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Research: Widespread and extensive lengthening of 3′ UTRs in the mammalian brain
- Pedro Miura,
- Sol Shenker,
- Celia Andreu-Agullo,
- Jakub O. Westholm,
- and Eric C. Lai
Genome Res. May 2013 23: 812-825; Published in Advance March 21, 2013, doi:10.1101/gr.146886.112
.... Green arrowheads indicate predicted mRNA length of Ensembl v65 gene model. Red arrowheads indicate inferred mRNA lengths of novel 39 UTR extension isoforms. Asterisks denote background hybridization to ribosomal RNAs. 39 UTR lengthening in the mammalian brain Genome Research 815 www..org Several...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...assessments of protein-coding and transcriptome annotations separately. To add CDS annotations to StringTie and Scallop annotations, we used TransDecoder (https://github.com/TransDecoder/TransDecoder) to predict open reading frames (ORFs) and explicitly label features as CDS or UTR. Although there are other...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...challenging.We previously developed RiboPlotR to visualize Ribo-seq reads for all annotated isoforms of individual genes within their gene structures, including 5′ and 3′ untranslated regions (UTRs) and introns. It displays both RNA-seq coverage and Ribo-seq periodicity by color-coding reads from each reading...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...features that predict plant alternative translation initiation sites (TISs). (A) Illustration of the identified true-positive (TP; blue) and true-negative (TN; gray) TISs that were categorized based on the location of initiation codons (i.e., 5′ UTR, CDS, or 3′ UTR) and their sequences in a transcript...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...regions (UTRs) (Shabalina et al. 2010, 2014), prompt questions about the extent of AS contributions in diversifying the proteome.Existing approaches to analyze splicing and associated events have relied predominantly on pairwise comparisons of transcript architectures. For instance, the numeric symbolic...
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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
...moment, resulting in k-mer-specific ion current shifts. RNA modifications can cause further shifts in the ion currents. Methods for detecting these alterations can be divided into two categories: de novo prediction, and comparative approaches. De novo prediction methods, including Tombo (Stoiber et al...
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Methods: Predicting essential genes in fungal genomes
- Michael Seringhaus,
- Alberto Paccanaro,
- Anthony Borneman,
- Michael Snyder,
- and Mark Gerstein
Genome Res. September 2006 16: 1126-1135; Published in Advance August 9, 2006, doi:10.1101/gr.5144106
...for predicting essential genes. Methods Preparing fungal s for study We used the S. cerevisiae coding ORF list ( orf_coding.fasta.gz , revision 12/16/2004, available at ftp://-ftp.stanford.edu/pub/yeast/data_download/sequence/genomic_sequence/orf_dna/). This excludes 5′-UTR, 3′-UTR, intron sequences, and bases...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...). Transcripts are often specified for decay through the binding of RNA and protein factors to cis-regulatory elements within the 3′ untranslated region (UTR) (Ray et al. 2013; Vejnar et al. 2019). Cross talk between factors can lead to differential mRNA decay, such as RNA-binding proteins stabilizing...
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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
...immunoprecipitation (ChIP) in 1984 followed by ChIP-qPCR and ChIP-seq, which allowed scientists to probe the full palette of DNA molecules bound by proteins of interest. A ChIP experiment begins by using formaldehyde to chemically cross-link DNA and protein molecules (Das et al. 2004). Nuclei are isolated...
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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
..., but there are multiple other reasons why clusters contain only moderately similar or unrelated protein sequences. These include cases in which one coding sequence has been predicted within introns, within UTRs, or on a different frame from another gene model. In a few cases, the differences could be the result of true...
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