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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
...decreases with genomic distance: Genes positioned at the periphery of the clusters more frequently exhibit biased expression toward one of the two parental alleles, rather than strictly monoallelic expression (Perez et al. 2015).Histone modifications, cis-spatial organization, long noncoding RNAs (lncRNAs...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...at both the 5′- and 3′-ends, representing the 5′ and 3′ untranslated regions (UTRs) of the transcripts. Comparing structure types, the incidence of piMs showed the most even distribution, whereas pG4s were preferentially localized at both the 5′- and 3′-ends for mRNA but only the 5′-end for lncRNA. G4s...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...-to-I editing occurs frequently in repetitive elements that fold into stable secondary structures(Wren et al. 1977; Porath et al. 2017). For example, the vast majority of mRNA editing in humans occurs within Alu repetitive elements. These ~300bp long elements are abundant and make up approximately 10...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...,G) Visualization of RNA-seq (blue) and ATAC-seq (orange) results at the MYH6 locus (F) and cCREs (G). Highlighted are cCRE regions: R1 (red), R2 (green), and R3 (purple) and a previously characterized MYH7 enhancer C3 (blue). (H) RT-qPCR analysis of transcript abundance for cCRE RNAs and CMTM5 transcripts in i...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...) depletion to ensure that the samples to be sequenced are enriched in miRNAs and not in rRNAs.miRNAs are short noncoding RNAs ∼22 nucleotides (nt) in length that play a crucial role in post-transcriptional regulation by targeting messenger RNA (mRNA) for degradation or translational repression (Shang et al...
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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
...region indicated with dashed rectangles in the upper plot. MHC-I, MHC-II and APG are marked and labeled individually, with the width of rectangles corresponding to gene lengths. Maximum relative expression: the maximum fraction of total MHC-I expression (FPKM) attributable to a sequence across all RNA...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...NPCs. We identified 8148 regions with enhancer activity in phNPCs. Of these regions, 6612 were replicated in two experiments, demonstrating strong evidence of enhancer activity. Additionally, we generated ATAC-seq data in iPSC-derived NPCs and RNA-seq data in the phNPCs, providing further characterization...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...and Bender 2006; Stroud et al. 2013, 2014; Zemach et al. 2013). SUVH2 and SUVH9 bind all methylated contexts but preferentially to mCG and mCHH, respectively (Johnson et al. 2008). They are partially redundant in the RdDM pathway, recruiting PolV for the generation of long noncoding RNAs that—in concert...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...at single-molecule resolution, characterize the full composition of exons on individual mRNAs (Tilgner et al. 2014; Tian et al. 2021; Wright et al. 2022b), and determine the connections between protein-coding and untranslated regions (UTRs) that regulate mRNA functions and expression. Furthermore...
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Method: CodonBERT large language model for mRNA vaccines
- Sizhen Li,
- Saeed Moayedpour,
- Ruijiang Li,
- Michael Bailey,
- Saleh Riahi,
- Lorenzo Kogler-Anele,
- Milad Miladi,
- Jacob Miner,
- Fabien Pertuy,
- Dinghai Zheng,
- Jun Wang,
- Akshay Balsubramani,
- Khang Tran,
- Minnie Zacharia,
- Monica Wu,
- Xiaobo Gu,
- Ryan Clinton,
- Carla Asquith,
- Joseph Skaleski,
- Lianne Boeglin,
- Sudha Chivukula,
- Anusha Dias,
- Tod Strugnell,
- Fernando Ulloa Montoya,
- Vikram Agarwal,
- Ziv Bar-Joseph,
- and Sven Jager
Genome Res. July 2024 34: 1027-1035; Published in Advance July 1, 2024, doi:10.1101/gr.278870.123
...candidates that encode the influenza hemagglutinin antigen (i.e., with fixed untranslated regions and a variable coding region) were designed, synthesized, and transfected into cells. The protein expression levels corresponding to these mRNA sequences were measured and used as labels for a supervised...

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