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Method: Global mapping of RNA homodimers in living cells
- Marta M. Gabryelska,
- Andrew P. Badrock,
- Jian You Lau,
- Raymond T. O'Keefe,
- Yanick J. Crow,
- and Grzegorz Kudla
Genome Res. May 2022 32: 956-967; Published in Advance March 24, 2022, doi:10.1101/gr.275900.121
...of interacting fragments of RNA, which are then detected as chimeric reads by high-throughput sequencing. We reasoned that chimeras that represent intra- and intermolecular interactions can be distinguished from each other by an analysis of sequence overlap between the arms of each chimera.When an RNA molecule...
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Method: Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
- Minjie Zhang,
- Irena T. Hwang,
- Kongpan Li,
- Jianhui Bai,
- Jian-Fu Chen,
- Tsachy Weissman,
- James Y. Zou,
- and Zhipeng Lu
Genome Res. May 2022 32: 968-985; Published in Advance March 24, 2022, doi:10.1101/gr.275979.121
...the largest human protein titin. In particular, the XIST RNA contains many repetitive elements across the entire transcript, making it challenging to analyze. The simulated reads cover the full length of these three genes, including both exons and introns (Supplemental Fig. S1B). We focused on two...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...a transposase domain derived from an Hsmar1 insertion conserved in primates, providing functional DNA-binding to target methylation (Cordaux et al. 2006). Such exaptation and domestication events can often be identified by the occurrence of chimeric transcripts, which are mRNAs with both gene- and TE...
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Research: LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans
- Shengjun Tan,
- Margarida Cardoso-Moreira,
- Wenwen Shi,
- Dan Zhang,
- Jiawei Huang,
- Yanan Mao,
- Hangxing Jia,
- Yaqiong Zhang,
- Chunyan Chen,
- Yi Shao,
- Liang Leng,
- Zhonghua Liu,
- Xun Huang,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. December 2016 26: 1663-1675; Published in Advance October 20, 2016, doi:10.1101/gr.204925.116
...-seq experiments showed that three of four retrocopies are capable of transcription from the sense strand relative to the parental genes. Analogously, by taking advantage of public strand-specific RNA-seq data from mosquito, chicken, zebrafish, and mouse (Methods), we found that recently evolved retrocopies...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...short-read RNA-seq as a modularized software that contains chimeric read extraction, fusion transcripts identification, expression quantification, gene fusion annotation, and interactive visualization. To benchmark existing tools, we collected or generated comprehensive simulation data sets to reflect...
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Review: Origins, evolution, and phenotypic impact of new genes
- Henrik Kaessmann
Genome Res. October 2010 20: 1313-1326; Published in Advance July 22, 2010, doi:10.1101/gr.101386.109
...RNA genes, genomic parasites were coopted as new genes, and that both protein and RNA genes were composed from scratch (i.e., from previously nonfunctional sequences). These mechanisms then also contributed to the formation of numerous novel chimeric gene structures. Detailed functional investigations...
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Perspective: Functional transcriptomics in the post-ENCODE era
- Jonathan M. Mudge,
- Adam Frankish,
- and Jennifer Harrow
Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
...manifests, for example, as alternative splicing within protein-coding genes, as well as in the discovery of thousands of long noncoding RNAs. It is also possible that significant numbers of human transcripts have not yet been described by annotation projects, while existing transcript models are frequently...
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Perspective: What does our genome encode?
- John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
...et al. 2011), long-range splicing and chimeric transcripts (Djebali et al. 2012b; Frenkel-Morgenstern et al. 2012), promoter-associated small RNAs (Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project 2009), and the splicing–chromatin connection (Tilgner et al. 2009), among other...
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Method: TransRate: reference-free quality assessment of de novo transcriptome assemblies
- Richard Smith-Unna,
- Chris Boursnell,
- Rob Patro,
- Julian M. Hibberd,
- and Steven Kelly
Genome Res. August 2016 26: 1134-1144; Published in Advance June 1, 2016, doi:10.1101/gr.196469.115
...://www.yeast. org/. The transcripts were quantified and mRNA abundances recorded using Salmon, and the same set of reads used in the de novo assembly evaluation is described in “Analysis of assemblies generated from real reads.” To simulate transcript chimeras, 1000 transcripts were selected at random without...
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ENSEMBL Special: ESTGenes: Alternative Splicing From ESTs in Ensembl
- Eduardo Eyras,
- Mario Caccamo,
- Val Curwen,
- and Michele Clamp
Genome Res. May 2004 14: 976-987; doi:10.1101/gr.1862204
...and produce a minimal set of putative transcript variants that have nonequivalent splicing structure and are compatible with the EST evidence. The resulting transcripts produced from ESTs are the ESTGenes as shown in the Ensembl Web site ( www.ensembl.org ). The algorithm can be applied to ESTs, mRNAs...

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