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Method: Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms
- Kerstin C. Maier,
- Saskia Gressel,
- Patrick Cramer,
- and Björn Schwalb
Genome Res. September 2020 30: 1332-1344; Published in Advance September 4, 2020, doi:10.1101/gr.257857.119
...(A)-tailed using the Escherichia coli Poly(A) Polymerase (NEB). The reaction was incubated for 5 min and stopped with 0.1 M EDTA. Poly(A)-tailed synthetic RNA pools were then purified with phenol:chloroform:isoamyl alcohol and precipitated. Purified poly(A)-tailed synthetic RNA pools were subsequently subjected...
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Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
- Isabel X. Wang,
- Christopher Grunseich,
- Youree G. Chung,
- Hojoong Kwak,
- Girish Ramrattan,
- Zhengwei Zhu,
- and Vivian G. Cheung
Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
...RNA chains ∼55 nt from the RNA Polymerase II active site (Wang et al. 2014). Because RDDs are found so soon after transcription, we posited that R-loops that often occur outside of the polymerase complex may be involved in RDD formation. Results from studying human cells with a gain...
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LETTER: A Microarray-Based Antibiotic Screen Identifies a Regulatory Role for Supercoiling in the Osmotic Stress Response of Escherichia coli
- Kevin J. Cheung,
- Vasudeo Badarinarayana,
- Douglas W. Selinger,
- Daniel Janse,
- and George M. Church
Genome Res. February 1, 2003 13: 206-215; Published in Advance January 14, 2003, doi:10.1101/gr.401003
...-induced transcription. RESULTS Microarray Studies of Genome-Wide E. coli Transcription in Response to Salt and a Panel of Microbial Antibiotics We examined whole- mRNA expression in E. coli MG1655 ( Blattner et al. 1997 ) following exposure to five different conditions: novobiocin, high salt, novobiocin plus salt...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...techniques have been developed that monitor transcription as it occurs. Pioneering work introduced methods such as global run-on sequencing (GRO-seq) (Core and Lis 2008) and precision nuclear run-on sequencing (PRO-seq) (Kwak et al. 2013), which measure the location and activity of engaged RNA polymerase II...
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Resource: Structural and operational complexity of the Geobacter sulfurreducens genome
- Yu Qiu,
- Byung-Kwan Cho,
- Young Seoub Park,
- Derek Lovley,
- Bernhard Ø. Palsson,
- and Karsten Zengler
Genome Res. September 2010 20: 1304-1311; Published in Advance June 30, 2010, doi:10.1101/gr.107540.110
.... Emergent properties of reduced- Escherichia coli. Science 312: 1044–1046. Rasmussen S, Nielsen HB, Jarmer H. 2009. The transcriptionally active regions in the of Bacillus subtilis. Mol Microbiol 73: 1043– 1057. Selinger DW, Saxena RM, Cheung KJ, ChurchGM, RosenowC. 2003. Global RNA half-life analysis...
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Method: CodonBERT large language model for mRNA vaccines
- Sizhen Li,
- Saeed Moayedpour,
- Ruijiang Li,
- Michael Bailey,
- Saleh Riahi,
- Lorenzo Kogler-Anele,
- Milad Miladi,
- Jacob Miner,
- Fabien Pertuy,
- Dinghai Zheng,
- Jun Wang,
- Akshay Balsubramani,
- Khang Tran,
- Minnie Zacharia,
- Monica Wu,
- Xiaobo Gu,
- Ryan Clinton,
- Carla Asquith,
- Joseph Skaleski,
- Lianne Boeglin,
- Sudha Chivukula,
- Anusha Dias,
- Tod Strugnell,
- Fernando Ulloa Montoya,
- Vikram Agarwal,
- Ziv Bar-Joseph,
- and Sven Jager
Genome Res. July 2024 34: 1027-1035; Published in Advance July 1, 2024, doi:10.1101/gr.278870.123
..., and Tc-riboswitch data sets are strongly affected by local and global secondary structure patterns encoded on top of RNA sequences. Although CodonBERT is a codon-based model, it outperforms RNABERT and RNA-FM, which were demonstrated to capture rich structural information from large-scale noncoding RNAs...
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Methods: Genome-wide identification of spliced introns using a tiling microarray
- Zhihong Zhang,
- Jay R. Hesselberth,
- and Stanley Fields
Genome Res. April 2007 17: 503-509; Published in Advance March 9, 2007, doi:10.1101/gr.6049107
...transcripts are processed by the spliceosome to remove introns, which are released as lariats. Lariat RNAs must be subsequently debranched prior to their turnover by cellular exonucleases ( Fig. 1A ). In wild-type cells, the half-life of lariats is short; however, in yeast cells that lack the debranching RNA...
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Research: Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons
- William Gao,
- Carlos J. Gallardo-Dodd,
- and Claudia Kutter
Genome Res. January 2022 32: 97-110; Published in Advance December 2, 2021, doi:10.1101/gr.275944.121
...the stability of tRNA transcripts, and hypomodified tRNA molecules are rapidly degraded (Kimura and Waldor 2019). Thus, absence of the m2,2G26 modification upon the deletion of TRM1L may reduce tRNAAla (AGC) pools in neurons and impact the rate of translation elongation. Future systematic studies may explore...
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Method: Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA
- Romualdas Vaisvila,
- V.K. Chaithanya Ponnaluri,
- Zhiyi Sun,
- Bradley W. Langhorst,
- Lana Saleh,
- Shengxi Guan,
- Nan Dai,
- Matthew A. Campbell,
- Brittany S. Sexton,
- Katherine Marks,
- Mala Samaranayake,
- James C. Samuelson,
- Heidi E. Church,
- Esta Tamanaha,
- Ivan R. Corrêa, Jr.,
- Sriharsa Pradhan,
- Eileen T. Dimalanta,
- Thomas C. Evans, Jr.,
- Louise Williams,
- and Theodore B. Davis
Genome Res. July 2021 31: 1280-1289; Published in Advance June 17, 2021, doi:10.1101/gr.266551.120
...the QIAamp Circulating Nucleic Acid Kit (Qiagen). pUC19 was extracted from dam-/dcm- Escherichia coli cells using the Monarch Plasmid Miniprep Kit (NEB), and then 10 µg of pUC19 was CpG methylated in vitro using 40 U of M.SssI (NEB) in a 200-µL final reaction volume for 2 h at 37°C. DNA was isolated using...
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Methods: Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
- Nitin Gupta,
- Stephen Tanner,
- Navdeep Jaitly,
- Joshua N. Adkins,
- Mary Lipton,
- Robert Edwards,
- Margaret Romine,
- Andrei Osterman,
- Vineet Bafna,
- Richard D. Smith,
- and Pavel A. Pevzner
Genome Res. September 2007 17: 1362-1377; Published in Advance August 9, 2007, doi:10.1101/gr.6427907
...predictions were 100% accurate, they would still provide incorrect protein sequences for ∼50% of bacterial genes! It is estimated that a single post-translational modification (N-terminal methionine cleavage, or NME) alters roughly half of proteins in Escherichia coli . NME is the process of cleaving N...

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