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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
..._SC5314/Assembly21/archive/C_albicans_SC5314_version_A21-s02-m09-r08_chromosomes.fasta.gz) (Van het Hoog et al. 2007) was used as a basis for a -wide study of niche characteristics on gene density, TE density, and GC content per 5000 kb window (see Supplemental Methods; Goodwin and Poulter 2000; Rice et...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...phenomenon. Because of the lack of strong co-phylogenetic signal, open questions remain about Blastocystis host association, including what the barriers to colonizing different hosts are and how multiple strains or subtypes (commonly termed “mixed infections”) are maintained, and will require a denser...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation...
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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
...(Weitzman and Fradet-Turcotte 2018). In the process of infection, a number of DNA viruses dominate chromatin epigenetic markers and restructure the host 3D architecture, thus reprogramming gene expression and modulating the infection status, including hepatitis B virus (HBV) (Yang et al. 2020), adenovirus...
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Method: Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing
- Lin Lyu,
- Xue Li,
- Ru Feng,
- Xin Zhou,
- Tuhin K. Guha,
- Xiaofei Yu,
- Guo Qiang Chen,
- Yufeng Yao,
- Bing Su,
- Duowu Zou,
- Michael P. Snyder,
- and Lei Chen
Genome Res. March 2023 33: 401-411; Published in Advance March 27, 2023, doi:10.1101/gr.277178.122
...and solutions, whereas the latter is a widespread bacteria found in soil and waterbodies (Fig. 1F,G; Ha et al. 2020; Dohlman et al. 2021).The localized host cell response to cytomegalovirus infection as captured by SMTAn advantage of SMT over 16S sequencing is that by using RNA-seq, SMT captures fungi and viral...
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Method: Arrayed CRISPR screen with image-based assay reliably uncovers host genes required for coxsackievirus infection
- Heon Seok Kim,
- Kyungjin Lee,
- Seong-Jun Kim,
- Sungchan Cho,
- Hye Jin Shin,
- Chonsaeng Kim,
- and Jin-Soo Kim
Genome Res. June 2018 28: 859-868; Published in Advance April 30, 2018, doi:10.1101/gr.230250.117
...to endocytosis, and Golgi-localized proteins, individually using 4542 sgRNAs (three sgRNAs per gene). This screen revealed host factors required for infection by coxsackievirus B3 (CVB3) from Picornaviridae, which includes human pathogens causing diverse diseases. Many host factors that had been overlooked...
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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
...processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization. Given Legionella infection is known to alter its host's cell cycle, to exploit the host...
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Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
- Divya Selvaraju,
- Filip Wierzbicki,
- and Robert Kofler
Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
...of transposable elements (TEs), hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major defense mechanism operates through PIWI-interacting RNAs (piRNAs). To investigate the establishment of the host defense, we introduced the P-element, one of the most widely studied...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
...that recruits additional transcriptional factors to the 11 integration locus, increases chromatin accessibility, changes 3D chromatin interactions, and enhances both 12 retroviral and host gene expression. We used 4 well-characterized HIV-1-infected cell line clones having 13 unique integration sites and low...
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