Searching journal content for articles similar to Denoeud et al. 17 (6): 746.

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  1. 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
    ...of transcriptional regulation whereby approximately 200 mammalian genes are expressed monoallelically according to their parental origin. This crucial developmental process is primarily controlled by discrete cis-regulatory elements known as imprinting control regions (ICRs), which play essential roles in directing...
  2. Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
    • Wiesław Babik,
    • Katarzyna Dudek,
    • Gemma Palomar,
    • Marzena Marszałek,
    • Grzegorz Dubin,
    • Maximina H. Yun,
    • and Magdalena Migalska
    Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
    ...is encoded by a separate exon (indicated as “ex” with the exon number inside the box). The remaining regions—including the transmembrane domain and cytosolic tail—are encoded by a variable number of exons (black boxes), typically ranging from one to four, depending on the molecule type.There are both...
  3. 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
    ...by the coding region (exons and introns); and ending with a terminator and polyadenylation signals that ensure proper transcript processing and stability. Before we can determine proteins that directly regulate GOI expression, we must identify the regulatory DNA sequences relevant to the GOI such as its...
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  4. Research: The human genome contains over a million autonomous exons
    • Nicholas Stepankiw,
    • Ally W.H. Yang,
    • and Timothy R. Hughes
    Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
    ...in length are cloned into the middle of the sixth intron from TRA2B (black boxes), in a pcDNA 3.1 vector backbone. First and terminal exons (gray boxes) are labeled with the transcriptional start site (TSS), start codon (ATG), stop codon (Stop), and the cleavage and polyadenylation site (CPA). Internal...
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  5. Resource: Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types
    • Jill E. Moore,
    • Xiao-Ou Zhang,
    • Shaimae I. Elhajjajy,
    • Kaili Fan,
    • Henry E. Pratt,
    • Fairlie Reese,
    • Ali Mortazavi,
    • and Zhiping Weng
    Genome Res. February 2022 32: 389-402; Published in Advance December 23, 2021, doi:10.1101/gr.275723.121
    ...% of K562 and GM12878 RAMPAGE rPeaks were not supported by one of the other assays (N = 301 and 212, respectively). These peaks had the lowest RAMPAGE signals and were more likely to overlap exons, introns, and intergenic regions (Fig. 2F,G; Supplemental Fig. S3D,E). These weaker transcription sites...
  6. Research: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
    • Wenli Xu,
    • Chang Liu,
    • Bing Deng,
    • Penghui Lin,
    • Zhenghua Sun,
    • Anrui Liu,
    • Jiajia Xuan,
    • Yuying Li,
    • Keren Zhou,
    • Xiaoqin Zhang,
    • Qiaojuan Huang,
    • Hui Zhou,
    • Qingyu He,
    • Bin Li,
    • Lianghu Qu,
    • and Jianhua Yang
    Genome Res. June 2022 32: 1026-1041; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
    ...still remains largely unclear.Although the definition of a lncRNA is an RNA transcript that does not encode a protein (Eddy 2001, 2002), recent studies have shown that a small subset of short open reading frames (sORFs) located on lncRNAs are actually activated in human cells (Slavoff et al. 2013; Ma et...
  7. Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
    • Terence Gall-Duncan,
    • Nozomu Sato,
    • Ryan K.C. Yuen,
    • and Christopher E. Pearson
    Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
    ...; also known as Baratela-Scott syndrome) and glutaminase deficiency (GD), expansions of GC-rich TR sequences in the promoter regions cause pathogenic transcriptional suppression (LaCroix et al. 2019; van Kuilenburg et al. 2019). Further exploration of suspected loss-of-function mechanisms may therefore...
  8. Resource: The transcription start site landscape of C. elegans
    • Taro Leo Saito,
    • Shin-ichi Hashimoto,
    • Sam Guoping Gu,
    • J. Jason Morton,
    • Michael Stadler,
    • Thomas Blumenthal,
    • Andrew Fire,
    • and Shinichi Morishita
    Genome Res. August 2013 23: 1348-1361; Published in Advance May 1, 2013, doi:10.1101/gr.151571.112
    ...the term ‘‘outron’’ (Blumenthal 2005) indicative of the sequence between the natural transcription start site and spliced leader attachment site of a relevant gene (Blumenthal 2005). We defined exon-TSSs as candidate TSSs with an annotated coding region with no SL1 transsplice sites that were not also...
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  9. Research: RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts
    • Yang I. Li,
    • Luis Sanchez-Pulido,
    • Wilfried Haerty,
    • and Chris P. Ponting
    Genome Res. January 2015 25: 1-13; Published in Advance December 18, 2014, doi:10.1101/gr.181990.114
    ...sharply as their sizes decrease below 100 nt (Fig. 1B).View larger version: In this window In a new window Figure 1. Identification of novel micro-exons. (A) Flowchart of our micro-exon discovery pipeline. Ensembl release 70 annotation was first used to build all cDNA transcripts on which RNA-seq reads...
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  10. Perspective: What does our genome encode?
    • John A. Stamatoyannopoulos
    Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
    ...everything from alternative transcriptional start sites to antisense transcripts, and it has anchored and empowered numerous integrative analyses. Indeed, the GENCODE annotation is used in some form by every ENCODE paper in this issue, and those contemporaneously published in other journals. Intensive...
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