territories is a hallmark of chromosomal conformation, affecting most domains in most nuclei. Single cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organisation underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns. Mouse Th1 single-cell Hi-C maps were produced and paired-end sequenced. 10 single-cell samples and a multi-sample pool together with a population Hi-C sample are included.

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