Post-transcriptional splicing can occur in a slow-moving zone around the gene

Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remains controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription site proximal zone through which RNA moves more slowly than in the nucleoplasm. Full-length pre-mRNA undergoes continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results m..., , , # Post-transcriptional splicing can occur in a slow-moving zone around the gene

[https://doi.org/10.5061/dryad.m0cfxppb7](https://doi.org/10.5061/dryad.m0cfxppb7)

## Description of the data and file structure

Matlab scripts in the **extraction_scripts** folder were used to generate data in the **extracted_data** and **extracted_images** folders. This data was analyzed by R and Matlab scripts in the **analysis_scripts** folder. Analyzed data was plotted into figure graphs using the R scripts in the **plot_scripts** folder.

### Folder structure:

#### Cote\_eLife\_scripts

* /analysis_scripts: R and .m files
* /extracted_data: CSV files with information about genes, etc., and .tif images, STORM density maps
* /extracted_images: organized .tif files
* /extraction_scripts: .m scripts
* /plot_scripts: R scripts for plots

#### Cote\_eLife\_raw\_data\_1 - Cote\_eLife\_raw\_data\_6

These folders contain .tif images of cells, and some contain matlab files with the corresponding d...

剪接（Splicing）是将内含子（intron）从前体mRNA（pre-mRNA）中移除，并将外显子（exon）连接以形成成熟mRNA序列的分步分子过程。关于该过程的时序与空间分布仍存在争议：两种对立模型分别认为剪接发生于转录过程中，或转录完成之后。本研究借助单分子RNA荧光原位杂交（single-molecule RNA FISH）、扩展显微镜技术（expansion microscopy）与活细胞成像（live-cell imaging），揭示了哺乳动物细胞内新生转录本的时空分布特征。在超分辨成像尺度下，我们观察到前体mRNA在转录位点周围形成云状聚集区；该区域即为转录位点近端区，RNA在此区域内的移动速率慢于核质（nucleoplasm）环境。全长前体mRNA在转录完成后穿过该区域的过程中会持续发生剪接，这提示一种新模型：剪接可在转录后发生，但仍局限于转录位点附近，因此在多数检测中表现为共转录过程。本研究结果表明…… # 转录后剪接可发生于基因周围的慢速移动区域

[https://doi.org/10.5061/dryad.m0cfxppb7](https://doi.org/10.5061/dryad.m0cfxppb7)

## 数据与文件结构说明

Matlab 脚本存放于**extraction_scripts**文件夹内，用于生成**extracted_data**与**extracted_images**文件夹中的数据。上述数据通过**analysis_scripts**文件夹内的R与Matlab脚本完成分析。利用**plot_scripts**文件夹内的R脚本，可将分析后的数据绘制成统计图。

### 文件夹结构：

#### Cote_eLife_scripts
* /analysis_scripts：R与.m格式文件
* /extracted_data：包含基因信息等内容的CSV文件，以及.tif格式图像、STORM密度图
* /extracted_images：已整理的.tif格式文件
* /extraction_scripts：.m格式脚本
* /plot_scripts：用于绘图的R脚本

#### Cote_eLife_raw_data_1 - Cote_eLife_raw_data_6
此类文件夹包含细胞的.tif格式图像，部分文件夹还包含带有对应d...的Matlab文件。