Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

2′-O-methylation-dependent installation of N2-methylguanosine in the U6 internal stem loop facilitates efficient spliceosome assembly

ABSTRACT: The internal stem loop (ISL) of the human U6 snRNA, which catalyzes pre-mRNA splicing, contains LARP7-dependent, snoRNA-guided 2′-O-methylations and an N2-methylguanosine (m2G) that is required for splicing of weak splice sites. Here, we show that installation of m2G72 by the THUMPD2-TRMT112 methyltransferase complex is one of the last maturation events during U6 snRNP biogenesis. We dissect features of THUMPD2 required for association with U6 and present an experimentally validated model of the THUMPD2-TRMT112-U6 complex. Using in vitro methylation assays as well as a newly developed m2G-sensitive deoxyribozyme to monitor U6-m2G72 levels in cellular RNAs, we reveal that 2′-O-methylations within the U6 ISL enhance methylation of G72. We show that m2G72 and the 2′-O-methylations in U6 independently and interdependently influence alternative splicing. Furthermore, our data demonstrate that 2′-O-methylations in the ISL are required for incorporation of U6 into snRNPs whereas m2G72 influences the progression of the U6 snRNP into larger assemblies, highlighting distinct roles of these modifications during spliceosome assembly.

ORGANISM(S): Homo sapiens

PROVIDER: GSE270753 | GEO | 2026/03/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

2′-O-methylation-dependent installation of N2-methylguanosine in the U6 internal stem loop facilitates efficient spliceosome assembly

Project description:The internal stem loop (ISL) of the human U6 snRNA, which catalyzes pre-mRNA splicing, contains LARP7-dependent, snoRNA-guided 2′-O-methylations and an N2-methylguanosine (m2G) that is required for splicing of weak splice sites. Here, we show that installation of m2G72 by the THUMPD2-TRMT112 methyltransferase complex is one of the last maturation events during U6 snRNP biogenesis. We dissect features of THUMPD2 required for association with U6 and present an experimentally validated model of the THUMPD2-TRMT112-U6 complex. Using in vitro methylation assays as well as a newly developed m2G-sensitive deoxyribozyme to monitor U6-m2G72 levels in cellular RNAs, we reveal that 2′-O-methylations within the U6 ISL enhance methylation of G72. We show that m2G72 and the 2′-O-methylations in U6 independently and interdependently influence alternative splicing. Furthermore, our data demonstrate that 2′-O-methylations in the ISL are required for incorporation of U6 into snRNPs whereas m2G72 influences the progression of the U6 snRNP into larger assemblies, highlighting distinct roles of these modifications during spliceosome assembly.

2026-03-12 | GSE270752 | GEO

2′-O-methylation-dependent installation of N2-methylguanosine in the U6 internal stem loop facilitates efficient spliceosome assembly

Project description:The internal stem loop (ISL) of the human U6 snRNA, which catalyzes pre-mRNA splicing, contains LARP7-dependent, snoRNA-guided 2?-O-methylations and an N2-methylguanosine (m2G) that is required for splicing of weak splice sites. Here, we show that installation of m2G72 by the THUMPD2-TRMT112 methyltransferase complex is one of the last maturation events during U6 snRNP biogenesis. We dissect features of THUMPD2 required for association with U6 and present an experimentally validated model of the THUMPD2-TRMT112-U6 complex. Using in vitro methylation assays as well as a newly developed m2G-sensitive deoxyribozyme to monitor U6-m2G72 levels in cellular RNAs, we reveal that 2?-O-methylations within the U6 ISL enhance methylation of G72. We show that m2G72 and the 2?-O-methylations in U6 independently and interdependently influence alternative splicing. Furthermore, our data demonstrate that 2?-O-methylations in the ISL are required for incorporation of U6 into snRNPs whereas m2G72 influences the progression of the U6 snRNP into larger assemblies, highlighting distinct roles of these modifications during spliceosome assembly.

2026-03-12 | GSE303357 | GEO

THUMPD2 catalyzes N2-methylation on the spliceosome catalytic center of U6 snRNA and regulates pre-mRNA splicing and retina degeneration

Project description:How the relatively evolutionarily conserved spliceosome is able to manage the enormously expanded number of splicing events that occur in humans (~200,000 vs. ~400 reported for yeast) is not well understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G)-on the G72 nucleoside of U6 snRNA (known to function as the catalytic center of the spliceosome) results in profoundly increased pre-mRNA splicing activity in human cells. This U6 m2G72 modification is conserved among vertebrates. Further, we demonstrate that THUMPD2 is the methyltransferase responsible for U6 m2G72 and show that it interacts with an auxiliary protein (TRMT112) to specifically recognize both sequence and structural elements of U6. THUMPD2 KO blocks U6 m2G72 and down-regulates the pre-mRNA splicing activity of major spliceosome, yielding thousands of changed alternative splicing events of endogenous pre-mRNAs. Notably, the aberrantly spliced pre-mRNA population of the THUMPD2 KO cells elicits the nonsense-mediated mRNA decay (NMD) pathway and restricts cell proliferation. We also show that THUMPD2-mediated control of the U6 m2G72 modification is associated with age-related macular degeneration and retinal function. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome differentially regulates global mRNA splicing and impacts physiology and disease.

2024-01-02 | GSE236689 | GEO

N2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing

Project description:Modified nucleotides in non-coding RNAs, such as tRNAs and snRNAs, represent an important layer of gene expression regulation through their ability to fine-tune mRNA maturation and translation. Dysregulation of such modifications and the enzymes installing them have been linked to various human pathologies including neurodevelopmental disorders and cancers. Several methyltransferases (MTases) are regulated allosterically by human TRMT112 (Trm112 in Saccharomyces cerevisiae), but the interactome of this regulator and targets of its interacting MTases remain incompletely characterized. Here, we have investigated the interaction network of human TRMT112 in intact cells and identify three poorly characterized putative MTases (TRMT11, THUMPD3 and THUMPD2) as direct partners. We demonstrate that these three proteins are active N2-methylguanosine (m2G) MTases and that TRMT11 and THUMPD3 methylate positions 10 and 6 of tRNAs, respectively. For THUMPD2, we discovered that it directly associates with the U6 snRNA, a core component of the catalytic spliceosome, and is required for the formation of m2G, the last “orphan” modification in U6 snRNA. Furthermore, our data reveal the combined importance of TRMT11 and THUMPD3 for optimal protein synthesis and cell proliferation as well as a role for THUMPD2 in fine-tuning pre-mRNA splicing.

2023-05-17 | GSE219260 | GEO

N2-methylguanosine modifications on human tRNAs and snRNA U6 are important for colon cancer cell proliferation, protein translation and pre-mRNA splicing

Project description:Modified nucleotides in non-coding RNAs, such as tRNAs and snRNAs, represent an important layer of gene expression regulation through their ability to fine-tune mRNA maturation and transla-tion. Growing evidences support important roles of tRNA/snRNAs modifications and hence the enzymes that install them, in eukaryotic cell development and their dysregulation has been linked to various human pathologies including neurodevelopmental disorders and cancers. Human TRMT112 (Trm112 in Saccharomyces cerevisiae) functions as an allosteric regulator of several methyltransfer-ases (MTases) targeting molecules (tRNAs, rRNAs and proteins) involved in protein synthesis. Here, we have investigated the interaction network of human TRMT112 in intact cells and identify three poorly characterized putative MTases (TRMT11, THUMPD3 and THUMD2) as direct part-ners. We demonstrate that these three proteins are active N2-methylguanosine (m2G) MTases and that TRMT11 and THUMPD3 methylate positions 10 and 6 of tRNAs, respectively. In contrast, we discovered that THUMPD2 directly associates with the U6 snRNA and is required for the for-mation of m2G in this core component of the catalytic spliceosome. Consistently, our data reveal the combined importance of TRMT11 and THUMPD3 for optimal protein synthesis and cancer cell proliferation as well as a role for THUMPD2 in fine-tuning pre-mRNA splicing.

2023-05-17 | PXD038967 | Pride

N2-methylguanosine modifications on human tRNAs and snRNA U6 are important for colon cancer cell proliferation, protein translation and pre-mRNA splicing

Project description:Modified nucleotides in non-coding RNAs, such as tRNAs and snRNAs, represent an important layer of gene expression regulation through their ability to fine-tune mRNA maturation and transla-tion. Growing evidences support important roles of tRNA/snRNAs modifications and hence the enzymes that install them, in eukaryotic cell development and their dysregulation has been linked to various human pathologies including neurodevelopmental disorders and cancers. Human TRMT112 (Trm112 in Saccharomyces cerevisiae) functions as an allosteric regulator of several methyltransfer-ases (MTases) targeting molecules (tRNAs, rRNAs and proteins) involved in protein synthesis. Here, we have investigated the interaction network of human TRMT112 in intact cells and identify three poorly characterized putative MTases (TRMT11, THUMPD3 and THUMD2) as direct part-ners. We demonstrate that these three proteins are active N2-methylguanosine (m2G) MTases and that TRMT11 and THUMPD3 methylate positions 10 and 6 of tRNAs, respectively. In contrast, we discovered that THUMPD2 directly associates with the U6 snRNA and is required for the for-mation of m2G in this core component of the catalytic spliceosome. Consistently, our data reveal the combined importance of TRMT11 and THUMPD3 for optimal protein synthesis and cancer cell proliferation as well as a role for THUMPD2 in fine-tuning pre-mRNA splicing.

2023-05-17 | PXD038997 | Pride

Identification of small RNAs interacting with LARP7

Project description:The La-related protein LARP7 has been mainly described as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, which negatively regulates RNA polymerase II by sequestering the positive transcription elongation factor b (P-TEFb). In our studies, we discovered a novel, 7SK snRNP-independent function of LARP7. We show that LARP7 interacts with the U6 spliceosomal RNA as well as with the small nucleolar RNAs (snoRNAs) directing the 2'-O-methylations of U6. Importantly, in the absence of LARP7, significantly less 2'-O-methylations are deposited on U6 affecting splicing fidelity. Mutations in the LARP7 gene have been associated with the Alazami syndrome, a form of primordial dwarfism characterized by intellectual disability. We describe a novel loss-of-function mutation of LARP7 occurring in Alazami patients and detect reduced 2'-O-methylations of U6 in patient-derived samples. Thus, aberrant posttranscriptional RNA modifications of the spliceosomal U6 snRNA may contribute to the development of this severe disease.

2020-02-03 | GSE126592 | GEO

Identification of small RNAs interacting with FLAG/HA(FH)-tagged LARP7

2020-02-03 | GSE126591 | GEO

Impact of LARP7 depletion on the transcriptome of HEK293 cells

2020-02-03 | GSE126682 | GEO

Impact of LARP7 depletion on the pA+ transcriptome of HEK293 cells upon heat shock

Project description:The La-related protein LARP7 has been mainly described as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, which negatively regulates RNA polymerase II by sequestering the positive transcription elongation factor b (P-TEFb). In our studies, we discovered a novel, 7SK snRNP-independent function of LARP7. We show that LARP7 interacts with the U6 spliceosomal RNA as well as with the small nucleolar RNAs (snoRNAs) directing the 2'-O-methylations of U6. Importantly, in the absence of LARP7, significantly less 2'-O-methylations are deposited on U6 affecting splicing fidelity. Mutations in the LARP7 gene have been associated with the Alazami syndrome, a form of primary dwarfism characterized by intellectual disability. We describe a novel loss-of-function mutation of LARP7 occurring in Alazami patients and detect reduced 2'-O-methylations of U6 in patient-derived samples. Thus, aberrant posttranscriptional RNA modifications of the spliceosomal U6 snRNA may contribute to the development of this severe disease.

2020-02-03 | GSE134813 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data