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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...also helped characterize novel cis-regulatory DNA elements and their combined effects in regulating transcription and associating genetic variation with differential gene expression and phenotypic diversity (Azodi et al. 2020a,b). Therefore, integrating high-throughput translation initiation sequencing...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...: a DIAMOND hit to NCBI nr, a PANNZER2 hit, or both (Supplemental Table S9).Mitochondrial Cnidarians are characterized by mitochondrial genomic diversity, varying in overall mtDNA conformation (circular or linear), gene content, gene organization, and the number of mitochondrial chromosomes within each...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...its genetics and genomics fully reproducible by C. elegans laboratories over many years. CGC1 is available at the Caenorhabditis Genetics Center stock center (https://cgc.umn.edu/strain/CGC1).Genome sequencing and assemblyWe harvested genomic DNA (gDNA) from CGC1 and sequenced it in two sets apiece...
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Research: Ribosomal DNA harbors an evolutionarily conserved clock of biological aging
- Meng Wang and
- Bernardo Lemos
Genome Res. March 2019 29: 325-333; Published in Advance February 14, 2019, doi:10.1101/gr.241745.118
...author: blemos@hsph.harvard.eduAbstractThe ribosomal DNA (rDNA) is the most evolutionarily conserved segment of the and gives origin to the nucleolus, an energy intensive nuclear organelle and major hub influencing myriad molecular processes from cellular metabolism to epigenetic states of the . The rDNA...
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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
...and function of the molecule. Despite this, many secondary structures in RNA, particularly noncanonical structures, are significantly less well characterized than their DNA counterparts. In this study, we focus on the formation of G-quadruplex (G4), intercalated-motif (iM), R-loop (RL), and Z-RNA noncanonical...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...the process of transcription as the nascent RNA strand exits RNA polymerase II (Pol II) and hybridizes to the template DNA strand (Ginno et al. 2012; Sanz et al. 2016). In addition, recent studies showed that some long noncoding RNAs (lncRNAs) can associate to distant genomic regions through the formation...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
...of CNSs in active regions of DNA replication in the early S phase suggests that regions of DNA replication initialization might be evolutionarily conserved. CNS knockout lines should be generated to gain a comprehensive understanding of their function (Gasperini et al. 2020). Taking advantage...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...promoter regions.Hydra chromatin is organized into localized contact domainsThe three-dimensional organization of DNA molecules in the nucleus is tightly linked to regulation (Szabo et al. 2019). Although several cnidarian Hi-C data sets have been published (Supplemental Table S4; Li et al. 2020; Nong et...
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Research: Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas
- Jonas Kjellin,
- Lotta Avesson,
- Johan Reimegård,
- Zhen Liao,
- Ludwig Eichinger,
- Angelika Noegel,
- Gernot Glöckner,
- Pauline Schaap,
- and Fredrik Söderbom
Genome Res. March 2021 31: 436-447; Published in Advance January 21, 2021, doi:10.1101/gr.272856.120
...far beyond being an intermediate transmitter of information between DNA and protein in its role as messenger (m)RNA. This has been appreciated for a long time for some noncoding RNAs (ncRNAs), such as transfer (t)RNAs, ribosomal (r)RNAs, small nuclear (sn)RNAs, and small nucleolar (sno)RNAs. Today, we...
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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
...genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted—or read—differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull...

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