3D Visualization and Analysis of Genome Organization

Coupling fluorescence in situ hybridization (FISH) with 3D microscopy and image reconstruction to study spatial organization of the nuclear genome, chromatin topology and interactions between chromosomes/chromatins, which play important roles in transcriptional and epigenetic regulation of the genome function.

Image 1: FISH using oligo probes reveals the helical organization of barley metaphase chromosomes.
Image 2: Loss of PRC1 reduces nuclear clustering with and without RING1B.

Chromosome Structure and Arrangement

Using FISH-based assay to reveal chromosome structures and rearrangements including translocations, segmental duplications/deletions, and presence-absence variations, which is essential for studying recombination between chromosomes, chromosome synteny and evolution, massive gene duplication and amplification events, etc.

Image 3: Meiotic crossovers characterized by haplotype-specific chromosome painting in maize.
Image 4: SAF-A Regulates Interphase Chromosome Structure through Ol in siControl cells.
Image 5: Multiplex DNA-FISH on human interphase WI 38 cells nuclei targeting adjacent regions on chromosome X.
Image 6: Mulitplex DNA-FISH applied to maize interphase nuclei.
Image 7: Fluorescent in situ hybridization (FISH) with chromosome-specific oligo probes on metaphase mitotic chromosomes.
Image 8: Oligo painting FISH on meiotic pachytene chromosome spreads of Musa.
Image 9: HEK 293 metaphase chromosomes hybridized with myTags chromosome paint probes.
Image 10: Loss of PRC1 reduces nuclear clustering at sites with and without RING1B.
Image 11: HEK 293 metaphase chromosomes hybridized with myTags chromosome paint probes for chromosome 13 and chromosome X.
Image 12: HT 1080 metaphase chromosomes hybridized with myTags chromosome indexed probes.
Image 13: HT 1080 metaphase chromosomes hybridized with myTags chromosome indexed probes.

Chromosome Identification, Karyotyping and Chromosome Painting

Using oligo-FISH to develop chromosome identification/barcode system, allowing karyotyping based on individually identified chromosomes and studies of chromosome-scale genetic adaptation and evolution; Chromosome/haplotype-specific painting using chromosome or haplotype-specific oligo probes can be applied to research in chromosomal evolution, monitoring chromosome pairing and transmission and assessing genomic sequence assembly.

Image 14: Multiplex DNA-FISH on human interphase WI 38 cells nuclei targeting adjacent regions on chromosome X
Image 15: HEK 293 metaphase chromosomes hybridized with myTags chromosome paint probes for chromosome 13 and chromosome X.
Image 16: Mulitplex DNA-FISH applied to maize interphase nuclei.
Image 17: Meiotic crossovers characterized by haplotype-specific chromosome painting in maize.
Image 18: FISH using the chromosome 9-specific oligo library and 45S rDNA probes on chromosomes of Nipponbare.
Image 19: Use of just two unique probe sets for complete chromosome sorting.
Image 20: myTags chromosome FISH painting on meiotic pachytene chromosome spreads of banana.
Image 21: Multiplex FISH with myTags probes specific to chromosome 5, 6, and 9 on sugar cane (S. spontaneum) metaphase mitotic chromosomes.
Image 22: Multiplex DNA-FISH on Drosophila salivary polytene chromosomes targeting adjacent regions.

Oligonucleotides Based Fluorescent in situ Hybridization (Oligo-FISH)

Oligo-FISH, which utilizes custom-designed synthetic single stranded oligonucleotides probes, is the fundamental technique required for chromosome identification, chromosome painting, chromosome rearrangement and study of three-dimensional chromatin organization, etc.

Image 23: Multiplex DNA-FISH on Drosophila salivary polytene chromosomes targeting adjacent regions on chromosome 2R.
Image 24: HEK 293 metaphase chromosomes hybridized with myTags chromosome paint probes.
Image 25: Multiplex DNA-FISH on human interphase WI 38 cells nuclei targeting adjacent regions on chromosome X.
Image 26: Mulitplex DNA-FISH applied to maize interphase nuclei Mulitplex DNA-FISH applied to maize interphase nuclei.
Image 27: Meiotic crossovers characterized by haplotype-specific chromosome painting in maize.
Image 28: FISH using the chromosome 9-specific oligo library and 45S rDNA probes on chromosomes of Nipponbare.

Evaluation of Gene Expression and Regulation

Visualization of chromatin interactions and spatial arrangement/localization of target genes or mRNA transcripts using oligo-FISH allows for investigation of transcriptional and epigenetic regulation activities.

Image 29: Combination of ICC and myTags RNA FISH. Huh7 cells infected with SARS-CoV2.
Image 30: Loss of PRC1 reduces nuclear clustering at sites with and without RING1B.
Image 31: Multiplex DNA-FISH on Drosophila salivary polytene chromosomes targeting adjacent regions on chromosome 2R
Image 32: Multiplex DNA-FISH on human interphase WI 38 cells nuclei targeting adjacent regions on chromosome X.

Super-resolution Imaging of Nuclear Organizations and Structures

Oligo-FISH in combination with super-resolution imaging techniques allows for analyzing the subcellular localization and spatial arrangement of targeted DNA sequences and RNA transcripts at the single cell level.

Image 33: FISH using oligo probes reveals the helical organization of barley metaphase chromosomes.

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