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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...) Collection and preprocessing of snRNA-seq and snATAC-seq data sets in physical space. (B) Multiple analysis to identify an AD-associated gene list including differential gene expression analysis; identification of cCRE; cell type–specific, AD-associated risk variants; and peak-to-gene linkages. (C) Two...
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Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
- Shelley Reich,
- Tobias Loschko,
- Julie Jung,
- Samantha Nestel,
- Ralf J. Sommer,
- and Michael S. Werner
Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
...that it is the pivotal environmental switch gene.Transcriptional effects of mutations in the mouth-form GRN are temporally restrictedTo explore the relationship between mouth-form genes, we performed RNA-seq on seven mutant lines of P. pacificus (Supplemental Fig. S1A) and quantified changes in gene expression relative...
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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
...). Enriched GO terms for slope included ATPase-coupled intramembrane lipid transporter activity (all traits) and RNA-directed 5′-3′ RNA polymerase activity (flowering time traits). Six GO terms, including plant hormone signal transduction, were identified as significantly enriched for intercept, all of which...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...occupancy of genes and TEs in Spirodela and Arabidopsis. (B) Size distribution and genomic feature annotation of TraPR-purified sRNA from Arabidopsis and Spirodela. Error bars represent SD of the mean of three biological replicates. (C) Metaplots of averaged weighted DNA methylation in all three contexts...
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Research: Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
- Bo Li,
- Karl A.G. Kremling,
- Penghao Wu,
- Robert Bukowski,
- Maria C. Romay,
- En Xie,
- Edward S. Buckler,
- and Mingsheng Chen
Genome Res. October 2018 28: 1555-1565; Published in Advance August 30, 2018, doi:10.1101/gr.229716.117
...five GO terms are exclusively related to protein synthesis or ribosome biogenesis (Fig. 6), suggesting that a considerable number of genes coexpressed with rRNA play roles in assisting rRNA into the ribosome complex. Further Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
.... Hierarchical clustering was performed on tRNA-seq libraries across different biological samples and across different tRNA genes (grouped according to the unique anticodons). (D) Scatterplots show that at the same or close stage, tsRNA abundances were correlated with tRNA gene copy numbers, tRNA abundances, tsRNA...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
...%) were paternally biased, 55 genes (20%) were maternally biased, and two genes (1%) switched their ASE bias direction across the cohorts (Fig. 2C). This heavy paternal skew is driven by a 672-kb cluster of 171 small nucleolar RNAs (snoRNAs) in the Prader-Willi/Angelman syndrome (PWS/AS) domain...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...toxic mechanism in particular has facilitated the development of therapeutics. Recently, gene silencing methods with antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) have made considerable progress toward clinical application. One such ASO in advances stages of development is RG6042...
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Research: Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair
- Kaitlynne A. Bohm,
- Amelia J. Hodges,
- Wioletta Czaja,
- Kathiresan Selvam,
- Michael J. Smerdon,
- Peng Mao,
- and John J. Wyrick
Genome Res. June 2021 31: 1047-1059; Published in Advance May 17, 2021, doi:10.1101/gr.274373.120
...promote repair of the TS through GG-NER or may affect TC-NER indirectly (by altering RNA polymerase II [RNAP] transcription) or directly. (D,E) CPD-seq analysis examining the repair of CPDs on both DNA strands across approximately 5000 genes of the in GG-NER-deficient rad16Δ WT-AA and rad16Δ Sth1-AA cells...
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Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
- Charlie George Barker,
- Eirini Petsalaki,
- Girolamo Giudice,
- Julia Sero,
- Emmanuel Nsa Ekpenyong,
- Chris Bakal,
- and Evangelia Petsalaki
Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
.... However, the exact regulatory systems that define these changes remain poorly characterized. In this study, we used a network-systems approach to integrate imaging data and RNA-seq expression data. Our workflow allowed the discovery of unbiased and context-specific gene expression signatures and cell...
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