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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...-cell RNA-seq methods to study the variation of the targets and the microRNAs themselves, and transcriptional inhibition to measure target half-lives. We find that microRNAs form four distinct coexpression groups across single cells. In particular, the mir-290 and the mir-182 clusters are abundantly...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...et al. 2019; Teets et al. 2023). Neural events also control the production and release of prothoracicotropic hormone (PTTH), as well as the production of ecdysone (Ahmadi et al. 2021). Additionally, downstream genes, such as microRNAs regulated by ecdysone titers (e.g., let-7, miR-252, and miR-8–3p...
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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
...directly rearranges the enhancer contacts. Such a rearrangement disturbs the intrinsic enhancer–gene connections in several antiviral genes, resulting in reduced expression of these genes, which accelerates viral infection. Overall, our results reveal the regulatory role of super-enhancers and shed new...
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Research: Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
- Isabela Gerdes Gyuricza,
- Joel M. Chick,
- Gregory R. Keele,
- Andrew G. Deighan,
- Steven C. Munger,
- Ron Korstanje,
- Steven P. Gygi,
- and Gary A. Churchill
Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
...to leakage of cytoplasmic proteins into the nucleus (D'Angelo et al. 2009). Transcripts in the cytoplasm can be modified post-transcriptionally by micro-RNAs (miRNAs), which are primarily processed by the DROSHA complex, a RNase that cleaves primary miRNAs releasing hairpin-shaped ones (Han et al. 2004...
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Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
- Xiaoli Ma,
- Tom Denyer,
- Marie Javelle,
- Antje Feller,
- and Marja C.P. Timmermans
Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
....timmermans@zmbp.uni-tuebingen.deAbstractDevelopment of complex organisms requires the delicate and dynamic spatiotemporal regulation of gene expression. Central to this are microRNAs (miRNAs). These mobile small RNAs offer specificity in conveying positional information and versatility in patterning the outcomes of gene expression. However, the parameters...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...RNA expression profiling in postmortem brains from individuals with ASD and controls and identified 60 circRNAs and three coregulated modules that were perturbed in ASD. By integrating circRNA, microRNA, and mRNA dysregulation data derived from the same cortex samples, we identified 8170 ASD-associated circRNA-microRNA...
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Research: Genome-wide redistribution of 24-nt siRNAs in rice gametes
- Chenxin Li,
- Hengping Xu,
- Fang-Fang Fu,
- Scott D. Russell,
- Venkatesan Sundaresan,
- and Jonathan I. Gent
Genome Res. February 2020 30: 173-184; Published in Advance January 2, 2020, doi:10.1101/gr.253674.119
...cell or tissue type, we prepared at least three biological replicates. After removing PCR duplicates as described in Methods, we aligned all reads of 20 to 25 nt in length to the MSU7 reference assembly (Supplemental Table S1; Kawahara et al. 2013).Distinct microRNA expression patterns in gametes...
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Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
- Mattia Furlan,
- Eugenia Galeota,
- Nunzio Del Gaudio,
- Erik Dassi,
- Michele Caselle,
- Stefano de Pretis,
- and Mattia Pelizzola
Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
...DTA (Sun et al. 2012), GRAND-SLAM (Jürges et al. 2018), pulseR (Uvarovskii and Dieterich 2017), and DRiLL (Rabani et al. 2014). Eventually, these approaches have started to unveil how the modulation of RNA dynamics can determine gene-specific regulatory modes and elicit complex transcriptional responses...
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Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...and chimpanzees (Gronau et al. 2013), (3) a conservation score calculated for the primate phylogeny (Pollard et al. 2010), and (4) a scaled measure of transcription factor binding site (TFBS) conservation.ResultsTo investigate different aspects associated with varying degrees of regulatory pleiotropy, we...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...at the next in-frame AUG (black arrowhead in the Ribo-seq panel and start/stop codon track). TSS-seq (purple lines) reveals two major transcription start site (TSS) clusters (red arrowheads): one upstream of and one downstream from the annotated start codon. The downstream TSS cluster will cause...
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