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Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
- Tim R. Mercer,
- Marcel E. Dinger,
- Cameron P. Bracken,
- Gabriel Kolle,
- Jan M. Szubert,
- Darren J. Korbie,
- Marjan E. Askarian-Amiri,
- Brooke B. Gardiner,
- Gregory J. Goodall,
- Sean M. Grimmond,
- and John S. Mattick
Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
...transcripts are simply transitional intermediates in the degradation and recycling ofmRNA, but could rather represent functional products generated from longer parental transcripts. Here, we show that post-transcriptional cleavage events are widespread, conserved among eukaryotes, and generate a range...
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Research: Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
- Chan-Shuo Wu,
- Chun-Ying Yu,
- Ching-Yu Chuang,
- Michael Hsiao,
- Cheng-Fu Kao,
- Hung-Chih Kuo,
- and Trees-Juen Chuang
Genome Res. January 2014 24: 25-36; Published in Advance October 16, 2013, doi:10.1101/gr.159483.113
...equally to this work. Abstract Trans -splicing is a post-transcriptional event that joins exons from separate pre-mRNAs. Detection of trans -splicing is usually severely hampered by experimental artifacts and genetic rearrangements. Here, we develop a new computational pipeline, TSscan, which...
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LETTER: Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22
- Leonard Lipovich and
- Mary-Claire King
Genome Res. January 2006 16: 45-54; Published in Advance December 12, 2005, doi:10.1101/gr.3883606
...conservation and localized to gaps in the human–mouse BLASTZ alignment. Novel TUs were richer in exonic primate-specific interspersed repetitive elements ( P = 0.001) and were more likely to rely on splice junctions provided by them, than were known genes: 19% of spliced TUs, versus 5% of spliced genes, had...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...regions. We recently characterized the abundance of snoRNAs and their host gene across several healthy human tissues and found that the level of most snoRNAs does not correlate with that of their host gene, with the observation that snoRNAs embedded within the same host gene often differ drastically...
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Research: Frac-seq reveals isoform-specific recruitment to polyribosomes
- Timothy Sterne-Weiler,
- Rocio Teresa Martinez-Nunez,
- Jonathan M. Howard,
- Ivan Cvitovik,
- Sol Katzman,
- Muhammad A. Tariq,
- Nader Pourmand,
- and Jeremy R. Sanford
Genome Res. October 2013 23: 1615-1623; Published in Advance June 19, 2013, doi:10.1101/gr.148585.112
...(Frac-seq) to assay partitioning of mRNA isoforms between the cytosolic and the polyribosome-associated fractions. Our data shows that ;30% of alternative splicing events exhibit isoformspecific polyribosome association. The sequences encompassing these events are more evolutionarily conserved compared...
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Research: Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation
- Maria Warnefors,
- Katharina Mössinger,
- Jean Halbert,
- Tania Studer,
- John L. VandeBerg,
- Isa Lindgren,
- Amir Fallahshahroudi,
- Per Jensen,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1961-1973; Published in Advance October 27, 2017, doi:10.1101/gr.225391.117
...; Nothnick et al. 2010), suggesting an additional layer of post-transcriptional, sex-biased regulation.Taken together, previous studies suggest that sex-biased miRNA expression might be widespread and have potentially profound functional implications. Even so, previous efforts to identify sex-biased mi...
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LETTER: Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
- Andrew J. Gentles,
- Matthew J. Wakefield,
- Oleksiy Kohany,
- Wanjun Gu,
- Mark A. Batzer,
- David D. Pollock,
- and Jerzy Jurka
Genome Res. July 2007 17: 992-1004; Published in Advance May 10, 2007, doi:10.1101/gr.6070707
...localizing in previously identified evolutionarily conserved regions in vertebrate s ( Siepel et al. 2005 ). The conserved regions identified by Siepel et al. represent 4.75% of the human and encompass &gt;30% of all repeat insertions from the newly described families. The genomic copy numbers can vary...
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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
...RNA-like regions consistently map more smRNAs, and, if so, of what size? The question of size is important because it is thought that dsRNA degradation via Dicer feeds into post-transcriptional gene silencing (PTGS) pathways, which tends to rely on 21- and 22-nt smRNAs. In contrast, pathways that lead...
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Method: New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes
- Brian J. Parker,
- Ida Moltke,
- Adam Roth,
- Stefan Washietl,
- Jiayu Wen,
- Manolis Kellis,
- Ronald Breaker,
- and Jakob Skou Pedersen
Genome Res. November 2011 21: 1929-1943; Published in Advance October 12, 2011, doi:10.1101/gr.112516.110
...networks, including large families of short hairpins enriched in immunity-related genes, e.g., TNF , FOS , and CTLA4 , which include known transcript destabilizing elements. Our findings exemplify the diversity of post-transcriptional regulation and provide a resource for further characterization of new...
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Research: High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface
- Bianca M. Schmitt,
- Konrad L.M. Rudolph,
- Panagiota Karagianni,
- Nuno A. Fonseca,
- Robert J. White,
- Iannis Talianidis,
- Duncan T. Odom,
- John C. Marioni,
- and Claudia Kutter
Genome Res. November 2014 24: 1797-1807; Published in Advance August 13, 2014, doi:10.1101/gr.176784.114
..., this correlation may be higher if considering post-transcriptional modifications such as tRNAdependent adenosine deaminases (Novoa et al. 2012). This molecular equilibrium canprevent a potential bottleneckwhen tRNAs facilitate translation of mRNAs into proteins and hence ensures optimal translational efficiencies...
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