Searching journal content for articles similar to Bar-Yaacov et al. 27 (10): 1696.

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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...), recoding is overrepresented in twomajor clades, coleoids (Cephalopoda) (Alon et al. 2015; Liscovitch-Brauer et al. 2017) and Drosophila (Insecta) (Yu et al. 2016; Yablonovitch et al. 2017a; Duan et al. 2024a). The temporospatial regulation of RNA editing circumvents the pleiotropic effects caused by DNA...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...and antisense transcripts, preventing stable dsRNA formation, and RNA-binding proteins may wrap RNA molecules, interfering with their ability to pair with complementary transcripts. Several limitations of our analysis warrant consideration. First, we conservatively excluded candidate cis-NAT editing regions...
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Research: Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
- Yang Li and
- Jianzhi Zhang
Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
...A are examined in multiple species, the loss of I but not the gain of II is expected to be conserved (He 2016). Indeed, deleting the transcription factor gene HAP4 in the budding yeast Saccharomyces cerevisiae (Sce) results in mRNA expression changes of 65 genes concentrated in related Gene Ontology (GO) terms...
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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
...necessitating additional molecules for their removal.Paramecium germline-limited sequences are thought to be targeted by two small noncoding RNA classes: scnRNAs and iesRNAs. scnRNAs are produced by Dicer-like proteins Dcl2 and Dcl3 in the MICs and loaded on Piwi proteins Ptiwi01/09 and transported to the old...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...the similarity of the translation initiation regulation in both species. To characterize the CU-rich elements in plant mRNAs, we swapped the TIS upstream regions between WT and mCU mutants from the 5′ to 3′ end in the 5′ UTR–AUG TIS of Solyc03g096920.3.1 (Fig. 5C). The protein signals of the GFP reporter were...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...of these TF genes in RNA-seq data from hESCs further differentiated beyond the PFG stage to pancreatic progenitors (PPs). This suggests that the HCNE CRMs these TFs act through bear functional marks prior to the expression of these TFs. Notably, multiple SOX family TFs, including SOX2, -3, -4, -6, -9, -15...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...primarily employed RNA sequencing(Jin et al. 2025), which, while 63 informative, does not fully elucidate the complex regulatory mechanisms underlying 64 transcriptional programs. Gene expression is regulated by cis-regulatory elements (CREs) in a 65 spatiotemporal manner through precise gene regulatory...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...; Van Oss and Carvunis 2019; Betrán and Long 2022; Zhang et al. 2022). New genes can be integrated into essential bioprocesses, such as transcriptional regulation, RNA synthesis, and DNA repair (Ciccarelli et al. 2005; Ding et al. 2021). In Drosophila species, lineage-specific genes may control the key...
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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...editing methods primarily rely on the simultaneous delivery of multiple sgRNAs targeting different genes. Various strategies have been explored, including using all-in-one plasmids containing multi-sgRNA/crRNA arrays (Zetsche et al. 2017; Breinig et al. 2019; Campa et al. 2019; Zhang et al. 2019b; Yuan...
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Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
- Brigitta Szabo,
- Therese C. Mandl,
- Bernhard Woldrich,
- Gregor Diensthuber,
- David Martin,
- Michael F. Jantsch,
- and Konstantin Licht
Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
...cells and editing level analysis suggests that regulation of editing levels also depends on transcription.Eukaryotic gene expression of protein-coding genes involves transcription, RNA processing, RNA export, translation, and degradation of transcripts (Maniatis and Reed 2002; Keene 2007; Bentley 2014...
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