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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
...of the best predictors for protein sequence and expression conservation. In this study, we investigated its effect on the evolution of cis-regulatory elements (CREs). To this end, we carefully reanalyzed the Epigenomics Roadmap data for nine fetal tissues, assigning a measure of pleiotropic degree to nearly...
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Research: Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a Drosophila knock-in tauopathy model
- Hassan Bukhari,
- Vanitha Nithianandam,
- Rachel A. Battaglia,
- Anthony Cicalo,
- Souvarish Sarkar,
- Aram Comjean,
- Yanhui Hu,
- Matthew J. Leventhal,
- Xianjun Dong,
- and Mel B. Feany
Genome Res. April 2024 34: 590-605; Published in Advance April 10, 2024, doi:10.1101/gr.278576.123
...correlate with a previously described functional role for transposable element mobilization in Drosophila models of tauopathy and in tauopathy patients (Guo et al. 2018; Sun et al. 2018). Mitochondrial function has been strongly linked to neurotoxicity in tauopathies (DuBoff et al. 2013; Frost et al. 2015...
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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
...(see below).View larger version: In this window In a new window Figure 3. Ubiquitous delivery of tsRNA sponges increases the levels of mRNAs with antisense target sites in early Drosophila pupae. (A) Construction of tsRNA sponges. The sponge element consists of 10 repetitive sequences (blue...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...to be older and primarily iesRNA and scnRNA independent, whereas younger, longer IESs require these and other molecules for excision (Sellis et al. 2021). Ptiwi01/09 was recently also suggested to interact with Polycomb repressive complex 2 (PRC2), which represses transposable elements (Miró-Pina et al. 2022...
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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
...Corresponding author: wuxiaofeng@zju.edu.cnAbstractAs influential regulatory elements in the , enhancers control gene expression under specific cellular conditions, and such connections are dynamic under different conditions. However, because of the lack of a -wide enhancer–gene connection map, the roles...
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Research: Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
- Boning Chen,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
...lethality in Drosophila (Houlard et al. 2006; Yu et al. 2013). In human cells, loss of CAF-1 halts S-phase progression and arrests cells in early or mid S phase (Hoek and Stillman 2003). In yeast, disruption of CAF-1 does not affect the viability of the cells, which is partly owing to the functional...
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Research: Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures
- Jiseon Lim,
- Wonjoo Kim,
- Jun Kim,
- and Junho Lee
Genome Res. November 2023 33: 1947-1957; Published in Advance November 2, 2023, doi:10.1101/gr.278124.123
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Research: TP53 regulates miRNA association with AGO2 to remodel the miRNA–mRNA interaction network
- Jonathan Krell,
- Justin Stebbing,
- Claudia Carissimi,
- Aleksandra F. Dabrowska,
- Alexander de Giorgio,
- Adam E. Frampton,
- Victoria Harding,
- Valerio Fulci,
- Giuseppe Macino,
- Teresa Colombo,
- and Leandro Castellano
Genome Res. March 2016 26: 331-341; Published in Advance December 23, 2015, doi:10.1101/gr.191759.115
...–induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA–mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find...
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Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
...developed to map replication origins in different organisms (Prioleau and MacAlpine 2016), mostly by mapping different replication elements such as nascent DNA strands (Besnard et al. 2012), replication bubbles (Mesner et al. 2013), Okazaki fragments (Petryk et al. 2016), replication initiation sites...
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Research: Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice
- Yuan Fang,
- Lifen Chen,
- Kande Lin,
- Yilong Feng,
- Pengyue Zhang,
- Xiucai Pan,
- Jennifer Sanders,
- Yufeng Wu,
- Xiu-e Wang,
- Zhen Su,
- Caiyan Chen,
- Hairong Wei,
- and Wenli Zhang
Genome Res. August 2019 29: 1287-1297; Published in Advance July 1, 2019, doi:10.1101/gr.246009.118
...and Tomizawa 1980; Kogoma 1997; Yu et al. 2003). Recently, R-loops have also been shown to be involved in impairment of transcription elongation (Huertas and Aguilera 2003), DNA replication obstacle (Gan et al. 2011), DNA-damage response (Sollier et al. 2014; Hamperl et al. 2017), environmental adaptation...

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