التفاصيل البيبلوغرافية
| العنوان: |
The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila |
| المؤلفون: |
Chen, Tao, Wei, Xiaolu, Courret, Cecile, Cui, Min, Cheng, Lin, Wu, Jing, Ahmad, Kami, Larracuente, Amanda, Rong, Yikang S. |
| بيانات النشر: |
Zenodo |
| سنة النشر: |
2022 |
| المجموعة: |
Zenodo |
| مصطلحات موضوعية: |
Drosophila telomere, chromatin profiling, ChIP-seq, GFP tagged proteins, CUT&RUN, CUT&TAG |
| الوصف: |
Advances in genomic technology lead to a more focused pattern for the distribution of chromosomal proteins and a better understanding of their functions. The recent development of the CUT&RUN technique marks one of the important such advances. Here we develop a modified CUT&RUN technique that we termed nanoCUT&RUN, in which a high affinity nanobody to GFP is used to bring micrococcal nuclease to the binding sites of GFP-tagged chromatin proteins. Subsequent activation of the nuclease cleaves the chromatin, and sequencing of released DNA identifies binding sites. We show that nanoCUT&RUN efficiently produces high quality data for the TRL transcription factor in Drosophila embryos, and distinguishes binding sites specific between two TRL isoforms. We further show that nanoCUT&RUN dissects the distributions of the HipHop and HOAP telomere capping proteins, and uncovers unexpected binding of telomeric proteins at centromeres. nanoCUT&RUN can be readily applied to any system in which a chromatin protein of interest, or its isoforms, carries the GFP tag. ; Bigwig files are indexed binary format. They can be open in IGV software to visualize the coverage track along the genome. We used them as input in our R script to make plots, using the package karyoploteR and the command kpPlotBigWig. Those coverage files were used to make Figure 2-4-S4-S5-S6-S10. The R scripts used to make the figures can be find here: https://github.com/LarracuenteLab/nanoCUTandRUN.github . File are organized by figure. The first part of the file name corresponds to the genotype (HipHop or HOAP transgenes). The second part corresponds to the replicate number ("_1", "_2") or digestion time ("_2min", "_15min"). The last part of the file name indicates whether we kept multi-mapping reads (".mapped.sorted.RPM.bw) or only report uniquely mapping reads (".unique.mapped.sorted.RPM.bw"). For example "hiphop_2.mapped.sorted.RPM" corresponds to normalized multi-mapping read coverage of the second replicate of nanoCUT&Run data ... |
| نوع الوثيقة: |
other/unknown material |
| اللغة: |
unknown |
| Relation: |
https://doi.org/10.1101/2022.04.20.488892; https://zenodo.org/communities/dryad; https://doi.org/10.5061/dryad.zcrjdfngc; oai:zenodo.org:7055717 |
| DOI: |
10.5061/dryad.zcrjdfngc |
| الاتاحة: |
https://doi.org/10.5061/dryad.zcrjdfngc |
| Rights: |
info:eu-repo/semantics/openAccess ; Creative Commons Zero v1.0 Universal ; https://creativecommons.org/publicdomain/zero/1.0/legalcode |
| رقم الانضمام: |
edsbas.C81DF3BE |
| قاعدة البيانات: |
BASE |