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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
...relative to miRNAs. This distinction may be reflective of the differences in size, abundance, modifications, and associated Argonaute proteins between tsRNAs and miRNAs. In Drosophila, miRNAs, siRNAs, and piRNAs execute post-transcriptional regulation by primarily binding to AGO1, AGO2, and AGO3/PIWI...
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Research: A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation
- Hala Al Adhami,
- Brendan Evano,
- Anne Le Digarcher,
- Charlotte Gueydan,
- Emeric Dubois,
- Hugues Parrinello,
- Christelle Dantec,
- Tristan Bouschet,
- Annie Varrault,
- and Laurent Journot
Genome Res. March 2015 25: 353-367; Published in Advance January 22, 2015, doi:10.1101/gr.175919.114
...whether alteration of IG expression did result in altered proliferation and/or differentiation. We selected several IGs based on their expression pattern in the adipogenic differentiation model and transiently transfected 3T3-L1 cells with siRNAs or cDNAs for 17 and 20 IGs, respectively. Si...
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Research: Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network
- Noor Jailkhani,
- Srikanth Ravichandran,
- Shubhada R. Hegde,
- Zaved Siddiqui,
- Shekhar C. Mande,
- and Kanury V.S. Rao
Genome Res. December 2011 21: 2067-2081; Published in Advance August 24, 2011, doi:10.1101/gr.116145.110
...and translate them into the output response of cell cycle progression. We next attempted to reconstruct the network of pathways through which the effects of the identified targets were likely enforced. Consequently, we defined the hits identified by our siRNA screen as ‘‘source nodes’’ (Fig. 2A, nodes in dark...
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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...). Although most approaches treat miRNA targets as sets of genes, disregarding the complex gene interactions that they form, network-based approaches can integrate protein–protein interactions (PPIs) and other regulators (e.g., transcription factors [TFs]) to achieve a systemic view of the mi...
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Research: Reprogramming of miRNA networks in cancer and leukemia
- Stefano Volinia,
- Marco Galasso,
- Stefan Costinean,
- Luca Tagliavini,
- Giacomo Gamberoni,
- Alessandra Drusco,
- Jlenia Marchesini,
- Nicoletta Mascellani,
- Maria Elena Sana,
- Ramzey Abu Jarour,
- Caroline Desponts,
- Michael Teitell,
- Raffaele Baffa,
- Rami Aqeilan,
- Marilena V. Iorio,
- Cristian Taccioli,
- Ramiro Garzon,
- Gianpiero Di Leva,
- Muller Fabbri,
- Marco Catozzi,
- Maurizio Previati,
- Stefan Ambs,
- Tiziana Palumbo,
- Michela Garofalo,
- Angelo Veronese,
- Arianna Bottoni,
- Pierluigi Gasparini,
- Curtis C. Harris,
- Rosa Visone,
- Yuri Pekarsky,
- Albert de la Chapelle,
- Mark Bloomston,
- Mary Dillhoff,
- Laura Z. Rassenti,
- Thomas J. Kipps,
- Kay Huebner,
- Flavia Pichiorri,
- Dido Lenze,
- Stefano Cairo,
- Marie-Annick Buendia,
- Pascal Pineau,
- Anne Dejean,
- Nicola Zanesi,
- Simona Rossi,
- George A. Calin,
- Chang-Gong Liu,
- Jeff Palatini,
- Massimo Negrini,
- Andrea Vecchione,
- Anne Rosenberg,
- and Carlo M. Croce
Genome Res. May 2010 20: 589-599; doi:10.1101/gr.098046.109
...network graphs (Supplemental Figs. 5, 6) show the functional effect of differentially expressed miRNAs on cellular pathways. The large majority of the affected pathways is related to cancer or signal transduction (i.e., Wnt, VEGF, TGF-beta, insulin, phosphatidylinositol signaling, focal adhesion...
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Research: Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis
- Marija Petrić Howe,
- Hamish Crerar,
- Jacob Neeves,
- Jasmine Harley,
- Giulia E. Tyzack,
- Pierre Klein,
- Andres Ramos,
- Rickie Patani,
- and Raphaëlle Luisier
Genome Res. October 2022 32: 1808-1825; Published in Advance September 30, 2022, doi:10.1101/gr.276898.122
...% of retained introns with cross-linking event. P-value from Fisher's exact test. (F) Bar graphs showing qPCR analysis of UPF1 (top) and IGF2BP1 (bottom) relative mRNA expression levels in MNs (DIV = 21) after being transfected with siRNA targeting UPF1 (UPF1i), IGF2BP1 (IGF2BP1i), or a scrambled control (CTRL...
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Method: Integrated analysis of motif activity and gene expression changes of transcription factors
- Jesper Grud Skat Madsen,
- Alexander Rauch,
- Elvira Laila Van Hauwaert,
- Søren Fisker Schmidt,
- Marc Winnefeld,
- and Susanne Mandrup
Genome Res. February 2018 28: 243-255; Published in Advance December 12, 2017, doi:10.1101/gr.227231.117
.... (*) indicates that the motif was identified with medium confidence. (B,C) The majority of the causal transcription factors predicted by IMAGE have an impact on lipid accumulation. (B) Representative images at low and high magnification of Oil Red O staining of hMSCs transfected with the indicated siRNAs...
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Perspective: Decrypting noncoding RNA interactions, structures, and functional networks
- Muller Fabbri,
- Leonard Girnita,
- Gabriele Varani,
- and George A. Calin
Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
.... 2017). Over the last decade, advances in bioinformatics and deep sequencing technology have allowed the identification and annotation of tens of thousands of short and long ncRNAs (lncRNAs). These include endogenous microRNAs (miRNAs), small interfering RNAs (endo-siRNAs), PIWI-interacting RNAs (pi...
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Research: Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis
- Kai Li,
- Jiayue Xu,
- Yanyun Luo,
- Dingfeng Zou,
- Ruiqin Han,
- Shunshun Zhong,
- Qing Zhao,
- Xinyu Mang,
- Mengzhen Li,
- Yanmin Si,
- Yan Lu,
- Pengyu Li,
- Cheng Jin,
- Zhipeng Wang,
- Fang Wang,
- Shiying Miao,
- Bo Wen,
- Linfang Wang,
- Yanni Ma,
- Jia Yu,
- and Wei Song
Genome Res. January 2021 31: 13-26; Published in Advance December 16, 2020, doi:10.1101/gr.264333.120
...then returned to the abdominal cavity, and the abdominal wall and skin were closed with sutures. The testes were harvested 4 wk after microinjection. All animal experimentation protocols were performed with the approval of the Peking Union Medical College Animal Care and Use Committees. The sequences of siRNAs...
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Method: Models of human core transcriptional regulatory circuitries
- Violaine Saint-André,
- Alexander J. Federation,
- Charles Y. Lin,
- Brian J. Abraham,
- Jessica Reddy,
- Tong Ihn Lee,
- James E. Bradner,
- and Richard A. Young
Genome Res. March 2016 26: 385-396; Published in Advance February 3, 2016, doi:10.1101/gr.197590.115
...; Kagey et al. 2010). To test whether the candidate core TFs play roles in control of ESC identity, we analyzed POU5F1 expression changes and cell nuclei number changes after depletion of each of these TFs using data from a -wide siRNA screen in H1 hESCs (Chia et al. 2010). These data confirm...

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