Next-generation sequencing technologies have revolutionized the study of small RNAs (sRNAs) on a genome-wide scale. However, classical sRNA library preparation methods introduce serious bias, mainly during adapter ligation steps. Several types including plant microRNAs (miRNA), piwi-interacting (piRNA) in insects, nematodes and mammals, interfering (siRNA) insects plants contain 2'-O-methyl (2'-OMe) modification at their 3′ terminal nucleotide. This inhibits makes particularly challenging....

The exosome is a complex of 3′–5′ exoribonucleases and RNA-binding proteins, which involved in processing or degradation different classes RNA. Previously, the characterization purified complexes from yeast human cells suggested that C1D KIAA0052/hMtr4p are associated with thus might regulate its functional activities. Subcellular localization experiments demonstrated co-localize subunit PM/Scl-100 nucleoli HEp-2 cells. Additionally, nucleolar accumulation appeared to be dependent on...

The 15 sibling species of the Paramecium aurelia cryptic complex emerged after a whole genome duplication that occurred tens millions years ago. Given extensive knowledge genetics and epigenetics acquired over last century, this offers uniquely powerful system to investigate consequences in unicellular eukaryote as well genetic epigenetic mechanisms drive speciation. High quality gene models are important for research using system. major aim work reported here was build an improved...

Horizontal gene transfer is a rapid and efficient way to diversify bacterial pools. Currently, little known about this flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging the same species isolated at microscale, we reveal frequent significant fraction pangenome. We show that it occurs time scale enabling population cope with its changing environment, notably, through production public goods.

Abstract Patients with Crohn’s disease exhibit abnormal colonization of the intestine by adherent invasive E. coli (AIEC). They adhere to epithelial cells, colonize them and survive inside macrophages. It appeared recently that AIEC LF82 adaptation phagolysosomal stress involves a long lag phase in which many cells become antibiotic tolerant. Later during infection, they proliferate vacuoles form colonies harboring dozens bacteria. In present work, we investigated mechanism sustaining this...

Eukaryotic mRNA degradation proceeds through two main pathways, both involving cap breakdown. In the 3′–5′ decay pathway, body generates free m7GpppN that is hydrolyzed by DcpS generating m7GMP. 5′–3′ recently identified human Dcp2 decapping enzyme cleaves of deadenylated mRNAs to produce m7GDP and 5′-phosphorylated mRNA. We investigated in cell extracts using a new assay for decapping. observed intermediates resulting from appear after incubation substrate RNA extracts, indicating presence...

The nucleoid-associated protein H-NS is a bacterial xenogeneic silencer responsible for preventing costly expression of genes acquired through horizontal gene transfer. silences several Salmonella Pathogenicity Islands (SPIs) essential host infection. stochastic SPI-1 required invasion epithelial cells but complicates investigation factors involved in chromatin structure and regulation. We performed functional genomics on sorted populations expressing or not, to characterize how activation...

The N6-methyladenosine (m6A) modification of HIV-1 RNAs plays an essential role in regulating viral infection. This has been widely studied but the number and precise positions m6A sites remain unclear due to lack precision detection methods. We used latest Nanopore chemistry direct base-calling option identify 18 m6As, 14 which were located at 3′ end genome, other four being central regions. Our data reveal differential methylation these between splicing isoforms. Eleven are clustered two...

Abstract Small nucleolar RNAs are non-coding transcripts that guide chemical modifications of RNA substrates and modulate gene expression at the epigenetic post-transcriptional levels. However, extent their regulatory potential underlying molecular mechanisms remain poorly understood. Here, we identify a conserved, previously unannotated intronic C/D-box snoRNA, termed snR107 , hosted in fission yeast long mamRNA carrying two independent cellular functions. On one hand, guides site-specific...

Summary Blackleg and soft rot are devastating diseases on potato stem tuber caused by Pectobacterium Dickeya pectinolytic enterobacteria. In European cultures, D. dianthicola solani species successively emerged in the past decades. Ecological traits associated to their settlement remain elusive, especially case of recent invader . this work, we combined genomic, metabolic transcriptomic comparisons unravel common distinctive genetic functional characteristics between two isolates. The...

During the summer of 2006, wound infections in bathers caused by Vibrio species were reported from several European countries. In Germany, three people to have developed vulnificus

Genome replication is highly regulated in time and space, but the rules governing remodeling of these programs during evolution remain largely unknown. We generated genome-wide timing profiles for ten Lachancea yeasts, covering a continuous evolutionary range from closely related to more divergent species. show that primarily evolve through dynamic renewal cohort active origins. found gained origins appear with low activity yet become efficient fire earlier as they evolutionarily age. By...

About 10% of bacteria have a multichromosome genome with primary replicon bacterial origin, called the chromosome, and other replicons plasmid chromids. Studies on revealed potential points coordination between replication/segregation chromids progression cell cycle. For example, replication chromid Vibrionales (called Chr2) is initiated upon duplication sequence carried by chromosome Chr1), in such way that both completed synchronously. Also, Chr2 uses Chr1 as scaffold for its partition...

The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage promote inflammatory gene expression, but its mechanism of action unknown. We show that accumulation contributes weakening the association H1 chromatin and increasing turnover. Decreased senescence is correlated increased expression some repeated sequences, STAT/IRF transcription factors, transcriptional activation Interferon-Stimulated Genes (ISGs). H2A.J-specific Val-11...

The family Flavobacteriaceae (phylum Bacteroidetes) is a major component of soil, marine and freshwater ecosystems. In this understudied family, Flavobacterium psychrophilum pathogen that infects salmonid fish worldwide, with critical environmental economic impact. Here, we report an extensive transcriptome analysis established the genome map transcription start sites transcribed regions, predicted alternative sigma factor regulons regulatory RNAs, documented gene expression profiles across...

Long non-coding RNAs (lncRNAs) have been shown to regulate gene expression, chromatin domains and chromosome stability in eukaryotic cells. Recent observations reported the existence of telomeric repeats containing long ncRNAs ⁻ TERRA mammalian yeast However, their functions remain poorly characterized. Here, we report S. cerevisiae several lncRNAs within Y' subtelomeric regions. We called them subTERRA. These belong Cryptic Unstable Transcripts (CUTs) Xrn1p-sensitive (XUTs) family. subTERRA...

Dissecting the genetic basis of intraspecific variations in life history traits is essential to understand their evolution, notably for potential biocontrol agents. Such are observed endoparasitoid Cotesia typhae (Hymenoptera: Braconidae), specialized on pest Sesamia nonagrioides (Lepidoptera: Noctuidae). Previously, we identified two strains C. that differed significantly an allopatric host population. To investigate underlying these phenotypic differences, used a quantitative trait locus...

Small nucleolar RNAs are non-coding transcripts that guide chemical modifications of RNA substrates and modulate gene expression at the epigenetic post-transcriptional levels. However, extent their regulatory potential underlying molecular mechanisms remain poorly understood. Here, we identify a conserved, previously unannotated intronic C/D-box snoRNA, termed snR107, hosted in fission yeast long mamRNA carrying two independent cellular functions. On one hand, snR107 guides site-specific 25S...

The mitochondrial genomes of Saccharomyces cerevisiae strains contain up to 13 introns. An intronless recombinant genome introduced into the nuclear background S. strain W303 gave CW252 strain, which is used model respiratory pathologies. complete sequence this was obtained using a hybrid assembling methodology.

The genomes of 11 conspecific Streptomyces strains, i.e., from the same species and inhabiting ecological niche, were sequenced assembled. This data set offers an ideal framework to assess genome evolution in their context.