Project description:The nature of chromatin as regular succession of nucleosomes has gained iconic status. The average nucleosome repeat length (NRL) determined by classical means serves as index for bulk chromatin of a given specimen. However, this value is dominated by regular heterochromatin since nucleosomal arrays are often not regular at individual single copy sequences. To obtain a measure for nucleosome regularity in euchromatin we subjected nucleosome dyad profiles to autocorrelation and spectral density analyses. This revealed variation in nucleosome regularity and NRL at different types of euchromatin and yielded a comprehensive catalog of regular phased nucleosome arrays (PNA). The absence of the nucleosome sliding factor ACF1 correlated with global loss of regularity in euchromatin and increased NRL and compromised phasing at a novel type of PNA. Our approach is generally applicable to characterize hallmarks of euchromatin organization.
Project description:The nature of chromatin as regular succession of nucleosomes has gained iconic status. The average nucleosome repeat length (NRL) determined by classical means serves as index for bulk chromatin of a given specimen. However, this value is dominated by regular heterochromatin since nucleosomal arrays are often not regular at individual single copy sequences. To obtain a measure for nucleosome regularity in euchromatin we subjected nucleosome dyad profiles to autocorrelation and spectral density analyses. This revealed variation in nucleosome regularity and NRL at different types of euchromatin and yielded a comprehensive catalog of regular phased nucleosome arrays (PNA). The absence of the nucleosome sliding factor ACF1 correlated with global loss of regularity in euchromatin and increased NRL and compromised phasing at a novel type of PNA. Our approach is generally applicable to characterize hallmarks of euchromatin organization.
Project description:The nature of chromatin as regular succession of nucleosomes has gained iconic status. The average nucleosome repeat length (NRL) determined by classical means serves as index for bulk chromatin of a given specimen. However, this value is dominated by regular heterochromatin since nucleosomal arrays are often not regular at individual single copy sequences. To obtain a measure for nucleosome regularity in euchromatin we subjected nucleosome dyad profiles to autocorrelation and spectral density analyses. This revealed variation in nucleosome regularity and NRL at different types of euchromatin and yielded a comprehensive catalog of regular phased nucleosome arrays (PNA). The absence of the nucleosome sliding factor ACF1 correlated with global loss of regularity in euchromatin and increased NRL and compromised phasing at a novel type of PNA. Our approach is generally applicable to characterize hallmarks of euchromatin organization.
Project description:The nature of chromatin as regular succession of nucleosomes has gained iconic status. However, since most nucleosomes in metazoans are poorly positioned it is unknown to which extent the bulk genomic nucleosome repeat length (NRL) reflects the regularity and spacing of nucleosome arrays at individual loci. We describe a new approach to map nucleosome fiber regularity and spacing through sequencing oligonucleosome-derived DNA by classical as well as emergent nanopore-technology. This revealed modulation of chromatin regularity and NRL depending on functional chromatin states independently of nucleosome positioning and even in unmappable regions. We also found that that nucleosome arrays downstream of silent promoters are considerably more regular than those downstream of highly expressed ones, despite most extensive nucleosome phasing of the latter. Our approach is generally applicable and provides an important parameter of chromatin organisation that so far had been missing.
Project description:MicroRNAs (miRNAs) are essential regulators of all developmental processes, including neurogenesis, when the production of large numbers of neurons from a limited number of neural stem cells depends on the precise control of determination, proliferation and differentiation. However, miRNA regulation of target mRNAs is highly promiscuous, a single miRNA can target many mRNAs and vice versa, raising the question of how specificity is achieved to elicit a precise regulatory response. Here we introduce in vivo AGO-APP, a novel approach to purify Argonaute-bound miRNAs directly from living cells and tissues. Using this technology, we isolate actively inhibiting miRNAs from different neural cell populations in the larval Drosophila central nervous system. We identify a defined group of miRNAs that redundantly target all iconic genes known to control the transition from neuroblasts to neurons. In vivo functional studies demonstrate that knockdown of individual miRNAs among this group does not induce detectable cellular phenotypes. However, simultaneous knockdown of multiple miRNAs leads to precocious stem cell differentiation, demonstrating functional interdependence. Our study shows that miRNAs cooperate within a regulatory module to specify the targeted gene network.
2023-08-11 | GSE240560 | GEO
Project description:The microbial aerosol composition of iconic fog systems in Coastal Maine and the Namib Desert