Genetic compensation: A phenomenon in search of mechanisms.
TLDR
This review revisits studies reporting genetic compensation in higher eukaryotes and outlines possible molecular mechanisms, which may include both transcriptional and posttranscriptional processes.Abstract:
Several recent studies in a number of model systems including zebrafish, Arabidopsis, and mouse have revealed phenotypic differences between knockouts (i.e., mutants) and knockdowns (e.g., antisense-treated animals). These differences have been attributed to a number of reasons including off-target effects of the antisense reagents. An alternative explanation was recently proposed based on a zebrafish study reporting that genetic compensation was observed in egfl7 mutant but not knockdown animals. Dosage compensation was first reported in Drosophila in 1932, and genetic compensation in response to a gene knockout was first reported in yeast in 1969. Since then, genetic compensation has been documented many times in a number of model organisms; however, our understanding of the underlying molecular mechanisms remains limited. In this review, we revisit studies reporting genetic compensation in higher eukaryotes and outline possible molecular mechanisms, which may include both transcriptional and posttranscriptional processes.read more
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Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish
Bernadett Bosze,Yosuke Ono,Benjamin Mattes,Claude Sinner,Victor Gourain,Thomas Thumberger,Sham Tlili,Joachim Wittbrodt,Timothy E. Saunders,Timothy E. Saunders,Uwe Strähle,Alexander Schug,Steffen Scholpp,Steffen Scholpp +13 more
TL;DR: It is found that Pcdh18a-mediated recycling of E-cadherin adhesion complexes transforms prechordal plate cells into a cohesive and fast migrating cell group, which influences the trailing mesodermal cell sheet by orchestrating the morphogenesis of the notochord.
Journal ArticleDOI
Site-directed RNA editing (SDRE): Off-target effects and their countermeasures.
TL;DR: The diverse strategies for combating off-target effects of site-directed RNA editing are discussed, drawing lessons from the published studies as well as ongoing research.
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Adaptation of the AID system for stem cell and transgenic mouse research.
TL;DR: It is demonstrated that the AID system can be successfully employed for rapid degradation of stable proteins in embryonic stem cells, which is crucial for investigation of protein functions in quickly changing environments, such as stem cell proliferation and differentiation.
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Mutagenesis of putative ciliary genes with the CRISPR/Cas9 system in zebrafish identifies genes required for retinal development.
Ruikun Hu,Weilai Huang,Jiangfang Liu,Miaomiao Jin,Yue Wu,Jingyu Li,Jingyi Wang,Zehao Yu,Hong Wang,Ying Cao +9 more
TL;DR: The potential function of the ciliary genes for the retinal development of zebrafish is uncovered by using the clustered regularly interspaced short palindromic repeats/ CRISPR‐associated protein 9 (CRISPR/Cas9) system.
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LIN28B affects gene expression at the hypothalamic-pituitary axis and serum testosterone levels
Jaakko T. Leinonen,Yu-Chia Chen,Jana Pennonen,Leevi Lehtonen,Nella Junna,Taru Tukiainen,Pertti Panula,Elisabeth Widen +7 more
TL;DR: Novel evidence is provided that LIN28B contributes to the regulation of sex hormone pathways, which might help explain why the gene associates with several distinct traits.
References
More filters
Journal ArticleDOI
Network biology: understanding the cell's functional organization
TL;DR: This work states that rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize the view of biology and disease pathologies in the twenty-first century.
Journal ArticleDOI
Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?
TL;DR: This Review summarizes the current understanding of the mechanistic aspects of microRNA-induced repression of translation and discusses some of the controversies regarding different modes of micro RNA function.
Journal ArticleDOI
Functional profiling of the Saccharomyces cerevisiae genome.
Guri Giaever,Angela M. Chu,Li Ni,Carla Connelly,Linda Riles,Steeve Veronneau,Sally Dow,Ankuta Lucau-Danila,Keith Anderson,Bruno André,Adam P. Arkin,Anna Astromoff,Mohamed El Bakkoury,Rhonda Bangham,Rocío Benito,Sophie Brachat,Stefano Campanaro,Matt Curtiss,Karen Davis,Adam M. Deutschbauer,K. D. Entian,Patrick Flaherty,Françoise Foury,David J. Garfinkel,Mark Gerstein,Deanna Gotte,Ulrich Güldener,Johannes H. Hegemann,Svenja Hempel,Zelek S. Herman,Daniel F. Jaramillo,Diane E. Kelly,Steven L. Kelly,Peter Kötter,Darlene LaBonte,David C. Lamb,Ning Lan,Hong Liang,Hong Liao,Lucy Y. Liu,Chuanyun Luo,Marc Lussier,Rong Mao,Patrice Menard,Siew Loon Ooi,José L. Revuelta,Christopher J. Roberts,Matthias Rose,Petra Ross-Macdonald,Bart Scherens,Greg Schimmack,Brenda Shafer,Daniel D. Shoemaker,Sharon Sookhai-Mahadeo,Reginald Storms,Jeffrey N. Strathern,Giorgio Valle,Marleen Voet,Guido Volckaert,Ching Yun Wang,Teresa R. Ward,Julie Wilhelmy,Elizabeth A. Winzeler,Yonghong Yang,Grace Yen,Elaine M. Youngman,Kexin Yu,Howard Bussey,Jef D. Boeke,Michael Snyder,Peter Philippsen,Ronald W. Davis,Mark Johnston +72 more
TL;DR: It is shown that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment, and less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal Growth in four of the tested conditions.
Journal ArticleDOI
Gene Action in the X -chromosome of the Mouse ( Mus musculus L.)
TL;DR: Ohno and Hauschka1 showed that in female mice one chromosome of mammary carcinoma cells and of normal diploid cells of the ovary, mammary gland and liver was heteropyKnotic and suggested that the so-called sex chromatin was composed of one heteropyknotic X-chromosome.
Journal ArticleDOI
The Transcriptional Landscape of the Mammalian Genome
Piero Carninci,Takeya Kasukawa,Shintaro Katayama,Julian Gough,Martin C. Frith,N. Maeda,Rieko Oyama,Timothy Ravasi,Boris Lenhard,Christine A. Wells,Christine A. Wells,Rimantas Kodzius,Kazuro Shimokawa,Vladimir B. Bajic,Steven E. Brenner,Serge Batalov,Alistair R. R. Forrest,Mihaela Zavolan,Melissa J. Davis,Laurens G. Wilming,Vassilis Aidinis,Jonathan E. Allen,Alberto Ambesi-Impiombato,Rolf Apweiler,Rajith N. Aturaliya,Timothy L. Bailey,Mukesh Bansal,Laura L. Baxter,Kirk W. Beisel,T. Bersano,Hidemasa Bono,Alistair M. Chalk,Kuo Ping Chiu,V. Choudhary,Alan Christoffels,D. R. Clutterbuck,Mark L. Crowe,Emiliano Dalla,Brian P. Dalrymple,Bernard de Bono,G. Della Gatta,Diego di Bernardo,Thomas A. Down,Pär G. Engström,Michela Fagiolini,Geoffrey J. Faulkner,Colin F. Fletcher,T. Fukushima,Masaaki Furuno,Sugiko Futaki,Manuela Gariboldi,P. Georgii-Hemming,Thomas R. Gingeras,Takashi Gojobori,Richard E. Green,Stefano Gustincich,Matthias Harbers,Yoshitaka Hayashi,Takao K. Hensch,Nobutaka Hirokawa,David E. Hill,Lukasz Huminiecki,M. Iacono,Kazuho Ikeo,Atsushi Iwama,T. Ishikawa,M. Jakt,Alexander Kanapin,Masaru Katoh,Yuka Imamura Kawasawa,Janet Kelso,Hiroshi Kitamura,Hiroaki Kitano,George Kollias,S. P. T. Krishnan,Adele Kruger,Sarah K. Kummerfeld,Igor V. Kurochkin,Liana F. Lareau,Dejan Lazarevic,Leonard Lipovich,Jinfeng Liu,Sabino Liuni,Sean McWilliam,M. Madan Babu,Martin Madera,Luigi Marchionni,Hideo Matsuda,Shu-ichi Matsuzawa,Harukata Miki,Flavio Mignone,Sou Miyake,Ken A. Morris,Salim Mottagui-Tabar,Salim Mottagui-Tabar,Nicola Mulder,Naoko Nakano,Hiromitsu Nakauchi,P. Ng,Roland Nilsson,S. Nishiguchi,Seishi Nishikawa,Franco Nori,Osamu Ohara,Yasushi Okazaki,Valerio Orlando,Ken C Pang,William J. Pavan,Giulio Pavesi,Graziano Pesole,Nikolai Petrovsky,Silvano Piazza,Jonathan C. Reed,James F. Reid,Brian Z. Ring,M. Ringwald,Burkhard Rost,Yijun Ruan,Steven L. Salzberg,Albin Sandelin,Claudio Schneider,Christian Schönbach,K. Sekiguchi,Colin A. Semple,Shigeto Seno,Luca Sessa,Y. Sheng,Y. Shibata,Hiroshi Shimada,Kiyo Shimada,D. Silva,B. Sinclair,Silke Sperling,Elia Stupka,Koji Sugiura,Razvan Sultana,Yoichi Takenaka,Kohei Taki,K. Tammoja,Sin Lam Tan,S. Tang,Martin S. Taylor,Jesper Tegnér,Sarah A. Teichmann,Hiroki R. Ueda,Erik van Nimwegen,Roberto Verardo,Chia-Lin Wei,Ken Yagi,H. Yamanishi,E. Zabarovsky,S. Zhu,Andreas Zimmer,Winston Hide,Carol J. Bult,Sean M. Grimmond,Rohan D. Teasdale,Edison T. Liu,Vladimir Brusic,John Quackenbush,Claes Wahlestedt,Claes Wahlestedt,John S. Mattick,David A. Hume,C. Kai,D. Sasaki,Yasuhiro Tomaru,S. Fukuda,Mutsumi Kanamori-Katayama,M. Suzuki,Junken Aoki,Taku Arakawa,J. Iida,Kengo Imamura,Masayoshi Itoh,T. Kato,Hideya Kawaji,N. Kawagashira,Tsugumi Kawashima,M. Kojima,S. Kondo,Hideaki Konno,K. Nakano,Noriko Ninomiya,T. Nishio,M. Okada,Charles Plessy,K. Shibata,Toshiyuki Shiraki,S. Suzuki,Michihira Tagami,Kazunori Waki,Akira Watahiki,Yuko Okamura-Oho,Harukazu Suzuki,Jun Kawai,Yoshihide Hayashizaki,Yoshihide Hayashizaki +197 more
TL;DR: Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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