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Atypical RNA polymerase subunits required for RNA-directed DNA methylation
TLDR
It is reported here that DRD2 and DRD3 correspond to the second-largest subunit and largest subunit, respectively, of a fourth class of DNA-dependent RNA polymerase (polymerase IV) that is unique to plants.
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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium
TLDR
The complete SEQC data sets, comprising >100 billion reads, provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings, and measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling.
View on Nature
Involvement of Putative SNF2 Chromatin Remodeling Protein DRD1 in RNA-Directed DNA Methylation
View on Elsevier
The transcriptome of syncytia induced by the cyst nematode Heterodera schachtii in Arabidopsis roots
TLDR
It is revealed that syncytia are transcriptionally clearly different from roots (and all other organs), as well as from other root tissues.
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The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
TLDR
RNA-seq outperforms microarray in DEG verification as assessed by quantitative PCR, with the gain mainly due to its improved accuracy for low-abundance transcripts, and classifiers to predict MOAs perform similarly when developed using data from either platform.
View on Nature
Identification of thermophilic species by the amino acid compositions deduced from their genomes.
TLDR
This study presents a careful statistical analysis of factors that affect amino acid composition and introduces the first example of a 'compositional tree' of species that takes into account not only homologous proteins, but also proteins unique to particular species.
View on PubMed
CAST: an iterative algorithm for the complexity analysis of sequence tracts
TLDR
A novel algorithm for low-complexity region detection and selective masking based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties that is sufficient for masking database query sequences without generating false positives.
View on PubMed
A structural-maintenance-of-chromosomes hinge domain–containing protein is required for RNA-directed DNA methylation
TLDR
This finding implicates a putative chromosome architectural protein that can potentially link nucleic acids in facilitating an RNAi-mediated epigenetic modification involving secondary siRNAs and spreading of DNA methylation.
View on Nature
Effects of Aneuploidy on Genome Structure, Expression, and Interphase Organization in Arabidopsis thaliana
TLDR
The analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and progressive genome instability.
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Hopfield Networks is All You Need
TLDR
A new PyTorch layer is provided, called "Hopfield", which allows to equip deep learning architectures with modern Hopfield networks as a new powerful concept comprising pooling, memory, and attention.
View PDF on arXiv
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