Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation

bioRxiv preprint: https://www.biorxiv.org/content/10.1101/2020.04.02.022566v4 <strong>Contact:</strong> Grigorios Georgolopoulos ([e-mail]); Jeff Vierstra ([e-mail]) Lineage commitment and differentiation is driven by the concerted action of master transcriptional regulators at their target chromatin sites. Multiple efforts have characterized the key transcription factors (TFs) that determine the various hematopoietic lineages. However, the temporal interactions between individual TFs and their chromatin targets during differentiation and how these interactions dictate lineage commitment remains poorly understood. Here we delineate the temporal interplay between the <em>cis</em>- and the <em>trans</em>-regulatory landscape in establishing lineage commitment and differentiation in human hematopoiesis by performing a dense timecourse of chromatin accessibility (DNase I-seq), and gene expression (total and single cell RNA-seq). All data uploaded correspond to human genome build version GRCh38. <strong>Contents</strong> <strong>DNase I Hotspot (DHS) metadata: </strong>Supplementary_Data_1.txt <strong>DNase I Hotspot quantile-normalized counts:</strong> A tab-separated matrix with quantile-normalized DNase I density counts from 79,085 FDR 5% hotspots, across 12 erythroid differentiation timepoints from 3 donors, present in at least n=2 samples. Rows correspond to DHS information in Supplementary_Data_1.txt (hotspots.fdr.0.05.qnorm.counts.tsv.gz) <strong>Column information for DNase I Hotspot quantile-normalized counts: </strong>hotspots.fdr.0.05.qnorm.counts.info.tsv <strong>Developmentally regulated gene metadata (erythroid): </strong>Supplementary_Data_2.csv <strong>Gene matrix of quantile-normalized FPKM values (erythroid): </strong>A tab-separated matrix with the quantile-normalized FPKM values of all detected genes, across 13 erythroid differentiation timepoints from 3 donors. (fpkm_erythroid_qnorm.tsv.gz) <strong>Column information for the quantile-normalized FPKM gene matrix (erythroid): </strong>A tab-separated table (fpkm_erythroid_qnorm.info.tsv) <strong>CD34+ HSPC TADs at 10kb resolution: </strong>Supplementary_Data_3.bed <strong>Day 11 <em>ex vivo</em> erythroid progenitor TADs at 10kb resolution: </strong>Supplementary_Data_4.bed <strong>Transcription factor motif enrichment per DHS cluster: </strong>Supplementary_Data_5.csv <strong>Correlation information (links) between developmentally regulated DHS and target genes: </strong>Supplementary_Data_6.csv <strong>Chromatin anchor loops called from 10kb resolution Hi-C data: </strong>Supplementary_Data_7.bedgraph <strong>Developmentally regulated gene metadata (megakaryocytic): </strong>Supplementary_Data_8.csv <strong>Gene matrix of quantile-normalized FPKM values (megakaryocytic): </strong>A tab-separated matrix with the quantile-normalized FPKM values of all detected genes, across 13 megakaryocytic differentiation timepoints from 3 donors. (fpkm_megakaryocyte_qnorm.tsv.gz) <strong>Column information for the quantile-normalized FPKM gene matrix (megakaryocytic): </strong>A tab-separated table (fpkm_megakaryocyte_qnorm.info.tsv) <strong>Marker (differentially expressed) genes per single cell population: </strong>Supplementary_Data_9.csv <strong>A SCANPY h5ad Annotated DataFrame object: </strong>Annotated Data frame `anndata` in h5ad format including the gene-by-cell count matrix, Velocyto splicing kinetics (RNA velocity) information layer, along with obs, obsm, var, varm, and uns layers. (SCANPY_anndata_object.h5ad)bioRxiv预印本：https://www.biorxiv.org/content/10.1101/2020.04.02.022566v4 <strong>联系方式：</strong>Grigorios Georgolopoulos（邮箱：[e-mail]）；Jeff Vierstra（邮箱：[e-mail]） 细胞谱系定型与分化由主转录调控因子在其靶染色质位点的协同作用所驱动。已有多项研究刻画了决定各类造血谱系的关键转录因子（transcription factor, TF）。然而，分化过程中单个转录因子与其染色质靶位点之间的时序互作，以及这些互作如何调控谱系定型，目前仍未得到充分阐释。 本研究通过对染色质开放状态（DNase I-seq）以及基因表达（总RNA-seq与单细胞RNA-seq）进行高密度时序采样，阐明了人类造血过程中顺式（cis）与反式（trans）调控图谱在建立谱系定型与分化过程中的时序互作关系。本研究上传的所有数据均对应人类基因组组装版本GRCh38。 <strong>数据内容</strong> <strong>DNase I超敏感位点（DNase I Hotspot, DHS）元数据：</strong>Supplementary_Data_1.txt <strong>DNase I超敏感位点分位数标准化计数：</strong>一张制表符分隔的矩阵，包含来自3名供体的12个红细胞分化时间点、至少在2个样本中检出的79085个FDR 5%超敏感位点的分位数标准化DNase I密度计数。行对应Supplementary_Data_1.txt中的DHS信息（文件：hotspots.fdr.0.05.qnorm.counts.tsv.gz） <strong>DNase I超敏感位点分位数标准化计数的列信息：</strong>hotspots.fdr.0.05.qnorm.counts.info.tsv <strong>发育调控基因元数据（红细胞系）：</strong>Supplementary_Data_2.csv <strong>红细胞系分位数标准化FPKM值基因矩阵：</strong>一张制表符分隔的矩阵，包含来自3名供体的13个红细胞分化时间点中所有检出基因的分位数标准化FPKM值（文件：fpkm_erythroid_qnorm.tsv.gz） <strong>红细胞系分位数标准化FPKM基因矩阵的列信息：</strong>一张制表符分隔的表格（文件：fpkm_erythroid_qnorm.info.tsv） <strong>10kb分辨率下的CD34+造血干祖细胞（hematopoietic stem and progenitor cell, HSPC）拓扑关联结构域（topologically associating domain, TAD）：</strong>Supplementary_Data_3.bed <strong>10kb分辨率下的第11天体外（ex vivo）红细胞祖细胞拓扑关联结构域：</strong>Supplementary_Data_4.bed <strong>每个DHS聚类的转录因子基序富集分析结果：</strong>Supplementary_Data_5.csv <strong>发育调控型DHS与其靶基因之间的关联信息：</strong>Supplementary_Data_6.csv <strong>从10kb分辨率Hi-C数据中鉴定得到的染色质锚定环：</strong>Supplementary_Data_7.bedgraph <strong>发育调控基因元数据（巨核细胞系）：</strong>Supplementary_Data_8.csv <strong>巨核细胞系分位数标准化FPKM值基因矩阵：</strong>一张制表符分隔的矩阵，包含来自3名供体的13个巨核细胞分化时间点中所有检出基因的分位数标准化FPKM值（文件：fpkm_megakaryocyte_qnorm.tsv.gz） <strong>巨核细胞系分位数标准化FPKM基因矩阵的列信息：</strong>一张制表符分隔的表格（文件：fpkm_megakaryocyte_qnorm.info.tsv） <strong>各单细胞群的标记基因（差异表达基因）：</strong>Supplementary_Data_9.csv <strong>SCANPY h5ad注释数据框对象：</strong>一个h5ad格式的注释数据框`anndata`，包含基因-细胞计数矩阵、Velocyto剪接动力学（RNA速率）信息层，以及obs、obsm、var、varm与uns层（文件：SCANPY_anndata_object.h5ad）