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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...decreases with genomic distance: Genes positioned at the periphery of the clusters more frequently exhibit biased expression toward one of the two parental alleles, rather than strictly monoallelic expression (Perez et al. 2015).Histone modifications, cis-spatial organization, long noncoding RNAs (lncRNAs...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
...al. 2022; Kong et al. 2023). Many sequencing-based approaches, using short- or long-read sequencing platforms, map RNA modifications across the transcriptome, revealing their patterns in normal and disease states across various cell types, tissues, organisms, and under different environmental...
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Method: Leveraging protein language models for accurate multiple sequence alignments
- Claire D. McWhite,
- Isabel Armour-Garb,
- and Mona Singh
Genome Res. July 2023 33: 1145-1153; Published in Advance July 6, 2023, doi:10.1101/gr.277675.123
...:10.1007/s00439-021-02411-y ↵Mirarab S, Nguyen N, Guo S, Wang L-S, Kim J, Warnow T. 2015. PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. J Comput Biol 22: 377–386. doi:10.1089/cmb.2014.0156 ↵Miyata T, Yasunaga T. 1980. Molecular evolution of mRNA: a method...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...by integrating RNA-seq and rare SVs genomic annotations. Notably, while STRVCTVRE (Sharo et al. 2022), CADD-SV (Kleinert and Kircher 2022), and PhenoSV (Xu et al. 2023) can prioritize putative pathogenic SVs, STRVCTRVE only scores coding SVs, CADD-SV do not explicitly identify the affected gene and is trained...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...and Ence 2012). Evidence-based annotation or evidence alignment methods use experimental data, such as RNA-seq, protein sequences, or expressed sequence tags (ESTs) from the organism of interest or related species, which are mapped to the to identify genes (Yandell and Ence 2012; Jung et al. 2020...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...closer toward meeting this fundamental goal (Linnarsson and Teichmann 2016). As single-cell RNA-sequencing (scRNA-seq) has been adopted earliest by the scientific community, its use has now become widespread and the technology has improved rapidly. At present, it is now common for laboratories to assay...
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Method: A universal framework for detecting cis-regulatory diversity in DNA regions
- Anushua Biswas and
- Leelavati Narlikar
Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
...resulted in a little over 9000 sequences (Fig. 6C). In spite of very few sequences overlapping between the STARR-seq regions and the eRNAs or EP300-bound regions (Supplemental Fig. S12), many motifs are common between the three sets. Only YY1 is discovered additionally in the STARR-seq regions (module 4...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...Project (https://www.encodeproject.org) for the alignment and only the unique mapped reads were kept for further analysis. The parameter “- -outWigType bedGraph” from STAR was used to generate files of the RNA-seq coverage in the bedGraph format, in which the coverage at each genomic locus was normalized...
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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
...of biochemical signatures that could be exploited on a genomic scale across multiple cell types (The ENCODE Project Consortium 2007; Heintzman et al. 2007; Mikkelsen et al. 2007). In a similar vein, RNA transcripts were increasingly used to annotate both sites of transcript origination (both coding and noncoding...
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