Mapping Whole-Transcriptome Splicing in Mouse Hematopoietic Stem Cells

Oron Goldstein; Karin Meyer; Yariv Greenshpan; Nir Bujanover; Mili Feigin; Hadas Ner-Gaon; Tal Shay; Roi Gazit

doi:10.1016/j.stemcr.2016.12.002

Mapping Whole-Transcriptome Splicing in Mouse Hematopoietic Stem Cells

Stem Cell Reports. 2017 Jan 10;8(1):163-176. doi: 10.1016/j.stemcr.2016.12.002. Epub 2016 Dec 29.

Authors

Oron Goldstein¹, Karin Meyer², Yariv Greenshpan¹, Nir Bujanover¹, Mili Feigin², Hadas Ner-Gaon³, Tal Shay³, Roi Gazit⁴

Affiliations

¹ The Shraga Segal Department for Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel.
² The Shraga Segal Department for Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel.
³ Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel.
⁴ The Shraga Segal Department for Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel; Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel. Electronic address: gazitroi@bgu.ac.il.

Abstract

Hematopoietic stem cells (HSCs) are rare cells that generate all the various types of blood and immune cells. High-quality transcriptome data have enabled the identification of significant genes for HSCs. However, most genes are expressed in various forms by alternative splicing (AS), extending transcriptome complexity. Here, we delineate AS to determine which isoforms are expressed in mouse HSCs. Our analysis of microarray and RNA-sequencing data includes differential expression of splicing factors that may regulate AS, and a complete map of splicing isoforms. Multiple types of isoforms for known HSC genes and unannotated splicing that may alter gene function are presented. Transcriptome-wide identification of genes and their respective isoforms in mouse HSCs will open another dimension for adult stem cells.

Keywords: HSC; ImmGen; RNA-sequencing analysis; adult stem cell splicing; alternative splicing; hematopoietic stem cell; splicing-function; unannotated splicing; whole-transcriptome splicing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alternative Splicing*
Animals
Cluster Analysis
Computational Biology / methods
DNA-Binding Proteins / genetics
Exons
Gene Expression Profiling
Gene Ontology
Hematopoietic Stem Cells / cytology
Hematopoietic Stem Cells / metabolism*
Homeodomain Proteins / genetics
Introns
Mice
Phenotype
Transcription Factors / genetics
Transcriptome*
Web Browser

Substances

DNA-Binding Proteins
Homeodomain Proteins
Prdm16 protein, mouse
Transcription Factors
homeobox protein HOXA9