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GenomicsChip-seq of S. cerevisiae to investigate post-transcriptional buffering of low nascent RNA transcription by Puf5
Gene expression is a dynamic process regulated on several layers starting with transcription, mRNA export, translation and finally, mRNA degradation. While subsequent layers heavily influence each other, it is not clear if the most extreme layers, chromatin architecture and mRNA decay are linked. He...
ORGANISM(S): Saccharomyces cerevisiae 
2021-07-19 | E-MTAB-10105 | biostudies-arrayexpress
GenomicsGlutamine methylation on Histone H2A is an RNA Polymerase I dedicated modification
Nucleosomes are decorated with numerous post-translational modifications capable of influencing many DNA processes. Here, we describe a new class of modification, methylation of glutamine, occurring on yeast histone H2A at position 105 (Q105) and human H2A at Q104. We identify Nop1 as the methyltran...
ORGANISM(S): Saccharomyces cerevisiae 
2014-01-21 | E-MTAB-1447 | biostudies-arrayexpress
ProteomicsMethylation of Q105 on histone H2A is part of a dynamic regulatory mechanism integrating metabolism with ribosome biogenesis through recruitment of Nhp2
Ribosome biogenesis is an essential process within cells that requires integration of extracellular cues such as metabolic states through signaling with transcriptional regulation and maintenance of accessible chromatin at the ribosomal DNA. Here, we demonstrate that the recently identified histone ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-08-06 | PXD023510 | Pride
Ip Lfq Silac 
TranscriptomicsscATAC-seq of mouse liver tissue derived from young and old mice II
We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 2259 nuclei prepared from 3 young liver tissues and 2490 nuclei from 3 o...
ORGANISM(S): Mus musculus 
2023-11-09 | E-MTAB-12560 | biostudies-arrayexpress
ProteomicsReduced polymerase pausing compensates for increased chromatin accessibility in the aging liver
Regulation of gene expression is linked to the organization of the genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes on the level of transcriptional regulation. Here, w...
ORGANISM(S): Mus musculus (Mouse) 
2022-09-15 | PXD034564 | Pride
Tmt Chromating Polymerase Liver Aging 
TranscriptomicsscATAC-seq of mouse liver tissue derived from young and old mice
We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 4838 nuclei prepared from 3 young liver tissues and 3361 nuclei from 3 o...
ORGANISM(S): Mus musculus 
2023-02-20 | E-MTAB-12706 | biostudies-arrayexpress
TranscriptomicsscRNA-seq of mouse liver tissue derived from young and old mice
We want to investigate how cells in the specific zones in murine liver are affected by age-related changes of the microenvironment. To this end, we generated high-quality scRNA-seq dataset of hepatocytes using Smart-seq3express from 2 young (3-5 months) and 2 old (18-20 months) male mice. Livers wer...
ORGANISM(S): Mus musculus 
2023-11-01 | E-MTAB-12579 | biostudies-arrayexpress
TranscriptomicsPost-transcriptional buffering of low nascent RNA transcription by Puf5
Gene expression is a dynamic process regulated on several layers starting with transcription, mRNA export, translation and finally, mRNA degradation. While subsequent layers heavily influence each other, it is not clear if the most extreme layers, chromatin architecture and mRNA decay are linked. He...
ORGANISM(S): Saccharomyces cerevisiae 
2021-07-19 | E-MTAB-10107 | biostudies-arrayexpress
TranscriptomicsBulk RNA-seq of organoids derived from young and old mice livers
We set up liver-derived organoids to study the ageing progenitor population. We detected epigenetic and transcriptional memory in organoids derived from old mice accompanied by alterations in drug and fatty acid metabolism pathways, similar to phenotypes observed in the liver itself.
ORGANISM(S): Mus musculus 
2024-11-30 | E-MTAB-11060 | biostudies-arrayexpress
TranscriptomicsSpatial Transcriptomics of ageing mouse liver tissues give insights into the zonation-specific lipid deposition
To gain in situ information on the transcriptional profile of the different zones upon ageing, we used the 10X Genomics Visium Platform and ran 5µm tissue cryosections from livers of 2 young and 2 old mice. We investigated the transcriptional events that differentiate lipid metabolism in ageing, acr...
ORGANISM(S): Mus musculus 
2023-11-09 | E-MTAB-12809 | biostudies-arrayexpress
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