Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis
Abstract Background Presently, there is no comprehensive analysis of the transcription regulation network in hematopoiesis. Comparison of networks arising from gene co-expression across species can facilitate an understanding of the conservation of functional gene modules in hematopoiesis. Results W...
Main Authors: | , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2020-12-01
|
Series: | BMC Genomics |
Subjects: | |
Online Access: | https://doi.org/10.1186/s12864-020-07241-2 |
id |
doaj-db7e8afad6d44868a9c53ab59fb2a036 |
---|---|
record_format |
Article |
spelling |
doaj-db7e8afad6d44868a9c53ab59fb2a0362021-01-03T12:10:19ZengBMCBMC Genomics1471-21642020-12-0121S1111510.1186/s12864-020-07241-2Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesisShouguo Gao0Zhijie Wu1Xingmin Feng2Sachiko Kajigaya3Xujing Wang4Neal S. Young5Hematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of HealthHematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of HealthHematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of HealthHematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of HealthDivision of Diabetes, Endocrinology, and Metabolic Diseases (DEM), NIDDK, National Institutes of HealthHematopoiesis and Bone Marrow Failure Laboratory, Hematology Branch, NHLBI, National Institutes of HealthAbstract Background Presently, there is no comprehensive analysis of the transcription regulation network in hematopoiesis. Comparison of networks arising from gene co-expression across species can facilitate an understanding of the conservation of functional gene modules in hematopoiesis. Results We used single-cell RNA sequencing to profile bone marrow from human and mouse, and inferred transcription regulatory networks in each species in order to characterize transcriptional programs governing hematopoietic stem cell differentiation. We designed an algorithm for network reconstruction to conduct comparative transcriptomic analysis of hematopoietic gene co-expression and transcription regulation in human and mouse bone marrow cells. Co-expression network connectivity of hematopoiesis-related genes was found to be well conserved between mouse and human. The co-expression network showed “small-world” and “scale-free” architecture. The gene regulatory network formed a hierarchical structure, and hematopoiesis transcription factors localized to the hierarchy’s middle level. Conclusions Transcriptional regulatory networks are well conserved between human and mouse. The hierarchical organization of transcription factors may provide insights into hematopoietic cell lineage commitment, and to signal processing, cell survival and disease initiation.https://doi.org/10.1186/s12864-020-07241-2HematopoiesisGene regulatory networkCo-expression networkSingle-cell RNA sequencingCross-species network analysis |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Shouguo Gao Zhijie Wu Xingmin Feng Sachiko Kajigaya Xujing Wang Neal S. Young |
spellingShingle |
Shouguo Gao Zhijie Wu Xingmin Feng Sachiko Kajigaya Xujing Wang Neal S. Young Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis BMC Genomics Hematopoiesis Gene regulatory network Co-expression network Single-cell RNA sequencing Cross-species network analysis |
author_facet |
Shouguo Gao Zhijie Wu Xingmin Feng Sachiko Kajigaya Xujing Wang Neal S. Young |
author_sort |
Shouguo Gao |
title |
Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis |
title_short |
Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis |
title_full |
Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis |
title_fullStr |
Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis |
title_full_unstemmed |
Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis |
title_sort |
comprehensive network modeling from single cell rna sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-12-01 |
description |
Abstract Background Presently, there is no comprehensive analysis of the transcription regulation network in hematopoiesis. Comparison of networks arising from gene co-expression across species can facilitate an understanding of the conservation of functional gene modules in hematopoiesis. Results We used single-cell RNA sequencing to profile bone marrow from human and mouse, and inferred transcription regulatory networks in each species in order to characterize transcriptional programs governing hematopoietic stem cell differentiation. We designed an algorithm for network reconstruction to conduct comparative transcriptomic analysis of hematopoietic gene co-expression and transcription regulation in human and mouse bone marrow cells. Co-expression network connectivity of hematopoiesis-related genes was found to be well conserved between mouse and human. The co-expression network showed “small-world” and “scale-free” architecture. The gene regulatory network formed a hierarchical structure, and hematopoiesis transcription factors localized to the hierarchy’s middle level. Conclusions Transcriptional regulatory networks are well conserved between human and mouse. The hierarchical organization of transcription factors may provide insights into hematopoietic cell lineage commitment, and to signal processing, cell survival and disease initiation. |
topic |
Hematopoiesis Gene regulatory network Co-expression network Single-cell RNA sequencing Cross-species network analysis |
url |
https://doi.org/10.1186/s12864-020-07241-2 |
work_keys_str_mv |
AT shouguogao comprehensivenetworkmodelingfromsinglecellrnasequencingofhumanandmouserevealswellconservedtranscriptionregulationofhematopoiesis AT zhijiewu comprehensivenetworkmodelingfromsinglecellrnasequencingofhumanandmouserevealswellconservedtranscriptionregulationofhematopoiesis AT xingminfeng comprehensivenetworkmodelingfromsinglecellrnasequencingofhumanandmouserevealswellconservedtranscriptionregulationofhematopoiesis AT sachikokajigaya comprehensivenetworkmodelingfromsinglecellrnasequencingofhumanandmouserevealswellconservedtranscriptionregulationofhematopoiesis AT xujingwang comprehensivenetworkmodelingfromsinglecellrnasequencingofhumanandmouserevealswellconservedtranscriptionregulationofhematopoiesis AT nealsyoung comprehensivenetworkmodelingfromsinglecellrnasequencingofhumanandmouserevealswellconservedtranscriptionregulationofhematopoiesis |
_version_ |
1724350765568360448 |