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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...the many introns of a human gene are removed can substantially influence AS, while nascent RNA polyadenylation can affect RNA stability and decay. However, how splicing order and poly(A) tail length are regulated by genetic variation has never been explored. Here, we used direct RNA nanopore sequencing...
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Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...curated from our deep RNA-seq resource of hIPSCs (Supplemental Table S3).GET-RI transcripts are resistant to RNA decayAfter identifying a high-confidence list of GET-RI isoforms, we investigated if they would have other distinct features that could make them GETs. We first tested how RNA stability could...
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Research: RNA editing in nascent RNA affects pre-mRNA splicing
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Yun Yang,
- Xianzhi Lin,
- Stephen Tran,
- Ei-Wen Yang,
- Giovanni Quinones-Valdez,
- and Xinshu Xiao
Genome Res. June 2018 28: 812-823; Published in Advance May 3, 2018, doi:10.1101/gr.231209.117
...in understanding their global RNA targets and regulatory pathways. However, the interplay between individual steps of RNA processing, an essential aspect of gene regulation, remains poorly understood. By sequencing the RNA of different subcellular fractions, we examined the timing of adenosine-to-inosine (A...
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Resource: Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
- Kyu-Hyeon Yeom,
- Zhicheng Pan,
- Chia-Ho Lin,
- Han Young Lim,
- Wen Xiao,
- Yi Xing,
- and Douglas L. Black
Genome Res. June 2021 31: 1106-1119; Published in Advance April 8, 2021, doi:10.1101/gr.273904.120
...with expression of mature cytoplasmic mRNA.ResultsBoth coding and noncoding RNAs show defined partitioning between cellular compartmentsTo broadly categorize RNAs enriched in different cellular locations and to gain insight into how this compartmentalization might be regulated across cell types, we generated deep...
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Method: Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome
- Hagen Tilgner,
- Fereshteh Jahanbani,
- Ishaan Gupta,
- Paul Collier,
- Eric Wei,
- Morten Rasmussen,
- and Michael Snyder
Genome Res. February 2018 28: 231-242; Published in Advance December 1, 2017, doi:10.1101/gr.230516.117
...ranges of expression (Supplemental Fig. S1B). It is therefore possible to produce high quality RNA-seq data with inputs as low as 125 pg using the GemCode system.Gene detection using deep isoform sequencingWe generated 2.01 billion paired-end 151-bp read-pairs (seven Illumina HiSeq lanes) from the 125-pg...
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Research: Long-read sequencing of nascent RNA reveals coupling among RNA processing events
- Lydia Herzel,
- Korinna Straube,
- and Karla M. Neugebauer
Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
...activity. (A) Schematic of nascent RNA (nRNA) purification from chromatin for short- (RNA-seq) and long-read RNA sequencing (LRS). (B) Enrichment of genomic DNA (DNA) and nRNA in the chromatin fraction and depletion of rRNA (18S and 28S) and tRNA revealed by gel electrophoresis and staining with Gel...
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Research: Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
- Marta Melé,
- Kaia Mattioli,
- William Mallard,
- David M. Shechner,
- Chiara Gerhardinger,
- and John L. Rinn
Genome Res. January 2017 27: 27-37; Published in Advance December 7, 2016, doi:10.1101/gr.214205.116
...Genome Research 29 www..org lincRNAs were less efficiently spliced than control mRNAs (Supplemental Fig. S19). This would suggest that inefficient splicing might be a common feature of lincRNAs across species. Last, we sought to determine if there might be sequence features that could account...
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Commentary: Decoding the human genome
- Kelly A. Frazer
Genome Res. September 2012 22: 1599-1601; doi:10.1101/gr.146175.112
..., Guigo´ R. 2012. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly cotranscriptional in the human but inefficient for lncRNAs. Genome Res (this issue). doi: 10.1101/gr.134445.111. Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA...
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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
...recent reports detailing deep probing of the RNA world (Mercer et al. 2011) affirm the centrality of the transcript in genomic organization, while highlighting both the opportunity and the daunting challenge of comprehensive transcriptome annotation. The chromatin–transcription continuum The interplay...
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Perspective: Toward mapping the biology of the genome
- Stephen Chanock
Genome Res. September 2012 22: 1612-1615; doi:10.1101/gr.144980.112
..., Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigo´ R. 2012. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly cotranscriptional in the human but inefficient for lncRNAs. Genome Res (this issue). doi: 10.1101/gr.134445.111. Verlaan DJ...
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