FelixKrueger/TrimGalore: v0.6.7 - DOI via Zenodo

Krueger, Felix; James, Frankie; Ewels, Philip; Afyounian, Ebrahim; Schuster-Böeckler, Benjamin

doi:10.5281/zenodo.5127899

Cited by 122 publications

(79 citation statements)

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“…Preprocessing of the fastq files were performed using the method mentioned above. Quality check was performed using fastQC [18] for single samples and MultiQC [19] for multi sample summary, followed by quality and adapter trimming by trimmomatic [22]. Next, the fastq was aligned to the Oar_rambouillet_v1.0 from Ensembl, using STAR [28] followed by read quantification using RSEM[29].…”

Section: Methodsmentioning

confidence: 99%

“…Phred score [20,21] Next, trimming was performed using Trim Galore [22] to get high quality reads for better methylation calls. It trims all reads having a Phred score less than 20 (i.e., 99% base call accuracy), read length less than 20bp after quality trimming and adapter contamination and/or when reads start with CAA or CGA (S1 File).…”

Section: Bioinformatic Analysismentioning

confidence: 99%

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Identification of differential hypothalamic DNA methylation and gene expression associated with sexual partner preferences in rams

Bhattacharya

Amodei

Vilain

et al. 2022

Preprint

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The sheep is a valuable model to test whether hormone mechanisms that sexually differentiate the brain underlie the expression of sexual partner preferences because as many as 8% of rams prefer same-sex partners. Epigenetic factors such as DNA methylation act as mediators in the interaction between steroid hormones and the genome. Variations in the epigenome could be important in determining morphological or behavior differences among individuals of the same species. In this study, we explored DNA methylation differences in the hypothalamus of male oriented rams (MORs) and female oriented rams (FORs). We employed reduced representation bisulfite sequencing (RRBS) to generate a genome-wide map of DNA methylation and RNA-Seq to profile the transcriptome. We found substantial DNA methylation and gene expression differences between FORs and MORs. Although none of the differentially methylated genes yielded significant functional terms directly associated with sex development, there were three differentially expressed genes that have been associated previously with sexual behaviors. We hypothesize that these differences are involved in the phenotypic variation in ram sexual partner preferences, whereas future studies will have to find the specific mechanisms. Our results add an intriguing new dimension to sheep behavior that should be useful for further understanding epigenetic and transcriptomic involvement.

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Section: Methodsmentioning

confidence: 99%

Section: Bioinformatic Analysismentioning

confidence: 99%

Identification of differential hypothalamic DNA methylation and gene expression associated with sexual partner preferences in rams

Bhattacharya

Amodei

Vilain

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Bioinformatic analysis was carried out using the Galaxy server [70], Raw reads were filtered for quality and adapter using Trim Galore! (version 0.4.3.1) [71]. Trimmed reads…”

Section: Small Rna-seqmentioning

confidence: 99%

“…Bioinformatic analysis was carried out using the Galaxy server [70], Raw reads were filtered for quality and adapters using Trim Galore! (version 0.4.3.1) [71]. Trimmed reads were then aligned to the S. japonicus reference genome SJ5 (GCA_000149845.2) using bowtie2 (version 2.3.4.3) [78].…”

Section: Chip-seqmentioning

confidence: 99%

Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus

2022

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RNA interference (RNAi) is a conserved mechanism of small RNA-mediated genome regulation commonly involved in suppression of transposable elements (TEs) through both post-transcriptional silencing, and transcriptional repression via heterochromatin assembly. The fission yeast Schizosaccharomyces pombe has been extensively utilised as a model for studying RNAi pathways. However, this species is somewhat atypical in that TEs are not major targets of RNAi, and instead small RNAs correspond primarily to non-coding pericentromeric repeat sequences, reflecting a specialised role for the pathway in promoting heterochromatin assembly in these regions. In contrast, in the related fission yeast Schizosaccharomyces japonicus, sequenced small RNAs correspond primarily to TEs. This suggests there may be fundamental differences in the operation of RNAi pathways in these two related species. To investigate these differences, we probed RNAi function in S. japonicus. Unexpectedly, and in contrast to S. pombe, we found that RNAi is essential in this species. Moreover, viability of RNAi mutants can be rescued by mutations implicated in enhancing RNAi-independent heterochromatin propagation. These rescued strains retain heterochromatic marks on TE sequences, but exhibit derepression of TEs at the post-transcriptional level. Our findings indicate that S. japonicus retains the ancestral role of RNAi in facilitating suppression of TEs via both post-transcriptional silencing and heterochromatin assembly, with specifically the heterochromatin pathway being essential for viability, likely due to a function in genome maintenance. The specialised role of RNAi in heterochromatin assembly in S. pombe appears to be a derived state that emerged after the divergence of S. japonicus.

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“…Bioinformatic analysis was carried out using the Galaxy server [63], Raw reads were filtered for quality and adapters using Trim Galore! (version 0.4.3.1) [64]. Trimmed reads were then aligned to the S. japonicus reference genome SJ5 (GCA_000149845.2) using bowtie2 (version 2.3.4.3) [71].…”

Section: Chip-seqmentioning

confidence: 99%

Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus

Chapman

Taglini

Bayne

2022

Preprint

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RNA interference (RNAi) is a conserved mechanism of small RNA-mediated genome regulation commonly involved in suppression of transposable elements (TEs) through both post-transcriptional silencing, and transcriptional repression via heterochromatin assembly. The fission yeast Schizosaccharomyces pombe has been extensively utilised as a model for studying RNAi pathways. However, this species is somewhat atypical in that TEs are not major targets of RNAi, and instead small RNAs correspond primarily to non-coding pericentromeric repeat sequences, reflecting a specialised role for the pathway in promoting heterochromatin assembly in these regions. In contrast, in the related fission yeast Schizosaccharomyces japonicus, sequenced small RNAs correspond primarily to TEs. This suggests there may be fundamental differences in the operation of RNAi pathways in these two related species. To investigate these differences, we probed RNAi function in S. japonicus. Unexpectedly, and in contrast to S. pombe, we found that RNAi is essential in this species. Moreover, viability of RNAi mutants can be rescued by mutations implicated in enhanching RNAi-independent heterochromatin propagation. These rescued strains retain heterochromatic marks on TE sequences, but exhibit derepression of TEs at the post-transcriptional level. Our findings indicate that S. japonicus retains the ancestral role of RNAi in facilitating suppression of TEs via both post-transcriptional silencing and heterochromatin assembly, with specifically the heterochromatin pathway being essential for viability, likely due to a function in genome maintenance. The specialised role of RNAi in heterochromatin assembly in S. pombe appears to be a derived state that emerged after the divergence of S. japonicus.

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FelixKrueger/TrimGalore: v0.6.7 - DOI via Zenodo

Cited by 122 publications

References 0 publications

Identification of differential hypothalamic DNA methylation and gene expression associated with sexual partner preferences in rams

Identification of differential hypothalamic DNA methylation and gene expression associated with sexual partner preferences in rams

Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus

Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus

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