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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
...: 814–825. doi:10.1016/j.molcel.2012.01.017 ↵Gómez-González B, Aguilera A. 2019. Transcription-mediated replication hindrance: a major driver of instability. Genes Dev 33: 1008–1026. doi:10.1101/gad.324517.119 ↵Gómez-González B, Aguilera A. 2023. Break-induced RNA-DNA hybrids (BIRDHs) in homologous...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain...
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Research: An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation
- Andrew M. Lerner,
- Austin J. Hepperla,
- Gregory R. Keele,
- Hashem A. Meriesh,
- Hayretin Yumerefendi,
- David Restrepo,
- Seth Zimmerman,
- James E. Bear,
- Brian Kuhlman,
- Ian J. Davis,
- and Brian D. Strahl
Genome Res. November 2020 30: 1605-1617; Published in Advance October 5, 2020, doi:10.1101/gr.264283.120
...highly transcribed genes results from multiple rounds of transcription, in which each round of transcription mediates a fixed amount of H3K36 methylation per nucleosome across the population of cells. Additionally, the linear rate of H3K36me3 gain across protein-coding genes also suggests that Set2...
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Research: Sense–antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit
- Yulong Song,
- Lishi Li,
- Wenbing Yang,
- Qiang Fu,
- Wanying Chen,
- Zeng Fang,
- Wen Li,
- Nannan Gu,
- and Rui Zhang
Genome Res. May 2020 30: 661-672; Published in Advance May 18, 2020, doi:10.1101/gr.257121.119
...Yulong Song1,2,4, Lishi Li1,2,4, Wenbing Yang1,2, Qiang Fu1,2, Wanying Chen1,2, Zeng Fang3, Wen Li3, Nannan Gu1,2 and Rui Zhang1,2 1MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; 2RNA...
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Research: Promoter-specific dynamics of TATA-binding protein association with the human genome
- Yuko Hasegawa and
- Kevin Struhl
Genome Res. December 2019 29: 1939-1950; Published in Advance November 15, 2019, doi:10.1101/gr.254466.119
...from those of yeast promoters with slow turnover. These observations suggest that TBP binding dynamics differentially affect promoter function and gene expression, possibly at the level of transcriptional reinitiation/bursting.Binding of transcription factors to specific genomic DNA sequences...
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Resource: The landscape of antisense gene expression in human cancers
- O. Alejandro Balbin,
- Rohit Malik,
- Saravana M. Dhanasekaran,
- John R. Prensner,
- Xuhong Cao,
- Yi-Mi Wu,
- Dan Robinson,
- Rui Wang,
- Guoan Chen,
- David G. Beer,
- Alexey I. Nesvizhskii,
- and Arul M. Chinnaiyan
Genome Res. July 2015 25: 1068-1079; Published in Advance June 10, 2015, doi:10.1101/gr.180596.114
...Wang, Rui Guoan Arul M, Chinnaiyan Y Wu A.M. Chinnaiyan OA Balbin Alexey I, Nesvizhskii Dhanasekaran, S.M R Malik SM Dhanasekaran 1549-5469 10.1101/gr.180596.114 genome;gr.180596.114 1088-9051 The landscape of antisense gene expression in human cancers Balbin et al. Landscape of antisense gene...
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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
..., the human malaria parasite, Plasmodium falciparum, is incapable of pyrimidine salvage for mRNA biogenesis. To capture cellular mRNA dynamics during Plasmodium development, we engineered parasites that can salvage pyrimidines through the expression of a single bifunctional yeast fusion gene, cytosine...
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Research: Multidimensional regulation of gene expression in the C. elegans embryo
- John Isaac Murray,
- Thomas J. Boyle,
- Elicia Preston,
- Dionne Vafeados,
- Barbara Mericle,
- Peter Weisdepp,
- Zhongying Zhao,
- Zhirong Bao,
- Max Boeck,
- and Robert H. Waterston
Genome Res. July 2012 22: 1282-1294; Published in Advance April 16, 2012, doi:10.1101/gr.131920.111
...Max, Boeck Murray, John Isaac Zhao Zhongying Dionne Vafeados Vafeados Weisdepp, P John Isaac, Murray 10.1101/gr.131920.111 1088-9051 genome;gr.131920.111 Multidimensional regulation of gene expression in the C. elegans embryo Research Multidimensional regulation of gene expression in the C. elegans...
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Research: Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts
- Milana Frenkel-Morgenstern,
- Vincent Lacroix,
- Iakes Ezkurdia,
- Yishai Levin,
- Alexandra Gabashvili,
- Jaime Prilusky,
- Angela del Pozo,
- Michael Tress,
- Rory Johnson,
- Roderic Guigo,
- and Alfonso Valencia
Genome Res. July 2012 22: 1231-1242; Published in Advance May 15, 2012, doi:10.1101/gr.130062.111
...by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/12; www..org Genome Research 1231 www..org For instance, gene fusion in chronicmyelogenous leukemia (CML) leads to an mRNA transcript that encompasses the 59 end of the BCR gene and the 39 end of the ABL gene. Notably, translation of this transcript...
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LETTER: Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
- Yijun Ruan,
- Hong Sain Ooi,
- Siew Woh Choo,
- Kuo Ping Chiu,
- Xiao Dong Zhao,
- K.G. Srinivasan,
- Fei Yao,
- Chiou Yu Choo,
- Jun Liu,
- Pramila Ariyaratne,
- Wilson G.W. Bin,
- Vladimir A. Kuznetsov,
- Atif Shahab,
- Wing-Kin Sung,
- Guillaume Bourque,
- Nallasivam Palanisamy,
- and Chia-Lin Wei
Genome Res. June 2007 17: 828-838; doi:10.1101/gr.6018607
...,824,953 and 56,824,980 (the 3′ end of BCAS3 ). ( B ) FISH analysis showed the amplification and colocalization of BCAS3 (green) and BCAS4 (red) genes. ( C ) Fusion transcript and inferred gene structures revealed by RT-PCR and sequencing analysis are shown. The exact breakpoint mapped by genomic PCR is displayed...
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