Searching journal content for articles similar to Makałowski et al. 6 (9): 846.

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  1. Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
    • Wenyu Zhang,
    • Anja Guenther,
    • Yuanxiao Gao,
    • Kristian Ullrich,
    • Bruno Huettel,
    • Aftab Ahmad,
    • Lei Duan,
    • Kaizong Wei,
    • and Diethard Tautz
    Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
    ...with hallmarks of both, a 5′ CAP and a poly(A) tail. It has been reported that the TeloPrime Full-Length cDNA Amplification Kit could selectively synthesize cDNA molecules from mRNAs carrying a 5′ CAP, in complement to the standard PacBio cDNA library preparation protocol that could only selectively synthesize c...
  2. Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
    • Rodrigo P. Baptista,
    • Yiran Li,
    • Adam Sateriale,
    • Mandy J. Sanders,
    • Karen L. Brooks,
    • Alan Tracey,
    • Brendan R.E. Ansell,
    • Aaron R. Jex,
    • Garrett W. Cooper,
    • Ethan D. Smith,
    • Rui Xiao,
    • Jennifer E. Dumaine,
    • Peter Georgeson,
    • Bernard J. Pope,
    • Matthew Berriman,
    • Boris Striepen,
    • James A. Cotton,
    • and Jessica C. Kissinger
    Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
    ...IRef, resulting in improved functional annotation. These changes increase the overall number of predicted genes, introns (100% supported by RNA-seq data), and exons (Table 2; Supplemental Results). The average mRNA length increased. These structural fixes led to the repair of the N terminus of the methylase...
    OPEN ACCESS ARTICLE
  3. ARTICLE: Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection
    • Koji Numata,
    • Akio Kanai,
    • Rintaro Saito,
    • Shinji Kondo,
    • Jun Adachi,
    • Laurens G. Wilming,
    • David A. Hume,
    • RIKEN GER Group,
    • GSL Members,
    • Yoshihide Hayashizaki,
    • and Masaru Tomita
    Genome Res. June 2003 13: 1301-1306; doi:10.1101/gr.1011603
    ...units, are processed like typical protein-coding mRNAs and are increasingly implicated in regulation of many cellular functions in eukaryotes. This study describes the identification of candidate functional ncRNAs from among the RIKEN mouse full-length cDNA collection, which contains 60,770 sequences...
  4. RESOURCE: Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS
    • Takeshi Nagashima,
    • Diego G. Silva,
    • Nikolai Petrovsky,
    • Luis A. Socha,
    • Harukazu Suzuki,
    • Rintaro Saito,
    • Takeya Kasukawa,
    • Igor V. Kurochkin,
    • Akihiko Konagaya,
    • and Christian Schönbach
    Genome Res. June 2003 13: 1520-1533; doi:10.1101/gr.1019903
    ...Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS Takeshi Nagashima 1 , 2 , Diego G. Silva 3 , 4 , Nikolai Petrovsky 3 , 4 , Luis A. Socha 3 , 4 , Harukazu Suzuki 5 , Rintaro Saito 5...
  5. Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
    • Daniel Siqueira de Oliveira,
    • Anaïs Larue,
    • William Vilas Boas Nunes,
    • Francois Sabot,
    • Alejandra Bodelón,
    • María Pilar García Guerreiro,
    • Cristina Vieira,
    • and Claudia Marcia Aparecida Carareto
    Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
    ...). This result indicates that almost all genes producing chimeras are dependent on the TE sequence to constitute their complete mRNA sequence. Because ∼88% of all chimeras detected with >25% contribution are from TE-exonized transcripts, for which 72.35% are from TEs embedded in exons, a high frequency...
  6. RESOURCE: Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling
    • Ryan D. Morin,
    • Elbert Chang,
    • Anca Petrescu,
    • Nancy Liao,
    • Malachi Griffith,
    • Robert Kirkpatrick,
    • Yaron S. Butterfield,
    • Alice C. Young,
    • Jeffrey Stott,
    • Sarah Barber,
    • Ryan Babakaiff,
    • Mark C. Dickson,
    • Corey Matsuo,
    • David Wong,
    • George S. Yang,
    • Duane E. Smailus,
    • Keith D. Wetherby,
    • Peggy N. Kwong,
    • Jane Grimwood,
    • Charles P. Brinkley III,
    • Mabel Brown-John,
    • Natalie D. Reddix-Dugue,
    • Michael Mayo,
    • Jeremy Schmutz,
    • Jaclyn Beland,
    • Morgan Park,
    • Susan Gibson,
    • Teika Olson,
    • Gerard G. Bouffard,
    • Miranda Tsai,
    • Ruth Featherstone,
    • Steve Chand,
    • Asim S. Siddiqui,
    • Wonhee Jang,
    • Ed Lee,
    • Steven L. Klein,
    • Robert W. Blakesley,
    • Barry R. Zeeberg,
    • Sudarshan Narasimhan,
    • John N. Weinstein,
    • Christa Prange Pennacchio,
    • Richard M. Myers,
    • Eric D. Green,
    • Lukas Wagner,
    • Daniela S. Gerhard,
    • Marco A. Marra,
    • Steven J.M. Jones,
    • and Robert A. Holt
    Genome Res. June 2006 16: 796-803; Published in Advance May 3, 2006, doi:10.1101/gr.4871006
    ...Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling 10,967 full-length cDNA clones from Xenopus Ryan D. Morin 1 , Elbert Chang 1 , Anca Petrescu 1...
  7. RESOURCE: The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC) Genome Res. October 15, 2004 14: 2121-2127; doi:10.1101/gr.2596504
    ...The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC) The MGC Project Team 1 , 2 Abstract The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly...
  8. Research: Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome
    • Sara González,
    • Alicia García,
    • Enrique Vázquez,
    • Rebeca Serrano,
    • Mar Sánchez,
    • Luis Quintales,
    • and Francisco Antequera
    Genome Res. November 2016 26: 1532-1543; Published in Advance September 23, 2016, doi:10.1101/gr.207241.116
    .... These signatures are present -wide and, in the case ofORFs, the finding that swapping of synonymous wild-type codons disrupts the regular nucleosomal profile of the S. pombe ura4 gene (Fig. 1, Shuffled; Supplemental Fig. S4) suggests the intriguing possibility that, in addition to modulating the stability of mRNA...
    OPEN ACCESS ARTICLE
  9. Research: Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis
    • Hai-Xi Sun,
    • Yan Li,
    • Qi-Wen Niu,
    • and Nam-Hai Chua
    Genome Res. August 2017 27: 1427-1436; Published in Advance May 18, 2017, doi:10.1101/gr.218669.116
    .... 2010). Alternative cleavage and polyadenylation (APA) generates mRNAs with different 3′ UTR sequences, and it is widespread in plants and animals. About 70% of mRNAs contain more than one poly(A) site in human (Derti et al. 2012), mouse (Hoque et al. 2013), and Arabidopsis (Wu et al. 2011). The 3′ UTR...
  10. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
    • Yuange Duan,
    • Min Huang,
    • Lin Ye,
    • Ling Ma,
    • Yashuai Wu,
    • Yating Du,
    • Jiyao Liu,
    • Fan Song,
    • Li Tian,
    • Wanzhi Cai,
    • Hu Li,
    • Xin Zhou,
    • and Shiqi Luo
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...in triplicate on the same plate, with a negative control using RNase-free water as the template. RACE of Adar gene in honeybee The full-length nucleotide sequence of Adar was amplified using the rapid-amplification of cDNA ends (RACE) technique with the HiScript-TS 5′/3′ RACE kit (Vazyme RA101). Gene...
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