deepTools2: a next generation web server for deep-sequencing data analysis

Ramírez, Fidel; Ryan, Devon P.; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S.; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

doi:10.1093/nar/gkw257

Cited by 6,179 publications

(5,306 citation statements)

References 19 publications

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“…The log2/ratio (33,34) between this latter profile and that of untreated cells (Fig. 4A, Bottom) confirmed that a gain of acetylation occurred in C-DOM in cells treated with both Shh and Fgf (Fig.…”

Section: Resultssupporting

confidence: 64%

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

Rodrigues

Yakushiji-Kaminatsui

Atsuta

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Significance Because structures in the developing embryo are organized by secreted signals, embryonic cells must integrate multiple inputs to turn on the target genes necessary for proper development. Little is known about how multiple signals can work together to regulate such target genes in an embryological context. In this work, we use cultured limb bud mesenchymal cells to investigate how two such signals, Sonic hedgehog (Shh) and fibroblast growth factor 8 (Fgf8), work together to control the activity of Hoxd genes, a set of transcription factors necessary for the patterning of developing tetrapod limbs.

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Section: Resultssupporting

confidence: 64%

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

Rodrigues

Yakushiji-Kaminatsui

Atsuta

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Paired-end alignments adjusted by MMR may lack conformity if the fragments are too small and/or the reads align entirely to direct repeats, so we removed these particular cases to avoid uncertainty. Genome-wide coverage was computed for every library by deepTools v2.5.3 [88], taking into consideration the extension of entire fragments for paired-end alignments and the fact that orphan R2 reads align to the opposite strand of the real RNA fragment. Furthermore, we used bedtools v2.2.26 [89] to compute 5ʹ and 3ʹ profiles for each library, employing the aligned R1 and R2 reads, respectively, once more taking into consideration the orientation of reads in relation to the original RNA fragment in the sample.…”

Section: Methodsmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

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Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.

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“…The resulting candidate peaks for MLE wt and its four mutants were used to calculate pairwise Spearman correlations between all replicates (Supplemental Fig. S1G), showing increased pairwise correlations between biological replicates within each condition over replicates of differing experimental conditions (deeptools version 2.3.5) (Ramírez et al 2016). JAMM combined the MLE-binding sites located on roX1 and roX2 into single large regions.…”

Section: Methodsmentioning

confidence: 99%

A mutually exclusive stem–loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

et al. 2017

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The X chromosome provides an ideal model system to study the contribution of RNA-protein interactions in epigenetic regulation. In male flies, roX long noncoding RNAs (lncRNAs) harbor several redundant domains to interact with the ubiquitin ligase male-specific lethal 2 (MSL2) and the RNA helicase Maleless (MLE) for X-chromosomal regulation. However, how these interactions provide the mechanics of spreading remains unknown. By using the uvCLAP (UV cross-linking and affinity purification) methodology, which provides unprecedented information about RNA secondary structures in vivo, we identified the minimal functional unit of roX2 RNA. By using wild-type and various MLE mutant derivatives, including a catalytically inactive MLE derivative, MLE GET , we show that the minimal roX RNA contains two mutually exclusive stem-loops that exist in a peculiar structural arrangement: When one stem-loop is unwound by MLE, an alternate structure can form, likely trapping MLE in this perpetually structured region. We show that this functional unit is necessary for dosage compensation, as mutations that disrupt this formation lead to male lethality. Thus, we propose that roX2 lncRNA contains an MLE-dependent affinity switch to enable reversible interactions of the MSL complex to allow dosage compensation of the X chromosome.[Keywords: dosage compensation; H4K16ac; MLE; X chromosome; acetylation; roX RNA] Supplemental material is available for this article. RNA helicases are a large family of proteins that have important roles in many aspects of RNA biology. Although the name "helicase" suggests that the main function of these proteins is to destabilize and remove RNA secondary structures, there are several RNA helicases, especially of the DEAD-box subfamily, that use their helicase domains to simply interact with RNA (such as eIF4A3) and not for remodeling. On the other hand, a closely related RNA helicase, eIF4A1, can unwind RNA structures but only when they are relatively weak and short (Rogers et al. 2001). At the other extreme, several helicases are proposed to act as annealers that facilitate the formation of structured RNA rather than the other way around (Jankowsky 2011).Thus, although the helicase family is quite large, specific functions assigned to helicases that involve the actual removal of secondary structures in vivo are rather sparse. Maleless (MLE), known primarily for its role in Drosophila dosage compensation, is an RNA helicase of the DExH family, which is composed of relatively large multidomain helicases that (unlike the DEAD-box family) are thought to work as processive RNA helicases.

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deepTools2: a next generation web server for deep-sequencing data analysis

Cited by 6,179 publications

References 19 publications

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

A mutually exclusive stem–loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

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