Lmst

The liver #transcriptome is highly sensitive to metabolic cues. By characterizing nuclear protein #OGlcNAcylation in mouse #liver during the day, this study shows how shifts in a nutrient-sensitive #PTM may shape transcriptional regulation @PLOSBiology https://plos.io/3KuS7m1

Model describing how daily rhythmic O-GlcNAc proteome integrates environmental and metabolic signals to regulate transcriptomic and physiological rhythms. Environmental cues signaling through the molecular clock and metabolic cues from feeding–fasting cycles regulate daily rhythms in the O-GlcNAc proteome. Rhythmic O-GlcNAcylation can directly shape daily rhythmicity in transcriptome and physiology. In addition, rhythmic O-GlcNAcylation can also interact with rhythmic phosphorylation. Different forms of crosstalk between O-GlcNAc proteome and phosphoproteome are shown in the middle box. The red solid arrows indicate the regulations described in this study, while the dashed arrow indicates regulations discovered by previous studies. Figure created using BioRender.com.

Wang et al. explore #adaptation to #karst geology in the medicinal plant Hemiboea subcapitata using a #chromosome-level #genome and #transcriptome analysis, revealing effects on flavonoid metabolism. #plantscience #evolution #botany
@wileyecolevol @wileyplantsci
https://doi.org/10.1111/jse.70007

Graphic showing a Circos plot of the genome and a drawing of the medicinal plant Hemiboea subcapitata, with "Facultative adaptation" underneath it and dashed lines to either side. The left side reads "non-karst" and leads to a bar graph depicting whole-genome duplications. the right side reads "karst" and leads to a diagram of gene regulation, showing various players forming MBW complexes.

Pipeline release! nf-core/denovotranscript v1.2.1 - nf-core/denovotranscript v1.2.1!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.2.1

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

The #spider #Tibellus #oblongus (#Philodromidae) has a #Holarcticdistribution and is common in Central Europe, thus not being protected. It prefers #sunexposed #habitats, whether dry or moist, and is a free #hunter that is very well #camouflaged due to its elongated #bodyshape. Y. Korolkova et al. (2023) examined the #venomgland #transcriptome and a venom proteome analysis.

Ref
Y. Korolkova et al. (2023)
https://doi.org/10.1038/s41597-023-02703-0

Photos
© S.F. Wirth

Tibellus oblongus lurking as an active hunter that builds no otb web on a flower head of common tansy on a semi-dry meadow in village Rosenthal (near Tegeler Fließ area) in Northern Berlin, © Stefan F. Wirth, August 2025

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

old paper on the development of sympatric morphs

#arcticcharr #transcriptome #rnaseq #fish #evolution #sympatry
#peerj #biology
https://peerj.com/articles/4345/

#Microbiota transplantation offers new hope against #cotton #leaf_curl #disease.

#CLCuD #rhizosphere #phylosphere #Gossypium # #microbiome #transcriptome

https://phys.org/news/2025-03-microbiota-transplantation-cotton-leaf-disease.html

Are you ready for #EMBLEpitrans? Prepare to deep dive into advances in RNA modification functions, their key roles in gene expression, disease, and transformative therapies. Be part of the community🔬💡

📩 Submit your abstract by 5 August
🗓️ 28 – 30 October
📍 EMBL Heidelberg and Virtual
➡️ https://s.embl.org/etc25-01-ma

#EMBLEvents #geneexpression #RNAmodification #mRNA #RNA #transcriptome

Pipeline release! nf-core/denovotranscript v1.2.0 - nf-core/denovotranscript v1.2.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.2.0

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

Random question for #transcriptome #bioinformatics folks - is there ever a reason to screen transcriptome assemblies (lots of small contigs) against database using ANI tools (i.e. skani)?

Curious to know if there's a usage case for it.

Do or die: How #soybeans tackle #nematode invaders.

#agriculture #transcriptome #RNA

https://phys.org/news/2025-01-die-soybeans-tackle-nematode-invaders.html

I've been seeing a few #transcriptome wide association studies (TWAS) papers lately. This is another example, from #sorghum, combining GWAS and TWAS to study flowering time. Bonus - I imagine that there's a lot more value that can be gained from the 822 #RNAseq samples made publicly available

https://www.biorxiv.org/content/10.1101/2024.12.12.628249v1.full.pdf

#PlantScience #PlantDevelopment #Sorghum

Manhattan plot and inferred pathway from combining GWAS and TWAS results

Pipeline release! nf-core/denovotranscript v1.1.0 - nf-core/denovotranscript v1.1.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.1.0

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

Luo et al. use comparative #transcriptome analysis with isolated two-celled #proembryos to explore the potential regulatory network underlying NtCP14-triggered programed #cell death in #embryos.
https://doi.org/10.1111/jipb.13795
@wileyplantsci
#PlantSci #JIPB #plant #development #embryogenesis #botany

Micrographs of suspensor cell PCD, annotated diagrams showing ROS expression in suspensor cell PCD, and a proposed molecular network underlying protease-triggered PCD.

Human molecular map contributes to understanding of disease mechanisms
https://www.sciencedaily.com/releases/2024/09/240911175947.htm

Roadmap to molecular human linking multiomics w. population traits, diabetes subtype
https://www.nature.com/articles/s41467-024-51134-x

6,304 quantitative molec. traits
1,221,345 genetic variants
methylation @ 470,837 DNA CpG sites
gene expression: 57,000 transcripts

#metabolome #connectome #interactome #genotype #phenotype #IndividualVariation #transcriptome #multiomics #omics #disease #MolecularEpidemiology #GeneExpression

Pipeline release! nf-core/denovotranscript v1.0.0 - nf-core/denovotranscript v1.0.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.0.0

#denovo-assembly #rna-seq #transcriptome #nfcore #openscience #nextflow #bioinformatics

#Genetic signatures of #domestication identified in #pigs and #chickens.

#agriculture #anthropology #transcriptome

https://phys.org/news/2024-08-genetic-signatures-domestication-pigs-chickens.html

Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. https://doi.org/10.1038/s41598-024-60593-7 #SpinalMuscularAtrophy,Sma #SurvivalMotorNeuron,Smn #CircularRna,Circrna #Proteome #Transcriptome

You know what really 🪲#bugs🪲me? Not having a stable framework for understanding the #evolutionary history of #Cucujiformia...
...Oh, hello there, Li et al.!
https://doi.org/10.1111/jse.13079
@WileyEcolEvol
#transcriptome #phylogenetics #data #Coleoptera #beetle #insect #entomology #evolution

Comprehensive phylogenomic analyses illustrate phylogenetic relationships within the Cucujiformia.

The #genetic interplay in Impatiens #downy_mildew: A #transcriptome-based approach to enhancing #disease resistance.

#plants #agriculture #RLK

https://phys.org/news/2024-05-genetic-interplay-impatiens-downy-mildew.html

Team reports on relationship between contents of #diosgenin and #brassinosteroids in #Dioscorea zingiberensis.

#hypomethylation #transcriptome

https://phys.org/news/2024-04-team-relationship-contents-diosgenin-brassinosteroids.html

#transcriptome

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