1
|
Rajendra KC, Cheng R, Zhou S, Lizarazo S, Smith D, Van Bortle K. Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.598009. [PMID: 38895345 PMCID: PMC11185800 DOI: 10.1101/2024.06.08.598009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
RNA polymerase (Pol) I, II, and III are most commonly described as having distinct roles in synthesizing ribosomal RNA (rRNA), messenger RNA (mRNA), and specific small noncoding (nc)RNAs, respectively. This delineation of transcriptional responsibilities is not definitive, however, as evidenced by instances of Pol II recruitment to genes conventionally transcribed by Pol III, including the co-transcription of RPPH1 - the catalytic RNA component of RNase P. A comprehensive understanding of the interplay between RNA polymerase complexes remains lacking, however, due to limited comparative analyses for all three enzymes. To address this gap, we applied a uniform framework for quantifying global Pol I, II, and III occupancies that integrates currently available human RNA polymerase ChIP-seq datasets. Occupancy maps are combined with a comprehensive multi-class promoter set that includes protein-coding genes, noncoding genes, and repetitive elements. While our genomic survey appropriately identifies recruitment of Pol I, II, and III to canonical target genes, we unexpectedly discover widespread recruitment of the Pol III machinery to promoters of specific protein-coding genes, supported by colocalization patterns observed for several Pol III-specific subunits. We show that Pol III-occupied Pol II promoters are enriched for small, nascent RNA reads terminating in a run of 4 Ts, a unique hallmark of Pol III transcription termination and evidence of active Pol III activity at these sites. Pol III disruption differentially modulates the expression of Pol III-occupied coding genes, which are functionally enriched for ribosomal proteins and genes broadly linked to unfavorable outcomes in cancer. Our map also identifies additional, currently unannotated genomic elements occupied by Pol III with clear signatures of nascent RNA species that are sensitive to disruption of La (SSB) - a Pol III-related RNA chaperone protein. These findings reshape our current understanding of the interplay between Pols II and III and identify potentially novel small ncRNAs with broad implications for gene regulatory paradigms and RNA biology.
Collapse
Affiliation(s)
- K C Rajendra
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruiying Cheng
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Simon Lizarazo
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Duncan Smith
- Department of Biology, New York University, New York, NY
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
2
|
Mattijssen S, Kerkhofs K, Stephen J, Yang A, Han CG, Tadafumi Y, Iben JR, Mishra S, Sakhawala RM, Ranjan A, Gowda M, Gahl WA, Gu S, Malicdan MC, Maraia RJ. A POLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.577363. [PMID: 38410490 PMCID: PMC10896340 DOI: 10.1101/2024.02.05.577363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B. Genome-edited POLR3B1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3'-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of ≥5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed that POLR3B1625A>G and patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3'-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 as POLR3-deficiency biomarkers.
Collapse
Affiliation(s)
- Sandy Mattijssen
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Kyra Kerkhofs
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Joshi Stephen
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Acong Yang
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - Chen G. Han
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Yokoyama Tadafumi
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - James R. Iben
- Molecular Genetics Core, NICHD, NIH, Bethesda, MD 20892, USA
| | - Saurabh Mishra
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rima M. Sakhawala
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Amitabh Ranjan
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mamatha Gowda
- Department of Obstetrics & Gynaecology, Jawaharlal Institute of Post-Graduate Medical Education and Research, Puducherry, India
| | - William A. Gahl
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Shuo Gu
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - May C. Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Richard J. Maraia
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| |
Collapse
|
3
|
Abe T, Sarentonglaga B, Nagao Y. Advancements in medical research using fetal sheep: Implications for human health and treatment methods. Anim Sci J 2024; 95:e13945. [PMID: 38651196 DOI: 10.1111/asj.13945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/13/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Sheep are typically considered as industrial animals that provide wool and meals. However, they play a significant role in medical research in addition to their conventional use. Notably, sheep fetuses are resistant to surgical invasions and can endure numerous manipulations, such as needle puncture and cell transplantation, and surgical operations requiring exposure beyond the uterus. Based on these distinguishing characteristics, we established a chimeric sheep model capable of producing human/monkey pluripotent cell-derived blood cells via the fetal liver. Furthermore, sheep have become crucial as human fetal models, acting as platforms for developing and improving techniques for intrauterine surgery to address congenital disorders and clarifying the complex pharmacokinetic interactions between mothers and their fetuses. This study emphasizes the significant contributions of fetal sheep to advancing human disease understanding and treatment strategies, highlighting their unique characteristics that are not present in other animals.
Collapse
Affiliation(s)
- Tomoyuki Abe
- Open Science Laboratory, Center for Development of Advanced Medical Technology, Jichi Medical University, Tochigi, Japan
| | | | - Yoshikazu Nagao
- Department of Agriculture, Utsunomiya University, Tochigi, Japan
| |
Collapse
|
4
|
Anwised P, Moorawong R, Samruan W, Somredngan S, Srisutush J, Laowtammathron C, Aksoy I, Parnpai R, Savatier P. An expedition in the jungle of pluripotent stem cells of non-human primates. Stem Cell Reports 2023; 18:2016-2037. [PMID: 37863046 PMCID: PMC10679654 DOI: 10.1016/j.stemcr.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023] Open
Abstract
For nearly three decades, more than 80 embryonic stem cell lines and more than 100 induced pluripotent stem cell lines have been derived from New World monkeys, Old World monkeys, and great apes. In this comprehensive review, we examine these cell lines originating from marmoset, cynomolgus macaque, rhesus macaque, pig-tailed macaque, Japanese macaque, African green monkey, baboon, chimpanzee, bonobo, gorilla, and orangutan. We outline the methodologies implemented for their establishment, the culture protocols for their long-term maintenance, and their basic molecular characterization. Further, we spotlight any cell lines that express fluorescent reporters. Additionally, we compare these cell lines with human pluripotent stem cell lines, and we discuss cell lines reprogrammed into a pluripotent naive state, detailing the processes used to attain this. Last, we present the findings from the application of these cell lines in two emerging fields: intra- and interspecies embryonic chimeras and blastoids.
Collapse
Affiliation(s)
- Preeyanan Anwised
- University Lyon, University Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France; Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Ratree Moorawong
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Worawalan Samruan
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Sirilak Somredngan
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Jittanun Srisutush
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Chuti Laowtammathron
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Irene Aksoy
- University Lyon, University Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France.
| | - Rangsun Parnpai
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
| | - Pierre Savatier
- University Lyon, University Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France.
| |
Collapse
|
5
|
Zhao C. Cell culture: in vitro model system and a promising path to in vivo applications. J Histotechnol 2023; 46:1-4. [PMID: 36691848 DOI: 10.1080/01478885.2023.2170772] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Chongbei Zhao
- Stowers Institute for Medical Research, Kansas City, MO, USA
| |
Collapse
|
6
|
Sarmah H, Sawada A, Hwang Y, Miura A, Shimamura Y, Tanaka J, Yamada K, Mori M. Towards human organ generation using interspecies blastocyst complementation: Challenges and perspectives for therapy. Front Cell Dev Biol 2023; 11:1070560. [PMID: 36743411 PMCID: PMC9893295 DOI: 10.3389/fcell.2023.1070560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Millions of people suffer from end-stage refractory diseases. The ideal treatment option for terminally ill patients is organ transplantation. However, donor organs are in absolute shortage, and sadly, most patients die while waiting for a donor organ. To date, no technology has achieved long-term sustainable patient-derived organ generation. In this regard, emerging technologies of chimeric human organ production via blastocyst complementation (BC) holds great promise. To take human organ generation via BC and transplantation to the next step, we reviewed current emerging organ generation technologies and the associated efficiency of chimera formation in human cells from the standpoint of developmental biology.
Collapse
Affiliation(s)
- Hemanta Sarmah
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Anri Sawada
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Youngmin Hwang
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Akihiro Miura
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Yuko Shimamura
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Junichi Tanaka
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| | - Kazuhiko Yamada
- Department of Surgery, Johns Hopkins University, Baltimore, MD, United States
| | - Munemasa Mori
- Department of Medicine, Columbia Center for Human Development, Columbia University Medical Center, New York, NY, United States
| |
Collapse
|