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Method: Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
- Qiao Rui Xing,
- Chadi A El Farran,
- Ying Ying Zeng,
- Yao Yi,
- Tushar Warrier,
- Pradeep Gautam,
- James J. Collins,
- Jian Xu,
- Peter Dröge,
- Cheng-Gee Koh,
- Hu Li,
- Li-Feng Zhang,
- and Yuin-Han Loh
Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
...–specific gene GYPB showed a high interaction frequency with GYPE only in cluster 3 (Fig. 4H).DiscussionIn this study, we presented an automated bimodal single-cell technology, ASTAR-seq, which allows for parallel profiling of whole-cell transcriptome and chromatin accessibility within the same single cell...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...a fundamental gap in the interpretation of their functional evolution. As a result of the whole- duplication, identifying orthologous and paralogous genomic regions across teleosts is challenging, hindering -wide investigations into their polyploid history. Here, we combine tailored gene phylogeny methodology...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
..., which is a hallmark of most bacterial chromosome structure (Le et al. 2013; Marbouty et al. 2017), was barely visible. Therefore, the protocol must first be improved to enrich for contacts in bacterial sequence before parallel analysis of changes in host and pathogen organization can be considered...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...of evolutionary change accrued during >260 Myr of independent evolution of trionychid softshell turtles and birds, paralleling the relatively lower rates of turtle molecular evolution compared to other sauropsids (Eo and DeWoody 2010; Shaffer et al. 2013; Takezaki 2018).Importantly, our analysis also uncovered...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
....We parallelized this process in a Nextflow (Di Tommaso et al. 2017) workflow available at GitHub (https://github.com/oist/plessy_pairwiseGenomeComparison/tree/v5.1.0). To load the alignment coordinates in the R environment for statistical computing (R Core Team 2023), we wrote a package called Genomic...
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Resource: Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution
- Flavia Angela Maria Maggiolini,
- Ashley D. Sanders,
- Colin James Shew,
- Arvis Sulovari,
- Yafei Mao,
- Marta Puig,
- Claudia Rita Catacchio,
- Maria Dellino,
- Donato Palmisano,
- Ludovica Mercuri,
- Miriana Bitonto,
- David Porubský,
- Mario Cáceres,
- Evan E. Eichler,
- Mario Ventura,
- Megan Y. Dennis,
- Jan O. Korbel,
- and Francesca Antonacci
Genome Res. November 2020 30: 1680-1693; Published in Advance October 22, 2020, doi:10.1101/gr.265322.120
...-altering inversions being subject to negative selection. One such inversion (Chr18_inv4) is depicted in Figure 4, A and B, along with chromatin domains predicted from a parallel analysis of paired human and rhesus Hi-C data generated for this study from LCLs (Methods), as well as previously published data from...
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Research: Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
- Alexandre Laverré,
- Eric Tannier,
- and Anamaria Necsulea
Genome Res. February 2022 32: 280-296; Published in Advance December 20, 2021, doi:10.1101/gr.275901.121
...understand the functional relevance and the phenotypic implications of the promoter–enhancer interactions predicted with PCHi-C data, we examined their relationship with gene expression evolution. We evaluated gene expression patterns using a comparative transcriptome collection spanning several organs...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...). Therefore, Hi-C can be used to conduct unbiased -wide chromatin 3D conformation analysis and establish the all-to-all DNA interaction landscape.In this study, Hi-C, epigenetic, and transcriptomic data were combined with biochemical assays to build the global and accurate -wide enhancer map in the silkworm...
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Resource: Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
- Ekaterina Khrameeva,
- Ilia Kurochkin,
- Dingding Han,
- Patricia Guijarro,
- Sabina Kanton,
- Malgorzata Santel,
- Zhengzong Qian,
- Shen Rong,
- Pavel Mazin,
- Marat Sabirov,
- Matvei Bulat,
- Olga Efimova,
- Anna Tkachev,
- Song Guo,
- Chet C. Sherwood,
- J. Gray Camp,
- Svante Pääbo,
- Barbara Treutlein,
- and Philipp Khaitovich
Genome Res. May 2020 30: 776-789; Published in Advance May 18, 2020, doi:10.1101/gr.256958.119
...), and cerebellar gray matter (CB), in three individuals per species (Supplemental Table S1). To reduce experimental variation among species, tissue samples from one individual of each species were pooled and processed in parallel in each brain region (Fig. 3A). The nuclei species’ identity was then recovered...
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Method: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
- Kyung Yeon Han,
- Kyu-Tae Kim,
- Je-Gun Joung,
- Dae-Soon Son,
- Yeon Jeong Kim,
- Areum Jo,
- Hyo-Jeong Jeon,
- Hui-Sung Moon,
- Chang Eun Yoo,
- Woosung Chung,
- Hye Hyeon Eum,
- Sangmin Kim,
- Hong Kwan Kim,
- Jeong Eon Lee,
- Myung-Ju Ahn,
- Hae-Ock Lee,
- Donghyun Park,
- and Woong-Yang Park
Genome Res. January 2018 28: 75-87; Published in Advance December 5, 2017, doi:10.1101/gr.223263.117
...inferred large-scale copy-number alterations for each cell by averaging relative expression levels over large regions. However, the parallel DNA and RNA sequencing also revealed inconsistencies between chromosome-wide genomic and transcriptomic variations. For example, Chromosome 3 displayed a relatively...
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