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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
..., Bruhm DC, Jensen SØ, Medina JE, Hruban C, White JR, et al. 2019. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature 570: 385–389. doi:10.1038/s41586-019-1272-6 ↵De Coster W, Weissensteiner MH, Sedlazeck FJ. 2021. Towards population-scale long-read sequencing. Nat Rev Genet 22: 572...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 46: 1311–1320. doi:10.1038/ng.3142 ↵Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, et al. 2006. Genome-wide mapping of DNase...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
...Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage Kavitha Uthanumallian1, Andrea Del Cortona2, Susana M. Coelho3, Olivier De Clerck2, Sebastian Duchene4,5 and Heroen Verbruggen1,6 1Melbourne Integrative Genomics, School of Bio...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
..., Isogai T, Suzuki Y, Akimitsu N. 2012. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res 22: 947–956. doi:10.1101/gr.130559.111 ↵Thomson DW, Bracken CP, Goodall GJ. 2011. Experimental strategies for microRNA target identification...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...regions and the stability of the Z-RNA sequences identified in this study will provide better understanding of Z-RNA formation in the noncoding transcriptome.In summary, we provide a comprehensive data set of predicted noncanonical secondary structures throughout the long noncoding transcriptome...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
..., revolutionizing the field of human genetics (Tam et al. 2019). Despite these successes, the interpretation of GWAS signals represents a challenging task as they are often located within noncoding regions of the and manifest as complex linkage disequilibrium (LD) blocks where identification of the causal variant...
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Research: Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- Yongbin Li,
- Xiao Liu,
- Peter Sarkies,
- and Zhongying Zhao
Genome Res. November/December 2022 32: 2015-2027; Published in Advance November 9, 2022, doi:10.1101/gr.277205.122
.... Misregulation of transposable elements, coding genes, and small regulatory RNAs was more widespread in the bB2 compared with the nB2 hybrids, which is a plausible explanation for the differential phenotypes between the two hybrids. Our results show that regulation of the C. briggsae is strongly affected...
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Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
- Jordan John,
- Javaid Jabbar,
- Nitika Badjatia,
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
...are enriched with YR nucleotides (IUPAC nomenclature), this determination was based on only 88 promoters (Hawley and McClure 1983). Genome-wide studies based on mapping RNA 5′ ends have found the YR motif to be enriched, with 79% of the +1 nucleotide being an R (Kim et al. 2012), whereas another study had R...
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Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
- Mattia Furlan,
- Eugenia Galeota,
- Nunzio Del Gaudio,
- Erik Dassi,
- Michele Caselle,
- Stefano de Pretis,
- and Mattia Pelizzola
Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
...transcripts, and, indeed, these were seen to be primarily controlled at the level of their stability, leading to a reduction in total RNA, whereas nontarget transcripts remained mostly unaffected (Fig. 5C).Altogether, these analyses illustrate how the quantification of RNA dynamics from total RNA-seq data...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...inhibitor JQ1 (Fig. 4). PRO-seq allows high-resolution mapping of active RNA polymerases across the at both coding and noncoding regions and provides information on both the abundance and directionality of transcripts. Analysis of the transcriptome in LBH589-treated ESCs revealed that the majority of genes...
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