Capsid-mediated chromatin state of the AAV vector genome controls host species range

A Gonzalez-Sandoval, S Tsuji, F Zhang, KL Hung… - bioRxiv, 2022 - biorxiv.org
… of vector copies in DNase I treated vs untreated nuclear … between species by treating
transduced cells with DNase I prior … from degradation in the +DNase I condition in both species. …

GTP‐dependent regulation of heterochromatin fluctuations at subtelomeric regions in Saccharomyces cerevisiae

T Ayano, T Yokosawa, M Oki - Genes to Cells, 2024 - Wiley Online Library
… , not all chromatin states are maintained throughout life; chromatinUsing budding yeast,
we have developed a system to track … The primers used for real-time PCR are listed in Table 2. …

[HTML][HTML] The AAV capsid can influence the epigenetic marking of rAAV delivered episomal genomes in a species dependent manner

A Gonzalez-Sandoval, K Pekrun, S Tsuji… - Nature …, 2023 - nature.com
… Programming viral chromatin states by capsid design may … between species by treating
transduced cells with DNAse I prior to … in the same manner as the nuclei were used as control. …

Mapping chromatin state and transcriptional response in CIC-DUX4 undifferentiated round cell sarcoma

NJ Thomas, C Luck, N Shlimon, RK Ponce, Z Kosibaty… - bioRxiv, 2023 - biorxiv.org
… -DUX4 directly binds and transcriptionally controls DUSP6, a negative regulator … control by
CIC-DUX4 (Figure 4A). To confirm CIC-DUX4 target gene regulation, we performed qRT-PCR

[HTML][HTML] Histone H3. 3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters

M Trovato, D Bunina, U Yildiz… - Nature …, 2024 - nature.com
… 3K9 and K27 crucially orchestrate repressive chromatin states at … Monitoring proliferation
over six days revealed decreased … described above (see “Quantitative real-time PCR” section). …

Cell-surface SLC nucleoside transporters and purine levels modulate BRD4-dependent chromatin states

KC Li, E Girardi, F Kartnig, S Grosche, T Pemovska… - Nature …, 2021 - nature.com
Real-time PCR analysis confirmed that 6-MP treatment or … To address this, we performed
stable isotope tracing … extracted using RNeasy Mini kit (Qiagen) including a DNase I …

Mammalian PERIOD2 regulates H2A. Z incorporation in chromatin to orchestrate circadian negative feedback

K Tartour, F Andriani, EG Folco, D Letkova… - Nature Structural & …, 2022 - nature.com
… Z mimicked the Per null chromatin state and disrupted cellular … 100 nM dexamethasone, and
real-time bioluminescence was … (Iprasense) by continuous monitoring of cell cultures inside …

[HTML][HTML] Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction

C Liu, J Yu, A Song, M Wang, J Hu, P Chen… - Nature …, 2023 - nature.com
… To track the dynamic restoration of H3K27me3 on nascent … Using epigenomic markers to
annotate chromatin states, we … Quantitative real-time PCR (qPCR) analyses were performed …

Spectroscopic label-free microscopy of changes in live cell chromatin and biochemical composition in transplantable organoids

G Pettinato, MF Coughlan, X Zhang, L Chen… - Science …, 2021 - science.org
… with quantitative real-time polymerase chain reaction (PCR), is … for monitoring the differentiation
state of organoids in real time. … , exhibiting a closed chromatin state. These domains are …

Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

S Battaglia, K Dong, J Wu, Z Chen, FJ Najm, Y Zhang… - Nature …, 2022 - nature.com
… gene regulatory elements by their chromatin state. However, … closely corresponded to the
real-time trajectory of activation (… known TF motifs using the motif track provided by HOMER v.…