Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts.
Kevin S. Lang,Houra Merrikh +1 more
TLDR
In this paper, the authors show that head-on, but not codirectional, conflict resolution requires the relaxation of positive supercoils by the type II topoisomerases DNA gyrase and Topo IV, at least in the Gram-positive model bacterium Bacillus subtilis.About:
This article is published in Cell Reports.The article was published on 2021-03-02 and is currently open access. It has received 12 citations till now. The article focuses on the topics: DNA gyrase & DNA supercoil.read more
Citations
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Walking a tightrope: The complex balancing act of R-loops in genome stability.
TL;DR: In this article , the authors discuss the cellular contexts in which R-loops contribute to genomic instability, particularly during DNA replication and double-strand break (DSB) repair.
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Harmful R-loops are prevented via different cell cycle-specific mechanisms.
Marta San Martin-Alonso,María E. Soler-Oliva,María L. García-Rubio,Tatiana García-Muse,Andrés Aguilera +4 more
TL;DR: In this paper, it was shown that R-loops form co-transcriptionally independently of DNA replication and Sen1 is an S-phase-specific R-loop resolvase.
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Toxic R-loops: Cause or consequence of replication stress?
TL;DR: In this paper, the authors discuss different scenarios in which R-loops directly or indirectly interfere with DNA replication and discuss alternative models in which toxic RNA:DNA hybrids form at stalled forks as a consequence - but not a cause - of replication stress and interfere with replication resumption.
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Bacillus subtilis PcrA Helicase Removes Trafficking Barriers.
TL;DR: In this paper, Bacillus subtilis PcrA interacts with the RNA polymerase and might contribute to mitigate replication-transcription conflicts (RTCs) by removing spontaneous or enzyme-driven R-loops.
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Transcription-Replication Collisions-A Series of Unfortunate Events.
TL;DR: In this paper, the authors discuss how transcription influences replication fork stability, and the safeguards that have evolved to navigate transcription-replication interactions and maintain genome integrity in mammalian cells, highlighting the importance of defining cellular pathways regulating transcriptionreplication interaction formation, evasion, and resolution.
References
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The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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Trimmomatic: a flexible trimmer for Illumina sequence data
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Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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Integrative genomics viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TL;DR: In this article, the authors present an approach for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz,Christopher Benner,Nathanael J. Spann,Eric Bertolino,Yin C. Lin,Peter Laslo,Jason X. Cheng,Cornelis Murre,Harinder Singh,Harinder Singh,Christopher K. Glass +10 more
TL;DR: It is demonstrated in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions.
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