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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...overwind or underwind DNA, creating DNA supercoils (Kouzine and Levens 2007). Supercoils can, in turn, induce formation of single-stranded DNA (ssDNA, hereafter SS DNA) or other non-B DNA structures.Genome-wide mapping of alternative DNA structures in cell lines and computational predictions in s suggested...
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LETTER: Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
- Leah O. Barrera,
- Zirong Li,
- Andrew D. Smith,
- Karen C. Arden,
- Webster K. Cavenee,
- Michael Q. Zhang,
- Roland D. Green,
- and Bing Ren
Genome Res. January 2008 18: 46-59; Published in Advance November 27, 2007, doi:10.1101/gr.6654808
...regulatory mechanisms in mammalian cells, we now directly identify active promoters by unbiased mapping of the RNA polymerase II pre-initiation complex (PIC) in the mouse across a panel of mouse organs—brain, heart, kidney, liver—and mouse embryonic stem cells (hereafter collectively referred to as “tissues...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...remodeling complex was proposed to play a crucial role in this rapid reignition of transcription upon nutrient addition (Cucinotta et al. 2021). However, the extent to which the transcription machinery is associated with the quiescent is still debated, with early studies indicating poised RNA polymerase II...
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Research: Distinctive regulatory architectures of germline-active and somatic genes in C. elegans
- Jacques Serizay,
- Yan Dong,
- Jürgen Jänes,
- Michael Chesney,
- Chiara Cerrato,
- and Julie Ahringer
Genome Res. December 2020 30: 1752-1765; Published in Advance October 22, 2020, doi:10.1101/gr.265934.120
...have provided important and increasingly detailed knowledge of features of transcription regulation in eukaryotes. Different regulatory architectures have been observed, ranging from single promoters to complex structures involving multiple regulatory elements, which can operate redundantly...
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Research: Widespread and precise reprogramming of yeast protein–genome interactions in response to heat shock
- Vinesh Vinayachandran,
- Rohit Reja,
- Matthew J. Rossi,
- Bongsoo Park,
- Lila Rieber,
- Chitvan Mittal,
- Shaun Mahony,
- and B. Franklin Pugh
Genome Res. March 2018 28: 357-366; Published in Advance February 14, 2018, doi:10.1101/gr.226761.117
...by yeast RNA polymerase II supports a scanning model. J Biol Chem 281: 14119–14128. ↵Kuras L, Kosa P, Mencia M, Struhl K. 2000. TAF-containing and TAF-independent forms of transcriptionally active TBP in vivo. Science 288: 1244–1248. ↵Lai WK, Pugh BF. 2017. Genome-wide uniformity of human ‘open’ pre-initiation...
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Perspective: Epigenomics and the structure of the living genome
- Nir Friedman and
- Oliver J. Rando
Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
...are packaged into an extensively folded state known as chromatin. Analysis of the structure of eukaryotic chromosomes has been revolutionized by development of a suite of genome-wide measurement technologies, collectively termed “epigenomics.” We review major advances in epigenomic analysis of eukaryotic...
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Research: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast
- Gregory T. Booth,
- Isabel X. Wang,
- Vivian G. Cheung,
- and John T. Lis
Genome Res. June 2016 26: 799-811; Published in Advance May 12, 2016, doi:10.1101/gr.204578.116
...al. 2013; Jonkers et al. 2014).Genome-wide increases in nascent transcription in spt4Δ are not reflected in mRNA abundanceTo test the possibility of a global elongation rate defect in S. cerevisiae and S. pombe lacking Spt4, we investigated the effects of the mutation on mRNA abundance. We postulated...
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Research: Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
- Gilad D. Evrony,
- Dwight R. Cordero,
- Jun Shen,
- Jennifer N. Partlow,
- Timothy W. Yu,
- Rachel E. Rodin,
- R. Sean Hill,
- Michael E. Coulter,
- Anh-Thu N. Lam,
- Divya Jayaraman,
- Dianne Gerrelli,
- Diana G. Diaz,
- Chloe Santos,
- Victoria Morrison,
- Antonella Galli,
- Ulrich Tschulena,
- Stefan Wiemann,
- M. Jocelyne Martel,
- Betty Spooner,
- Steven C. Ryu,
- Princess C. Elhosary,
- Jillian M. Richardson,
- Danielle Tierney,
- Christopher A. Robinson,
- Rajni Chibbar,
- Dana Diudea,
- Rebecca Folkerth,
- Sheldon Wiebe,
- A. James Barkovich,
- Ganeshwaran H. Mochida,
- James Irvine,
- Edmond G. Lemire,
- Patricia Blakley,
- and Christopher A. Walsh
Genome Res. August 2017 27: 1323-1335; Published in Advance June 19, 2017, doi:10.1101/gr.219899.116
...associated with PCNA, (4) components of the DNA replication pre-initiation and replication fork complexes: CG3430 [MCMBP], Mcm3 [MCM3], Cdc45 [CDC45], (5) Orc2 [ORC2], a component of the origin recognition complex, and (6) regulators of the cell cycle: Lethal-(2)-denticleless [DTL]—which codes...
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Research: Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing
- Joshua A. Arribere and
- Wendy V. Gilbert
Genome Res. June 2013 23: 977-987; Published in Advance April 11, 2013, doi:10.1101/gr.150342.112
...and its associated eukaryotic initiation factors (eIFs) to form a pre-initiation complex (PIC). The PIC scans in a net 5′-to-3′ direction until it locates a start codon (AUG), triggering complex rearrangements that eventually result in formation of an elongating 80S ribosome (for review, see Jackson et al...
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Research: RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast
- Dwaipayan Ganguli,
- Răzvan V. Chereji,
- James R. Iben,
- Hope A. Cole,
- and David J. Clark
Genome Res. October 2014 24: 1637-1649; Published in Advance July 11, 2014, doi:10.1101/gr.177014.114
...; Hota and Bartholomew 2011; Narlikar et al. 2013). Genome-wide studies of nucleosomal DNA isolated from cells by digestion with micrococcal nuclease (MNase) and analyzed using tiling microarrays or massively parallel sequencing have revealed that most yeast genes have a nucleosome-depleted region (NDR...

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