Mapping the splicing landscape of the human immune system

Most human genes code for more than one transcript. Different ratios of transcripts of the same gene can be found in different cell types or states, indicating differential use of transcription start sites or differential splicing. Such differential transcript use (DTUs) events provide an additional...

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Bibliographic Details
Published in:	Frontiers in immunology Vol. 14; p. 1116392
Main Authors:	Ner-Gaon, Hadas, Peleg, Ronnie, Gazit, Roi, Reiner-Benaim, Anat, Shay, Tal
Format:	Journal Article
Language:	English
Published:	Switzerland Frontiers Media S.A 30-08-2023
Subjects:	alternative promoters alternative splicing Blood Grouping and Crossmatching differential splicing Health Status Humans immune related diseases Immune System Immunology RNA Splicing RNA Splicing Factors sepsis immune related diseases immune system alternative splicing differential splicing alternative promoters sepsis
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Summary:	Most human genes code for more than one transcript. Different ratios of transcripts of the same gene can be found in different cell types or states, indicating differential use of transcription start sites or differential splicing. Such differential transcript use (DTUs) events provide an additional layer of regulation and protein diversity. With the exceptions of PTPRC and CIITA, there are very few reported cases of DTU events in the immune system. To rigorously map DTUs between different human immune cell types, we leveraged four publicly available RNA sequencing datasets. We identified 282 DTU events between five human healthy immune cell types that appear in at least two datasets. The patterns of the DTU events were mostly cell-type-specific or lineage-specific, in the context of the five cell types tested. DTUs correlated with the expression pattern of potential regulators, namely, splicing factors and transcription factors. Of the several immune related conditions studied, only sepsis affected the splicing of more than a few genes and only in innate immune cells. Taken together, we map the DTUs landscape in human peripheral blood immune cell types, and present hundreds of genes whose transcript use changes between cell types or upon activation.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: Charles Jay Malemud, Case Western Reserve University, United States Reviewed by: Martin Hemberg, Brigham and Women’s Hospital and Harvard Medical School, United States; Dr. Vikram Dalal, Washington University in St. Louis, United States
ISSN:	1664-3224 1664-3224
DOI:	10.3389/fimmu.2023.1116392