Searching journal content for articles similar to Nikolaev et al. 19 (8): 1471.

Displaying results 1-10 of 247
For checked items
  1. Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
    • Shruthi Rengarajan,
    • Jason Derks,
    • Daniel W. Bellott,
    • Nikolai Slavov,
    • and David C. Page
    Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
    ...dosage sensitive. Studying cells of individuals with sex chromosome aneuploidy, we observe that when the number of Y Chromosomes increases, DDX3X transcript levels fall; conversely, when the number of X Chromosomes increases, DDX3Y transcript levels fall. In 46,XY cells, CRISPRi knockdown of either DDX3X...
    OPEN ACCESS ARTICLE
  2. Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
    • Kevin Moyung,
    • Yulong Li,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
    ...-based transcriptional regulatory networks. Overall, these results illustrate the power of an approach combining genetic perturbation with high-resolution epigenomic profiling; the latter enables a close examination of the interplay between TFs and nucleosomes -wide, providing a deeper, more mechanistic understanding...
  3. Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
    • Tim R. Mercer,
    • Marcel E. Dinger,
    • Cameron P. Bracken,
    • Gabriel Kolle,
    • Jan M. Szubert,
    • Darren J. Korbie,
    • Marjan E. Askarian-Amiri,
    • Brooke B. Gardiner,
    • Gregory J. Goodall,
    • Sean M. Grimmond,
    • and John S. Mattick
    Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
    ...Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome Tim R. Mercer 1 , 4 , Marcel E. Dinger 1 , 4 , Cameron P. Bracken 2 , 3 , Gabriel Kolle 1 , Jan M. Szubert 2 , Darren J. Korbie 1...
  4. Research: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity
    • Stacia K. Wyman,
    • Emily C. Knouf,
    • Rachael K. Parkin,
    • Brian R. Fritz,
    • Daniel W. Lin,
    • Lucas M. Dennis,
    • Michael A. Krouse,
    • Philippa J. Webster,
    • and Muneesh Tewari
    Genome Res. September 2011 21: 1450-1461; Published in Advance August 3, 2011, doi:10.1101/gr.118059.110
    ...suggest multiple enzymes affect the post-transcriptional modification of miRNAs by 39 NTA. To validate the accuracy of the assays in Figure 7B, we tested the ability of our adapted nCounter miRNA variant profiling assay Figure 5. Development of the nCounter miRNA assay to detect miRNA 39 variants. (A...
  5. Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
    • Alexandra Dallaire,
    • Bethan F. Manley,
    • Maya Wilkens,
    • Iliana Bista,
    • Clement Quan,
    • Edouard Evangelisti,
    • Charles R. Bradshaw,
    • Navin B. Ramakrishna,
    • Sebastian Schornack,
    • Falk Butter,
    • Uta Paszkowski,
    • and Eric A. Miska
    Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
    ...Fig. S1A), we hypothesized that repetitiveness may correlate with transcriptional silencing by DNA methylation. We profiled mCG levels in gene bodies and observed that, although the majority of genes displayed very low mCG levels, 18% of all R. irregularis genes are highly methylated (Fig. 3A...
    OPEN ACCESS ARTICLE
  6. Resource: A limited set of transcriptional programs define major cell types
    • Alessandra Breschi,
    • Manuel Muñoz-Aguirre,
    • Valentin Wucher,
    • Carrie A. Davis,
    • Diego Garrido-Martín,
    • Sarah Djebali,
    • Jesse Gillis,
    • Dmitri D. Pervouchine,
    • Anna Vlasova,
    • Alexander Dobin,
    • Chris Zaleski,
    • Jorg Drenkow,
    • Cassidy Danyko,
    • Alexandra Scavelli,
    • Ferran Reverter,
    • Michael P. Snyder,
    • Thomas R. Gingeras,
    • and Roderic Guigó
    Genome Res. July 2020 30: 1047-1059; Published in Advance July 29, 2020, doi:10.1101/gr.263186.120
    ...that departures from the normal cellular composition correlate with histological phenotypes associated with disease.Transcriptional profiles reflect cell type, condition, and function. In tissues and organs, they are monitored in RNA extracted from millions to billions of cells (116–109) (Haque et al. 2017...
    OPEN ACCESS ARTICLE
  7. 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
    ..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
    OPEN ACCESS ARTICLE
  8. Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
    • Sahin Naqvi,
    • Daniel W. Bellott,
    • Kathy S. Lin,
    • and David C. Page
    Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
    ...and avian sex chromosomes and reveal an important role for post-transcriptional regulatory sequences (miRNA target sites) in sex chromosome evolution.The mammalian X and Y Chromosomes evolved from a pair of ordinary autosomes over the past 300 myr (Lahn and Page 1999). Only 3% of genes on the ancestral pair...
    OPEN ACCESS ARTICLE
  9. Method: Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum
    • Heather J. Painter,
    • Manuela Carrasquilla,
    • and Manuel Llinás
    Genome Res. June 2017 27: 1074-1086; Published in Advance April 17, 2017, doi:10.1101/gr.217356.116
    ...(Lelli et al. 2012). Similarly, Plasmodium differentiation and growth within various cell types and hosts involves complex regulatory mechanisms that govern both transcriptional and post-transcriptional processes (Hughes et al. 2010; Cui et al. 2015; Vembar et al. 2016). Development during the IDC...
  10. Research: Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol
    • Noah Dukler,
    • Gregory T. Booth,
    • Yi-Fei Huang,
    • Nathaniel Tippens,
    • Colin T. Waters,
    • Charles G. Danko,
    • John T. Lis,
    • and Adam Siepel
    Genome Res. November 2017 27: 1816-1829; Published in Advance October 12, 2017, doi:10.1101/gr.222935.117
    ...are fundamentally limited in temporal resolution owing to the substantial lag between changes in transcriptional activity and detectable changes in the level of mRNAs. This lag results in part from the time required for transcription and post-transcriptional processing, and in part because pre-existing mRNAs buffer...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research