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Method: System-wide analyses of the fission yeast poly(A)⁺ RNA interactome reveal insights into organization and function of RNA–protein complexes
- Cornelia Kilchert,
- Tea Kecman,
- Emily Priest,
- Svenja Hester,
- Ebru Aydin,
- Krzysztof Kus,
- Oliver Rossbach,
- Alfredo Castello,
- Shabaz Mohammed,
- and Lidia Vasiljeva
Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
...is colored black, tRNAs bound in the ribosomal A- and P-sites in red, and the small and large ribosomal subunits in beige and white, respectively.RIC/WCE ratios support the proposed topology of CPF on RNA in vivoTo further validate our approach, we turned to the mRNA 3′ end processing machinery (Zhao et al...
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Research: Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest
- Andrea Orioli,
- Viviane Praz,
- Philippe Lhôte,
- and Nouria Hernandez
Genome Res. May 2016 26: 624-635; Published in Advance March 3, 2016, doi:10.1101/gr.201400.115
...by global tRNA levels but also by the balance between the supply of different tRNA isoacceptors and the decoding requirements of the mRNAs expressed in a certain tissue or developmental state (Gingold et al. 2014; Schmitt et al. 2014). These studies point to a more subtle regulation of Pol III transcription...
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Research: Independent RNA polymerase II preinitiation complex dynamics and nucleosome turnover at promoter sites in vivo
- Yoselin Grimaldi,
- Paolo Ferrari,
- and Michel Strubin
Genome Res. January 2014 24: 117-124; Published in Advance December 2, 2013, doi:10.1101/gr.157792.113
...polymerases (Vannini and Cramer 2012). RNA polymerase I (Pol I) transcribes rRNA genes, RNA Pol II transcribes mRNA genes, while RNA Pol III synthesizes tRNA and other small RNA species. Transcription by the three RNA polymerases involves the assembly of a large preinitiation complex (PIC) at gene promoters...
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Research: Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots
- Loris Mularoni,
- Yulian Zhou,
- Tyson Bowen,
- Sunil Gangadharan,
- Sarah J. Wheelan,
- and Jef D. Boeke
Genome Res. April 2012 22: 693-703; Published in Advance January 4, 2012, doi:10.1101/gr.129460.111
...revealed an exquisitely specific pattern of Ty1 insertions relative to the global pattern of nucleosome phasing upstream of tRNA genes. In this pattern, pairs of peaks separated by 70 bp rather preciselymirror the positions of peak nucleosome occupancy. The pattern is somewhat asymmetric with regard to Ty1...
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Research: Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
- Guojie Zhang,
- Guangwu Guo,
- Xueda Hu,
- Yong Zhang,
- Qiye Li,
- Ruiqiang Li,
- Ruhong Zhuang,
- Zhike Lu,
- Zengquan He,
- Xiaodong Fang,
- Li Chen,
- Wei Tian,
- Yong Tao,
- Karsten Kristiansen,
- Xiuqing Zhang,
- Songgang Li,
- Huanming Yang,
- Jian Wang,
- and Jun Wang
Genome Res. May 2010 20: 646-654; Published in Advance March 19, 2010, doi:10.1101/gr.100677.109
...candidates, we performed the following analyses: (1) We excluded small RNA reads that might be from known noncoding RNAs by comparing with known noncodingRNAs (only consider rRNA, tRNA, snRNA, and snoRNA) deposited in the Rfam database (http://www.sanger.ac.uk/ Software/Rfam/, release 9.0); (2) small RNAs...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
.... Forward- and reverse-strand protein-coding genes are shown in red and blue, respectively, in the inner tile layer; ribosomal RNAs and tRNAs are shown in the outer tile layers. The red histogram shows the cumulative GC skew (Grigoriev 1998), with the inflection points corresponding to the replication...
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Research: Common genomic elements promote transcriptional and DNA replication roadblocks
- Kevin Roy,
- Jason Gabunilas,
- Abigail Gillespie,
- Duy Ngo,
- and Guillaume F. Chanfreau
Genome Res. October 2016 26: 1363-1375; Published in Advance August 18, 2016, doi:10.1101/gr.204776.116
...of Nrd1p or Nab3p also resulted in low levels of SNR53 readthrough (Fig. 6C). These results suggested that NNS is dependent on tRNA transcription for efficient SNR53 termination. The results obtained by nuclear depletion of Bdp1p were confirmed by deleting tG(GCC)E in WT and rrp6Δ backgrounds (Fig. 6C...
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LETTER: Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
- Marcel E. Dinger,
- Paulo P. Amaral,
- Tim R. Mercer,
- Ken C. Pang,
- Stephen J. Bruce,
- Brooke B. Gardiner,
- Marjan E. Askarian-Amiri,
- Kelin Ru,
- Giulia Soldà,
- Cas Simons,
- Susan M. Sunkin,
- Mark L. Crowe,
- Sean M. Grimmond,
- Andrew C. Perkins,
- and John S. Mattick
Genome Res. September 2008 18: 1433-1445; Published in Advance June 18, 2008, doi:10.1101/gr.078378.108
.... 2005 ). The limited number of functional studies of long ncRNAs reveal that they act via a diverse range of mechanisms in many regulatory processes, including transcription ( Feng et al. 2006 ), splicing ( Yan et al. 2005 ), translation ( Wang et al. 2005 ), nuclear factor trafficking ( Willingham et...

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