Searching journal content for articles similar to Kakrana et al. 28 (9): 1333.

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Method: A versatile type VI CRISPR-based approach for targeted m⁶A demethylation in mRNAs
- Panagiotis G. Adamopoulos,
- Konstantina Athanasopoulou,
- and Andreas Scorilas
Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
...in various organisms, including fission yeast, plants, and mammalian cells (Abudayyeh et al. 2016; Gupta et al. 2022). Besides the identification of several Cas13 enzymes with different features, including Cas13b and Cas13d (CasRx), findings have also confirmed that specific mutations in Cas13 can produce...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...for phages destroyed by RecBCD in cells, we tested more than 125 sources for phages that could grow in the absence of RecBCD but not in its presence in cells (Zheng et al. 2024). These sources were the feces of warm-blooded animals (mammals and birds), ponds and streams visited by them, and sewage plant...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...and epigenetic structure for the observed accelerated rates of evolution within and between species, including the role of recombination.Monocentric satellite array architectureDiverse plant species display a monocentric architecture, with a single chromosome constriction observed at metaphase, which contains...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...is functionally negligible, having little to no effect on TF binding or downstream mRNA production (Hu et al. 2013; Pacis et al. 2015; Kribelbauer et al. 2020; Kreibich et al. 2023). In addition to many regions of the being functionally insensitive to methylation, others display DNAm-expression relationships...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
...assembly statistics for S. lycopersicum and Z. mays compared to existing reference sDiscussionHere, we have demonstrated the complete assembly of human and plant chromosomes using a single sequencing platform. The high accuracy of ONT Duplex data (exceeding 99.9%) makes it a suitable alternative to Pac...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...of neurobiology.One mechanism well described to generally contribute to signal-regulated alternative splicing is alterations in expression or function of RBPs that directly bind pre-mRNAs and direct the recognition or skipping of exons by the splicing machinery (Heyd and Lynch 2011; Fu and Ares 2014...
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Research: The predicted RNA-binding protein regulome of axonal mRNAs
- Raphaëlle Luisier,
- Catia Andreassi,
- Lisa Fournier,
- and Antonella Riccio
Genome Res. September 2023 33: 1497-1512; Published in Advance August 15, 2023, doi:10.1101/gr.277804.123
.... The targeting of RNA transcripts to axons is one of the mechanisms that allows rapid local translation of proteins in response to extracellular signals. 3′ Untranslated regions (UTRs) of mRNA are noncoding sequences that play a critical role in determining transcript localization and translation by interacting...
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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
...′-nucleotide (Mi et al. 2008). For post-transcriptional gene silencing (PTGS), majorly undertaken in plants by cleavage of target mRNA, 21- to 22-nt size class sRNAs with 5′-uracil (U) are loaded into the AGO1, leading to slicing of the target mRNA between positions 10 and 11 in the sRNA:mRNA duplex regions...
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Resource: Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants
- Alice Lunardon,
- Nathan R. Johnson,
- Emily Hagerott,
- Tamia Phifer,
- Seth Polydore,
- Ceyda Coruh,
- and Michael J. Axtell
Genome Res. March 2020 30: 497-513; Published in Advance March 16, 2020, doi:10.1101/gr.256750.119
...(Liu et al. 2014; Zhang et al. 2019). This is consistent with the fact that monocots, in contrast to dicots, produce phasiRNAs mainly from noncoding RNAs (Zheng et al. 2015; Komiya 2017).The conservation of sRNAs across plants has been widely investigated for miRNAs. There are deeply conserved mi...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...community with more than 10 strains and an HIV-1 coinfection data set. We use devider to investigate the within-host diversity of a long-read bovine gut meta enriched for AMR genes, discovering 13 distinct haplotypes for a tet(Q) tetracycline-resistance gene with >18,000× coverage and six haplotypes...

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