IlLycPorp1
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB61622 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Lycophotia porphyrea (true lover's knot) genome assembly, ilLycPorp1, alternate haplotype
| PRJEB61623 | ENA
Project description:Lycophotia porphyrea (true lover's knot), genomic and transcriptomic data
| PRJEB61364 | ENA
Project description:We investigated the reported binding of telomere associated factor TERF1 and TERF2 to internal telomere sites using ChIP-Seq for these two factors in a lymphoblastoid cell line. We mapped over 40 million reads for each sample to a custom reference genome that incorporates our subtelomere assembly, and generated signal tracks using only uniquely mapping reads, and also using a multimapping pipeline we developed. We find that peaks are misshapen and made up of reads that cannot be distinguished from true telomere sequence. Removing telomere identified reads removes all internal signal. Examination of TRF1 and TRF2
2014-02-18 | E-GEOD-55053 | biostudies-arrayexpress
Project description:The histone lysine acetyltransferase TIP60 is the main enzyme that catalyzes histone H4 acetylation in cells. Domains on TIP60 regulate its enzymatic activity from different aspects. Here we use a CRISPR-Cas9 tiling screen to scan for essential domains on TIP60 protein and found that the Tudor-knot domain is essential for cell survival and intercellular H4 acetylation. We performed in-vitro biochemical assays and demonstrated Tudor-knot domain is not a histone reader. And deficiency of the Tudor-knot domain has mild effects on TIP60 intracellular localization, as well as the TIP60 complex’s constitution. But Tudor-knot deficiency significantly reduces TIP60 HAT activity both in vivo and in vitro. By comparing the catalytic efficiency of nucleosome substrate and histone octamer substrate, as well as TIP60 protein alone or TIP60 complex, we found the nucleosomal structure and other TIP60 complex components are required for Tudor-knot relative HAT activity regulation. We propose that the Tudor-knot domain function to increase nucleosome accessibility. Finally, we show that the Tudor-knot domain is required for TIP60-dependent transcription regulation. Altogether, our study reveals a mechanism that the Tudor-knot domain that regulates TIP60-dependent transcription through the regulation of TIP60 substrate catalytic efficiency.
2023-12-24 | GSE245116 | GEO
Project description:KAT8 is a lysine acetyltransferase and is involved in multiple important biological processes including cancer. The well-known function of KAT8 is catalyzing acetylation on histone H4, which regulates gene expression and chromatin decompaction. Besides catalytic HAT domain, the function of Tudor-knot domain of KAT8 remains largely unclear. Here, we report a novel function of Tudor-knot domain in facilitates histone acetyltransferase activity on H4K16ac. One hot-spot cancer mutation on Tudor-knot domain of KAT8 inhibits its interaction with nucleosome and reduces H4K16ac level both in vitro and in cells without altering the chromatin occupancy. Interestingly, this Tudor-knot mutation does not influence acetylation activity of KAT8 on p53, a non-histone substrate, suggests the important function of KAT8 Tudor-knot domain in the substrate specific catalytic regulation.
2023-12-24 | GSE245007 | GEO
Project description:We investigated the reported binding of telomere associated factor TERF1 and TERF2 to internal telomere sites using ChIP-Seq for these two factors in a lymphoblastoid cell line. We mapped over 40 million reads for each sample to a custom reference genome that incorporates our subtelomere assembly, and generated signal tracks using only uniquely mapping reads, and also using a multimapping pipeline we developed. We find that peaks are misshapen and made up of reads that cannot be distinguished from true telomere sequence. Removing telomere identified reads removes all internal signal.
2014-02-18 | GSE55053 | GEO
Project description:The aim of study is to investigate DEGs, long non-coding RNAs and alternative splicing events in the development of galls and neighboring region compared to the non-infected whole root induced by root-knot nematode (RKN, Meloidogyne incognita). Total RNA was extracted, ribosomal depleted libraries were prepared, and then high throughput RNA sequencing was performed using the Illumina NovaSeq 6000. High quality, paired-end reads were then aligned to the tomato reference genome (Heinz1706 assembly SL4.0) and uniquely mapped reads were counted using Htseq. Finally, differentially expressed genes (DEGs) between whole roots-galls and whole roots-neighboring region were identified using DESeq package and downstream analyses were performed.
2024-07-29 | GSE232828 | GEO
Project description:The histone lysine acetyltransferase TIP60 is the main enzyme that catalyzes histone H4 acetylation in cells. Domains on TIP60 regulate its enzymatic activity from different aspects. Here we use a CRISPR-Cas9 tiling screen to scan for essential domains on TIP60 protein and found that the Tudor-knot domain is essential for cell survival and intercellular H4 acetylation. We performed in-vitro biochemical assays and demonstrated Tudor-knot domain is not a histone reader. And deficiency of the Tudor-knot domain has mild effects on TIP60 intracellular localization, as well as the TIP60 complex’s constitution. But Tudor-knot deficiency significantly reduces TIP60 HAT activity both in vivo and in vitro. By comparing the catalytic efficiency of nucleosome substrate and histone octamer substrate, as well as TIP60 protein alone or TIP60 complex, we found the nucleosomal structure and other TIP60 complex components are required for Tudor-knot relative HAT activity regulation. We propose that the Tudor-knot domain function to increase nucleosome accessibility. Finally, we show that the Tudor-knot domain is required for TIP60-dependent transcription regulation. Altogether, our study reveals a mechanism that the Tudor-knot domain that regulates TIP60-dependent transcription through the regulation of TIP60 substrate catalytic efficiency.
2023-12-24 | GSE245115 | GEO