OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

Beliveau, Brian J.; Kishi, Jocelyn Y.; Nir, Guy; Sasaki, Hiroshi; Saka, Sinem K.; Nguyen, Son C.; Wu, Chao-ting; Yin, Peng

doi:10.1073/pnas.1714530115

Cited by 199 publications

(206 citation statements)

References 73 publications

(104 reference statements)

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“…Current models suggest that TADs are functional regulons, which spatially separate into 3D structures to insulate gene regulation. However, an emerging theme from recent single-cell based assays is that genome packaging is extremely dynamic and heterogeneous across a cell population (Bintu et al, 2018;Cardozo Gizzi et al, 2019;Finn et al, 2019;Flyamer et al, 2017;Nir et al, 2018). Yet, it remains unclear how these heterogeneous structures form, interact with one another, and impact genome function.…”

Section: Discussionmentioning

confidence: 99%

“…To measure the frequency and extent of interactions between entire TADs at the single chromosome level, we designed a FISH-based assay that tiles probes across population-based contact domains using the programmable Oligopaint technology (Beliveau et al, 2014;Beliveau et al, 2015;Beliveau et al, 2017;Beliveau et al, 2012;Beliveau et al, 2018). We then applied our "TAD FISH" assay in HCT-116, a human colorectal carcinoma cell line from which highresolution Hi-C maps were previously generated (Rao et al, 2017).…”

Section: Cell-to-cell Variability Of Inter-tad Association Is a Widesmentioning

confidence: 99%

“…We then applied the OligoMiner design pipeline to design DNA FISH probes to the coordinates found in Table S2 ( Beliveau et al, 2018). Oligopaints were designed to have 42 bases of homology with an average of five probes per kb (Beliveau, Joyce EF, et al 2012) and…”

Section: Oligopaint Design and Synthesismentioning

confidence: 99%

“…To address this issue, we generated Oligopaint-based probes for fluorescence in situ hybridization (FISH) (Beliveau et al, 2015;Beliveau et al, 2012;Beliveau et al, 2018) to precisely target entire Hi-C-defined TADs in single cells. We use a combination of superresolution and diffraction-limited microscopy to quantify the frequency and extent of spatial intermingling between neighboring domains of different length scales and chromatin types.…”

Section: Introductionmentioning

confidence: 99%

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Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes

Luppino

Park

Nguyen

et al. 2019

Preprint

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The mammalian genome has been segmented into thousands of topologically associated domains (TADs) based on chromosome conformation capture studies, such as Hi-C.TADs have been proposed to act as insulated neighborhoods, spatially sequestering and insulating the enclosed genes and regulatory elements through self-association and chromatin looping. Recent results indicate that inter-TAD interactions can also occur. However, the nature, extent, and function of these inter-TAD interactions remains unclear. Here, we combine Hi-C data with Oligopaint technology to precisely visualize neighboring TADs and quantify their interaction frequency in human cells. We find that intra-TAD interactions are indeed more enriched than inter-TAD interactions. However, we also observe extensive intermingling between neighboring domains in the majority of cells. Moreover, we find that cohesin depletion, which is known to abolish TADs at the population-average level, does not induce ectopic interactions but instead reduces interactions between neighboring domains. We find that cohesin loss preferentially alters locus topology and transcriptional bursting frequencies at genes close to domain boundaries, potentially explaining the gene expression changes observed in the cohesinopathy Cornelia de Lange syndrome. Together, our results challenge the notion that cohesin forms spatially insulated domains to regulate gene expression. Instead, we propose that cohesin normally antagonizes domain insulation by frequently bypassing boundaries to promote proper gene regulation at a subset of boundary-proximal genes.We would like to thank Leah Rosin, Melike Lakadamyali, and members of the Joyce lab for helpful discussions and critical reading of the manuscript. Additionally, we thank Masato Kanemaki for the HCT-116-RAD21-AID cell line and Suhas Rao and Erez Lieberman-Aiden for sharing critical primary datasets. We also thank Andrea Stout at the Penn Cell and Developmental Biology Microscopy core and Carl Eberling from Bruker for assistance with super-resolution imaging and analysis.

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Section: Discussionmentioning

confidence: 99%

Section: Cell-to-cell Variability Of Inter-tad Association Is a Widesmentioning

confidence: 99%

Section: Oligopaint Design and Synthesismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes

Luppino

Park

Nguyen

et al. 2019

Preprint

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“…We designed Oligopaint probes that target single copy genome regions, following (47,93). Each targeted euchromatic region has at least 500 probes designed to label it, with at least 12 probes/kb (Table S6).…”

Section: Oligopaint Fish Probesmentioning

confidence: 99%

Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin

Lee

Ogiyama

Martins

et al. 2019

Preprint

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1Membraneless pericentromeric heterochromatin (PCH) domains play vital roles in 2 chromosome dynamics and genome stability. However, our current understanding of 3D 3 genome organization does not include PCH domains because of technical challenges 4 associated with repetitive sequences enriched in PCH genomic regions. We investigated the 5 3D architecture of Drosophila melanogaster PCH domains and their spatial associations 6 with euchromatic genome by developing a novel analysis method that incorporates 7 genome-wide Hi-C reads originating from PCH DNA. Combined with cytogenetic analysis, 8 we reveal a hierarchical organization of the PCH domains into distinct "territories." 9 Strikingly, H3K9me2/3-enriched regions embedded in the euchromatic genome show 10 prevalent 3D interactions with the PCH domain. These spatial contacts require H3K9me2/3 11 enrichment, are likely mediated by liquid-liquid phase separation, and may influence 12 organismal fitness. Our findings have important implications for how PCH architecture 13 influences the function and evolution of both repetitive heterochromatin and the gene-rich 14 euchromatin. 15 16 17Author summary 18 The three dimensional (3D) organization of genomes in cell nuclei can influence a wide 19 variety of genome functions. However, most of our understanding of this critical 20 architecture has been limited to the gene-rich euchromatin, and largely ignores the gene-21 poor and repeat-rich pericentromeric heterochromatin, or PCH. PCH comprises large part 22 of most eukaryotic genomes, forms 3D PCH domains in nuclei, and plays vital role in 23 3 chromosome dynamics and genome stability. In this study, we developed a new method 1 that overcomes the technical challenges imposed by the highly repetitive PCH DNA, and 2 generated a comprehensive picture of its 3D organization. Combined with image analyses, 3 we revealed a hierarchical organization of the PCH domains. Surprisingly, we showed that 4 distant euchromatic regions enriched for repressive epigenetic marks also dynamically 5 interact with the main PCH domains. These 3D interactions are mediated by liquid-liquid 6 phase separation mechanisms, similar to how oil and vinegar separate in salad dressing, 7 and can influence the fitness of individuals. Our discoveries have strong implications for 8 how seemingly "junk" DNA could impact functions in the gene-rich euchromatin. 9 13 comprehensive picture of the 3D structure of PCH domains in late-stage D. melanogaster 14 embryos. Our analysis reveals highly heterogeneous contact frequencies among PCH 15 regions, suggesting hierarchical ordering within the domain. Surprisingly, despite being far 16 from PCH on linear chromosomes, euchromatic loci enriched with H3K9me2/3 can 17 dynamically interact with the main PCH domain, and such interactions show properties 18 consistent with liquid-liquid phase separation and influence individual fitness. Our study 19 demonstrates that the spatial interactions among H3K9me2/3 enriched regions both in 20 PCH and the euchromatic genome...

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Lung injury in axolotl salamanders induces an organ‐wide proliferation response

Jensen

Giunta

Schultz

et al. 2021

Developmental Dynamics

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Background: Ambystoma mexicanum, the axolotl salamander, is a classic model organism used to study vertebrate regeneration. It is assumed that axolotls regenerate most tissues, but the exploration of lung regeneration has not been performed until now. Results: Unlike the blastema-based response used during appendage regeneration, lung amputation led to organ-wide proliferation. Pneumocytes and mesenchymal cells responded to injury by increased proliferation throughout the injured lung, which led to a recovery in lung mass and morphology by 56 days post-amputation. Receptors associated with the Neuregulin signaling pathway were upregulated at one and 3 weeks post lung amputation. We show expression of the ligand, neuregulin, in the I/X cranial nerve that innervates the lung and cells within the lung. Supplemental administration of Neuregulin peptide induced widespread proliferation in the lung similar to an injury response, suggesting that neuregulin signaling may play a significant role during lung regeneration. Conclusion:Our study characterizes axolotl lung regeneration. We show that the lung responds to injury by an organ-wide proliferative response of multiple cell types, including pneumocytes, to recover lung mass.

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OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

Cited by 199 publications

References 73 publications

Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes

Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes

Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin

Lung injury in axolotl salamanders induces an organ‐wide proliferation response

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