What are housekeeping genes?
The concept of "housekeeping gene" has been used for four decades but remains loosely defined. Housekeeping genes are commonly described as "essential for cellular existence regardless of their specific function in the tissue or organism", and "stably expressed irrespective...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-07-01
|
| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1010295 |
| _version_ | 1828151359041437696 |
|---|---|
| author | Chintan J Joshi Wenfan Ke Anna Drangowska-Way Eyleen J O'Rourke Nathan E Lewis |
| author_facet | Chintan J Joshi Wenfan Ke Anna Drangowska-Way Eyleen J O'Rourke Nathan E Lewis |
| author_sort | Chintan J Joshi |
| collection | DOAJ |
| description | The concept of "housekeeping gene" has been used for four decades but remains loosely defined. Housekeeping genes are commonly described as "essential for cellular existence regardless of their specific function in the tissue or organism", and "stably expressed irrespective of tissue type, developmental stage, cell cycle state, or external signal". However, experimental support for the tenet that gene essentiality is linked to stable expression across cell types, conditions, and organisms has been limited. Here we use genome-scale functional genomic screens together with bulk and single-cell sequencing technologies to test this link and optimize a quantitative and experimentally validated definition of housekeeping gene. Using the optimized definition, we identify, characterize, and provide as resources, housekeeping gene lists extracted from several human datasets, and 10 other animal species that include primates, chicken, and C. elegans. We find that stably expressed genes are not necessarily essential, and that the individual genes that are essential and stably expressed can considerably differ across organisms; yet the pathways enriched among these genes are conserved. Further, the level of conservation of housekeeping genes across the analyzed organisms captures their taxonomic groups, showing evolutionary relevance for our definition. Therefore, we present a quantitative and experimentally supported definition of housekeeping genes that can contribute to better understanding of their unique biological and evolutionary characteristics. |
| first_indexed | 2024-04-11T21:55:42Z |
| format | Article |
| id | doaj.art-427b3e577d694634be26acfd89426dff |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-04-11T21:55:42Z |
| publishDate | 2022-07-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-427b3e577d694634be26acfd89426dff2022-12-22T04:01:07ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582022-07-01187e101029510.1371/journal.pcbi.1010295What are housekeeping genes?Chintan J JoshiWenfan KeAnna Drangowska-WayEyleen J O'RourkeNathan E LewisThe concept of "housekeeping gene" has been used for four decades but remains loosely defined. Housekeeping genes are commonly described as "essential for cellular existence regardless of their specific function in the tissue or organism", and "stably expressed irrespective of tissue type, developmental stage, cell cycle state, or external signal". However, experimental support for the tenet that gene essentiality is linked to stable expression across cell types, conditions, and organisms has been limited. Here we use genome-scale functional genomic screens together with bulk and single-cell sequencing technologies to test this link and optimize a quantitative and experimentally validated definition of housekeeping gene. Using the optimized definition, we identify, characterize, and provide as resources, housekeeping gene lists extracted from several human datasets, and 10 other animal species that include primates, chicken, and C. elegans. We find that stably expressed genes are not necessarily essential, and that the individual genes that are essential and stably expressed can considerably differ across organisms; yet the pathways enriched among these genes are conserved. Further, the level of conservation of housekeeping genes across the analyzed organisms captures their taxonomic groups, showing evolutionary relevance for our definition. Therefore, we present a quantitative and experimentally supported definition of housekeeping genes that can contribute to better understanding of their unique biological and evolutionary characteristics.https://doi.org/10.1371/journal.pcbi.1010295 |
| spellingShingle | Chintan J Joshi Wenfan Ke Anna Drangowska-Way Eyleen J O'Rourke Nathan E Lewis What are housekeeping genes? PLoS Computational Biology |
| title | What are housekeeping genes? |
| title_full | What are housekeeping genes? |
| title_fullStr | What are housekeeping genes? |
| title_full_unstemmed | What are housekeeping genes? |
| title_short | What are housekeeping genes? |
| title_sort | what are housekeeping genes |
| url | https://doi.org/10.1371/journal.pcbi.1010295 |
| work_keys_str_mv | AT chintanjjoshi whatarehousekeepinggenes AT wenfanke whatarehousekeepinggenes AT annadrangowskaway whatarehousekeepinggenes AT eyleenjorourke whatarehousekeepinggenes AT nathanelewis whatarehousekeepinggenes |