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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
...is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
...KO of Dicer and Drosha, which act upstream of Ago2 in the miRNA pathway, resulted in spermatogenic cell apoptosis, abnormal sperm morphology, and infertility, depending on the stage of spermatogenesis that was targeted (Hayashi et al. 2008; Maatouk et al. 2008; Romero et al. 2011; Wu et al. 2012). Together...
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Research: Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval development
- Marek Wojciechowski,
- Robert Lowe,
- Joanna Maleszka,
- Danyal Conn,
- Ryszard Maleszka,
- and Paul J. Hurd
Genome Res. October 2018 28: 1532-1542; Published in Advance August 22, 2018, doi:10.1101/gr.236497.118
...methylated regions are mainly localized to exons and are thought to mediate alternative splicing (Foret et al. 2012; Kucharski et al. 2016). More recently, proteomic analysis of histone modifications (Dickman et al. 2013) and miRNAs (Ashby et al. 2016) also suggested potential roles in caste determination...
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Research: Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains
- Ying-Tao Zhao,
- Deborah Y. Kwon,
- Brian S. Johnson,
- Maria Fasolino,
- Janine M. Lamonica,
- Yoon Jung Kim,
- Boxuan Simen Zhao,
- Chuan He,
- Golnaz Vahedi,
- Tae Hoon Kim,
- and Zhaolan Zhou
Genome Res. July 2018 28: 933-942; Published in Advance May 30, 2018, doi:10.1101/gr.233775.117
..._m1). Results were quantified on an ABI 7900 system. All RNA expression levels were normalized to Gapdh or Hprt.Genome annotationThe mouse annotation file of Ensembl release 75 was used. Genes annotated as protein_coding, lincRNA, miRNA, snRNA, and snoRNA were included in the analyses.GRO-seq and RNA...
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Research: TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
- Morgan A. Sammons,
- Jiajun Zhu,
- Adam M. Drake,
- and Shelley L. Berger
Genome Res. February 2015 25: 179-188; Published in Advance November 12, 2014, doi:10.1101/gr.181883.114
...and a concomitant increase in significantly enriched regions (FDR < 1) of TP53 (Fig. 1A; Supplemental Fig. S1A; Vassilev et al. 2004). Themajority of induced TP53 binding events occur >5 kb from the TSS of a protein-coding gene, with themodal group between5 and 50 kb from the nearest TSS (Fig. 1B). Genome...
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Resource: Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
- Daniel E. Goszczynski,
- Michelle M. Halstead,
- Alma D. Islas-Trejo,
- Huaijun Zhou,
- and Pablo J. Ross
Genome Res. April 2021 31: 732-744; Published in Advance March 15, 2021, doi:10.1101/gr.267336.120
...disabled. Antisense RNAs mapping to the gene body were identified using featureCounts in the opposite stranded mode (-s 2). Putative protein-coding and lncRNA genes were predicted based on k-mer frequency, codon use, and ORF coverage using the FEELnc software (Wucher et al. 2017). Lastly, prediction of pre-miRNA...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...the downstream target gene transcription. Nonetheless, our current finding is an extension to the formerly studied role of noncoding RNA (Mosig and Kojima 2022) such as miRNA (Xue and Zhang 2018; Zhou et al. 2021) in fine-tuning circadian clock by influencing the phase, amplitude, and period of the rhythm...
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Errata: Errata Genome Res. December 2009 19: 2343

...genome;19/12/2343 1088-9051 Errata Errata Genome Research 19: 1742–1751 (2009) Chromatin poises miRNA- and protein-coding genes for expression Artem Barski, Raja Jothi, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E. Schones, and Keji Zhao Several errors in equations appear on page 1749...
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Research: Polycomb preferentially targets stalled promoters of coding and noncoding transcripts
- Daniel Enderle,
- Christian Beisel,
- Michael B. Stadler,
- Moritz Gerstung,
- Prashanth Athri,
- and Renato Paro
Genome Res. February 2011 21: 216-226; Published in Advance December 22, 2010, doi:10.1101/gr.114348.110
...core promoter of pri-mir-275 maps exactly to the cuckold mutation (chr2L: 7,423,896– 7,423,995) (Castrillon et al. 1993), strongly suggesting that the observed behavioral defect for cuc1 is caused by a deregulation of the pri-mir-275 transcript. InDrosophila, <50% of all miRNA loci overlap with protein-coding...
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Resource: The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures
- Ron A.-J. Chen,
- Thomas A. Down,
- Przemyslaw Stempor,
- Q. Brent Chen,
- Thea A. Egelhofer,
- LaDeana W. Hillier,
- Tess E. Jeffers,
- and Julie Ahringer
Genome Res. August 2013 23: 1339-1347; Published in Advance April 2, 2013, doi:10.1101/gr.153668.112
..., with a peak of transcriptional pairing at 120 bp. We assign transcription initiation sites to 7691 protein-coding genes and find that they display features typical of eukaryotic promoters. Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. Based...
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