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Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...) Scatterplot representing the nuclear to total ratio of RNA abundance and indication of nuclear or cytoplasmic localization. Fisher's exact test: P-value < 2.2 × 10−16.GRADseq: identification of gradient-enriched transcripts (GETs)Our goal is to purify native RNPs using GRADseq that exhibit discrete...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...stability, or alternative splicing between the alleles due to genetic variation (Nembaware et al. 2008; Pai et al. 2012; Amoah et al. 2021). That is, local genetic variants can influence transcriptional or posttranscriptional processes to modulate the mRNA abundance of each allele (Robles-Espinoza et al...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...down, 3% of coding genes remain active. Furthermore, RNA polymerase II (RNAPII) accumulates at one-third of gene promoters. The corresponding genes are highly enriched among those showing a high level of transcription and high frequency of expression in individual cells, shortly after cells are refed...
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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...by bacterial DNA modifications (Rand et al. 2017; Wick et al. 2019). Bacterial DNA methylation can occur frequently in diverse sequence contexts. In nanopore direct RNA sequencing, mismatches in modified RNA molecules can be used to detect modifications (Liu et al. 2019). However, this feature has not been...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...been extensively assessed, their impact on epigenetics has been poorly studied and limited to specific genomic regions. Here, we investigated the hypothesis that some STRs act as independent regulators of local DNA methylation in the human and modify risk of common human traits. To address...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...m6A readers and erasers. We found that infection with SARS-CoV-2 variants causes a loss of m6A in cellular RNAs, whereas m6A is detected abundantly in viral RNA. METTL3, the m6A methyltransferase, shows an unusual cytoplasmic localization postinfection. The B.1.351 variant has a less...
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Research: Human contamination in bacterial genomes has created thousands of spurious proteins
- Florian P. Breitwieser,
- Mihaela Pertea,
- Aleksey V. Zimin,
- and Steven L. Salzberg
Genome Res. June 2019 29: 954-960; Published in Advance May 7, 2019, doi:10.1101/gr.245373.118
...-coding gene.” However, both the human protein and mRNA entries, as well as the Chlamydia psittaci entries, are still present in GenBank, nr, and TrEMBL. Another example is a 10,174-bp contig (accession FPIH01000010.1) in a Chlamydia abortus assembly that is a mouse contaminant (and that also matches the human...
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Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
- Seung Cho Lee,
- Evan Ernst,
- Benjamin Berube,
- Filipe Borges,
- Jean-Sebastien Parent,
- Paul Ledon,
- Andrea Schorn,
- and Robert A. Martienssen
Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
...PPTs promote nuclear localization. For one member of the ATCOPIA52 subfamily (SISYPHUS), cPPT intermediates were not observed, but abundant circular DNA indicated transposon “suicide” by auto-integration within the VLP. easiRNA targeted EVADE genomic RNA, polysome association of GYPSY (ATHILA) subgenomic RNA...
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Research: Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection
- Chun Jimmie Ye,
- Jenny Chen,
- Alexandra-Chloé Villani,
- Rachel E. Gate,
- Meena Subramaniam,
- Tushar Bhangale,
- Mark N. Lee,
- Towfique Raj,
- Raktima Raychowdhury,
- Weibo Li,
- Noga Rogel,
- Sean Simmons,
- Selina H. Imboywa,
- Portia I. Chipendo,
- Cristin McCabe,
- Michelle H. Lee,
- Irene Y. Frohlich,
- Barbara E. Stranger,
- Philip L. De Jager,
- Aviv Regev,
- Tim Behrens,
- and Nir Hacohen
Genome Res. December 2018 28: 1812-1825; Published in Advance November 16, 2018, doi:10.1101/gr.240390.118
...interferon stimulation induce widespread alternate isoform usageWe used paired-end RNA-seq to profile the transcriptomes of primary MoDCs from healthy donors at rest (N = 99), and following stimulation with either recombinant interferon beta (IFNB1), a type 1 interferon that stimulates anti-viral effectors...
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