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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
.... 2016; Jan et al. 2017; Rolland et al. 2019; Gamble et al. 2020; Tan et al. 2020). Further in-depth genomic examination of spermatogenesis reveals individual features of lnRNAs, including germ cell specificity, longer exon length, or high representation of antisense (AS) lncRNAs, which have shown...
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Resource: The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting
- Lishi Li,
- Yulong Song,
- Xinrui Shi,
- Jianheng Liu,
- Shaolei Xiong,
- Wanying Chen,
- Qiang Fu,
- Zichao Huang,
- Nannan Gu,
- and Rui Zhang
Genome Res. January 2018 28: 132-143; Published in Advance December 12, 2017, doi:10.1101/gr.224386.117
..., Guangzhou 510275, PR China ↵2 Co-first authors, listed alphabetically Corresponding authors: zhangrui3@mail.sysu.edu.cn, gnannan3@mail.sysu.edu.cnAbstractAdenosine-to-inosine (A-to-I) RNA editing regulates miRNA biogenesis and function. To date, fewer than 160 miRNA editing sites have been identified. Here...
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Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung,
- Phaedra Agius,
- Jakub O. Westholm,
- Michael Chen,
- Katsutomo Okamura,
- Nicolas Robine,
- Christina S. Leslie,
- and Eric C. Lai
Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
...the Drosophila melanogaster transcriptome. These included 17 known and six confident novel mirtrons among the top 51 candidates, and additional candidates had limited read evidence in available small RNA data. Our computational model also proved effective on Caenorhabditis elegans , for which...
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Research: Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
- Wei Niu,
- Zhi John Lu,
- Mei Zhong,
- Mihail Sarov,
- John I. Murray,
- Cathleen M. Brdlik,
- Judith Janette,
- Chao Chen,
- Pedro Alves,
- Elicia Preston,
- Cindie Slightham,
- Lixia Jiang,
- Anthony A. Hyman,
- Stuart K. Kim,
- Robert H. Waterston,
- Mark Gerstein,
- Michael Snyder,
- and Valerie Reinke
Genome Res. February 2011 21: 245-254; Published in Advance December 22, 2010, doi:10.1101/gr.114587.110
.... Such sites might mediate higher-order genomic interactions and influence nuclear organization, instead. To tease apart the diverse effects that a binding event might have will require many future studies, both -wide and at the level of singlegene analysis. The binding of many TFs to non-coding RNA genes...
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LETTER: Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray
- Housheng He,
- Jie Wang,
- Tao Liu,
- X. Shirley Liu,
- Tiantian Li,
- Yunfei Wang,
- Zuwei Qian,
- Haixia Zheng,
- Xiaopeng Zhu,
- Tao Wu,
- Baochen Shi,
- Wei Deng,
- Wei Zhou,
- Geir Skogerbø,
- and Runsheng Chen
Genome Res. October 2007 17: 1471-1477; Published in Advance September 4, 2007, doi:10.1101/gr.6611807
...) A high-resolution map of transcription in the yeast . Proc. Natl. Acad. Sci. 103 : 5320 – 5325 . ↵ Deng, W. , Zhu, X. , Skogerbø, G. , Zhao, Y. , Fu, Z. , Wang, Y. , He, H. , Cai, L. , Sun, H. , Liu, C. , et al. ( 2006 ) Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic...
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Method: RIP-chip-SRM—a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans
- Marko Jovanovic,
- Lukas Reiter,
- Alejandra Clark,
- Manuel Weiss,
- Paola Picotti,
- Hubert Rehrauer,
- Andreas Frei,
- Lukas J. Neukomm,
- Ethan Kaufman,
- Bernd Wollscheid,
- Martin J. Simard,
- Eric A. Miska,
- Ruedi Aebersold,
- André P. Gerber,
- and Michael O. Hengartner
Genome Res. July 2012 22: 1360-1371; Published in Advance March 27, 2012, doi:10.1101/gr.133330.111
...-confidence miRNA targets in the nematode Caenorhabditis elegans . We used differential RIP-chip analysis of miRNA-induced silencing complexes from wild-type and miRNA mutant animals, followed by quantitative targeted proteomics via selected reaction monitoring to identify and validate mRNA targets of the C...
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Method: Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
- Zhi John Lu,
- Kevin Y. Yip,
- Guilin Wang,
- Chong Shou,
- LaDeana W. Hillier,
- Ekta Khurana,
- Ashish Agarwal,
- Raymond Auerbach,
- Joel Rozowsky,
- Chao Cheng,
- Masaomi Kato,
- David M. Miller,
- Frank Slack,
- Michael Snyder,
- Robert H. Waterston,
- Valerie Reinke,
- and Mark B. Gerstein
Genome Res. February 2011 21: 276-285; Published in Advance December 22, 2010, doi:10.1101/gr.110189.110
...characterization of the candidates. Results Single features and feature pairs only partially separate different types of annotated genomic elements We gathered a large compendium of sequence, structure, and expression features of C. elegans that could potentially identify ncRNAs. The expression features were...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...genes in the model organism Caenorhabditis elegans. Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.Nematodes are one of the most diverse, abundant, and widespread metazoan phylum on earth...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...unprecedented resolution to study the transcriptome. The technique has provided new insights into the features of the transcripts expressed in several eukaryotic species, including human, C. elegans, and Arabidopsis (Workman et al. 2019; Li et al. 2020; Roach et al. 2020; Zhang et al. 2020). Here we applied d...
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Research: Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles
- Jianbin Wang,
- Benjamin Czech,
- Amanda Crunk,
- Adam Wallace,
- Makedonka Mitreva,
- Gregory J. Hannon,
- and Richard E. Davis
Genome Res. September 2011 21: 1462-1477; Published in Advance June 17, 2011, doi:10.1101/gr.121426.111
...development. Heatmap expression profiles represent normalized mature miRNA read numbers. Wang et al. 1468 Genome Research www..org Ascaris As.26G RNAs are specifically expressed in testis (Figs. 2G,H and 5C,F). These RNAs have features similar to C. elegans Class I 26G-RNAs that are involved...

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