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Article ; Online: Concurrent peripheral T-cell lymphoma and T-cell lymphoblastic leukemia/lymphoma with identical

Khanlari, Mahsa / Wang, Wei / Liu, Yen-Chun / Wang, Lu / Rubnitz, Jeffrey E / Dixon, Stephanie / Orr, Brent A / Anelo, Obianuju M / Cheng, Zhongshan / Balagopal, Vidya / Klco, Jeffery M

Haematologica

2024 Volume 109, Issue 3, Page(s) 994–999

MeSH term(s)	Humans ; Intracellular Signaling Peptides and Proteins ; Lymphoma, T-Cell ; Lymphoma, T-Cell, Peripheral/diagnosis ; Lymphoma, T-Cell, Peripheral/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma ; T-Cell Acute Lymphocytic Leukemia Protein 1 ; T-Lymphocytes
Chemical Substances	Intracellular Signaling Peptides and Proteins ; STIL protein, human ; T-Cell Acute Lymphocytic Leukemia Protein 1 ; TAL1 protein, human (135471-20-4)
Language	English
Publishing date	2024-03-01
Publishing country	Italy
Document type	Case Reports ; Journal Article
ZDB-ID	2333-4
ISSN	1592-8721 ; 0017-6567 ; 0390-6078
ISSN (online)	1592-8721
ISSN	0017-6567 ; 0390-6078
DOI	10.3324/haematol.2023.283585
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Article ; Online: Rous Sarcoma Virus RNA Stability Element Inhibits Deadenylation of mRNAs with Long 3'UTRs.

Balagopal, Vidya / Beemon, Karen L

Viruses

2017 Volume 9, Issue 8

Abstract: All retroviruses use their full-length primary transcript as the major mRNA for Group-specific antigen (Gag) capsid proteins. This results in a long 3' untranslated region (UTR) downstream of the termination codon. In the case of Rous sarcoma virus (RSV), ...

Abstract	All retroviruses use their full-length primary transcript as the major mRNA for Group-specific antigen (Gag) capsid proteins. This results in a long 3' untranslated region (UTR) downstream of the termination codon. In the case of Rous sarcoma virus (RSV), there is a 7 kb 3'UTR downstream of the
MeSH term(s)	3' Untranslated Regions ; Codon, Terminator ; Gene Knockdown Techniques ; Gene Products, gag/genetics ; Gene Products, gag/metabolism ; Humans ; Nonsense Mediated mRNA Decay ; Protein Biosynthesis ; RNA Stability ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Rous sarcoma virus/genetics ; Rous sarcoma virus/metabolism
Chemical Substances	3' Untranslated Regions ; Codon, Terminator ; Gene Products, gag ; RNA, Messenger ; RNA, Viral
Language	English
Publishing date	2017-08-01
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v9080204
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Article: SJPedPanel: A pan-cancer gene panel for childhood malignancies.

medRxiv : the preprint server for health sciences

2024

Abstract: Background: Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive ... ...

Abstract	Background: Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results: SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., Conclusions: SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
Language	English
Publishing date	2024-02-09
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.27.23299068
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Article ; Online: Integration of ALV into

Winans, Shelby / Flynn, Alyssa / Malhotra, Sanandan / Balagopal, Vidya / Beemon, Karen L

Oncotarget

2017 Volume 8, Issue 34, Page(s) 57302–57315

Abstract: Avian leukosis virus induces tumors in chickens by integrating into the genome and altering expression of nearby genes. Thus, ALV can be used as an insertional mutagenesis tool to identify novel genes involved in tumorigenesis. Deep sequencing analysis ... ...

Abstract	Avian leukosis virus induces tumors in chickens by integrating into the genome and altering expression of nearby genes. Thus, ALV can be used as an insertional mutagenesis tool to identify novel genes involved in tumorigenesis. Deep sequencing analysis of viral integration sites has identified
Language	English
Publishing date	2017-07-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.19328
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Article ; Online: Stm1 modulates translation after 80S formation in Saccharomyces cerevisiae.

Balagopal, Vidya / Parker, Roy

RNA (New York, N.Y.)

2011 Volume 17, Issue 5, Page(s) 835–842

Abstract: The control of translation is a critical aspect of gene regulation. It is often inversely related to mRNA degradation and is typically controlled during initiation. The Stm1 protein in Saccharomyces cerevisiae has been shown to interact with ribosomes, ... ...

Abstract	The control of translation is a critical aspect of gene regulation. It is often inversely related to mRNA degradation and is typically controlled during initiation. The Stm1 protein in Saccharomyces cerevisiae has been shown to interact with ribosomes, affect the interaction of eEF3 with ribosomes, and promote the decapping of a subclass of mRNAs. We demonstrate that in vitro Stm1 inhibits translation after formation of an 80S complex. This suggests that Stm1 modulates translation and mRNA decapping by controlling translation elongation.
MeSH term(s)	Amino Acid Sequence ; Conserved Sequence ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Molecular Sequence Data ; Mutation ; Protein Biosynthesis ; Ribosome Subunits, Large, Eukaryotic/metabolism ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Alignment
Chemical Substances	DNA-Binding Proteins ; Saccharomyces cerevisiae Proteins ; Stm1 protein, S cerevisiae
Language	English
Publishing date	2011-04-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.2677311
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Article ; Online: Polysomes, P bodies and stress granules: states and fates of eukaryotic mRNAs.

Balagopal, Vidya / Parker, Roy

Current opinion in cell biology

2009 Volume 21, Issue 3, Page(s) 403–408

Abstract: The control of translation and mRNA degradation plays a key role in the regulation of eukaryotic gene expression. In the cytosol, mRNAs engaged in translation are distributed throughout the cytosol, while translationally inactive mRNAs can accumulate in ... ...

Abstract	The control of translation and mRNA degradation plays a key role in the regulation of eukaryotic gene expression. In the cytosol, mRNAs engaged in translation are distributed throughout the cytosol, while translationally inactive mRNAs can accumulate in P bodies, in complex with mRNA degradation and translation repression machinery, or in stress granules, which appear to be mRNAs stalled in translation initiation. Here we discuss how these different granules suggest a dynamic model for the metabolism of cytoplasmic mRNAs wherein they cycle between different mRNP states with different functional properties and subcellular locations.
MeSH term(s)	Cytoplasmic Granules/metabolism ; Eukaryotic Cells/metabolism ; Humans ; Polyribosomes/metabolism ; Protein Biosynthesis ; RNA Caps/metabolism ; RNA Stability ; RNA, Messenger/metabolism ; Ribonucleoproteins/metabolism
Chemical Substances	RNA Caps ; RNA, Messenger ; Ribonucleoproteins ; messenger ribonucleoprotein
Language	English
Publishing date	2009-04-23
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1026381-0
ISSN	1879-0410 ; 0955-0674
ISSN (online)	1879-0410
ISSN	0955-0674
DOI	10.1016/j.ceb.2009.03.005
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Article: The decapping activator Edc3 and the Q/N-rich domain of Lsm4 function together to enhance mRNA stability and alter mRNA decay pathway dependence in Saccharomyces cerevisiae.

Huch, Susanne / Müller, Maren / Muppavarapu, Mridula / Gommlich, Jessie / Balagopal, Vidya / Nissan, Tracy

Biology open

2016 Volume 5, Issue 10, Page(s) 1388–1399

Abstract: The rate and regulation of mRNA decay are major elements in the proper control of gene expression. Edc3 and Lsm4 are two decapping activator proteins that have previously been shown to function in the assembly of RNA granules termed P bodies. Here, we ... ...

Abstract	The rate and regulation of mRNA decay are major elements in the proper control of gene expression. Edc3 and Lsm4 are two decapping activator proteins that have previously been shown to function in the assembly of RNA granules termed P bodies. Here, we show that deletion of edc3, when combined with a removal of the glutamine/asparagine rich region of Lsm4 (edc3Δ lsm4ΔC) reduces mRNA stability and alters pathways of mRNA degradation. Multiple tested mRNAs exhibited reduced stability in the edc3Δ lsm4ΔC mutant. The destabilization was linked to an increased dependence on Ccr4-mediated deadenylation and mRNA decapping. Unlike characterized mutations in decapping factors that either are neutral or are able to stabilize mRNA, the combined edc3Δ lsm4ΔC mutant reduced mRNA stability. We characterized the growth and activity of the major mRNA decay systems and translation in double mutant and wild-type yeast. In the edc3Δ lsm4ΔC mutant, we observed alterations in the levels of specific mRNA decay factors as well as nuclear accumulation of the catalytic subunit of the decapping enzyme Dcp2. Hence, we suggest that the effects on mRNA stability in the edc3Δ lsm4ΔC mutant may originate from mRNA decay protein abundance or changes in mRNPs, or alternatively may imply a role for P bodies in mRNA stabilization.
Language	English
Publishing date	2016-10-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2632264-X
ISSN	2046-6390
ISSN	2046-6390
DOI	10.1242/bio.020487
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Article ; Online: Stm1 Modulates mRNA Decay and Dhh1 Function in Saccharomyces cerevisiae

Balagopal, Vidya / Parker, Roy

Genetics. 2009 Jan., v. 181, no. 1 p.93-103

2009

MeSH term(s)	Cytoplasmic Structures/metabolism ; DEAD-box RNA Helicases/genetics/metabolism. ; DNA-Binding Proteins/genetics/metabolism. ; Gene Expression Regulation, Fungal ; Genes, Suppressor ; Half-Life ; Models, Genetic ; Mutation/genetics ; Protein Biosynthesis ; RNA Stability ; RNA, Messenger/genetics/metabolism. ; Saccharomyces cerevisiae/cytology/genetics/metabolism. ; Saccharomyces cerevisiae Proteins/genetics/metabolism. ; Temperature
Keywords	Saccharomyces cerevisiae ; yeasts ; messenger RNA ; degradation ; binding proteins ; ribosomes ; translation (genetics) ; half life ; Stm1 protein ; Dhh1 protein ; decapping ; messenger RNA decapping
Language	English
Dates of publication	2009-01
Size	p. 93-103.
Document type	Article ; Online
Note	Resource is Open Access
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.108.092601
Database	NAL-Catalogue (AGRICOLA)

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Article: Ways and means of eukaryotic mRNA decay.

Balagopal, Vidya / Fluch, Lydia / Nissan, Tracy

Biochimica et biophysica acta

2012 Volume 1819, Issue 6, Page(s) 593–603

Abstract: Messenger RNA degradation is an important point of control for gene expression. Genome-wide studies on mRNA stability have demonstrated its importance in adaptation and stress response. Most of the key players in mRNA decay appear to have been identified. ...

Abstract	Messenger RNA degradation is an important point of control for gene expression. Genome-wide studies on mRNA stability have demonstrated its importance in adaptation and stress response. Most of the key players in mRNA decay appear to have been identified. The study of these proteins brings insight into the mechanism of general and specific targeting of transcripts for degradation. Recruitment and assembly of mRNP complexes enhance and bring specificity to mRNA decay. mRNP complexes can form larger structures that have been found to be ubiquitous in nature. Discovery of P-Bodies, an archetype of this sort of aggregates, has generated interest in the question of where mRNA degrades. This is currently an open question under extensive investigation. This review will discuss in detail the recent developments in the regulation of mRNA decay focusing on yeast as a model system. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
MeSH term(s)	Active Transport, Cell Nucleus ; DEAD-box RNA Helicases/chemistry ; DEAD-box RNA Helicases/genetics ; Eukaryotic Cells ; Membrane Transport Proteins/chemistry ; Membrane Transport Proteins/metabolism ; Molecular Conformation ; Nuclear Proteins/chemistry ; Nuclear Proteins/metabolism ; Nucleocytoplasmic Transport Proteins/chemistry ; Nucleocytoplasmic Transport Proteins/genetics ; Nucleocytoplasmic Transport Proteins/metabolism ; Protein Structure, Tertiary ; RNA Stability/genetics ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA-Binding Proteins/chemistry ; RNA-Binding Proteins/metabolism ; Ribonucleoproteins/chemistry ; Ribonucleoproteins/genetics ; Ribonucleoproteins/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	MEX67 protein, S cerevisiae ; Membrane Transport Proteins ; Mtr2 protein, S cerevisiae ; Nuclear Proteins ; Nucleocytoplasmic Transport Proteins ; RNA, Messenger ; RNA-Binding Proteins ; Ribonucleoproteins ; Saccharomyces cerevisiae Proteins ; messenger ribonucleoprotein ; DBP5 protein, S cerevisiae (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2012-06
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbagrm.2012.01.001
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Article: Stm1 modulates mRNA decay and Dhh1 function in Saccharomyces cerevisiae.

Balagopal, Vidya / Parker, Roy

Genetics

2008 Volume 181, Issue 1, Page(s) 93–103

Abstract: The control of mRNA degradation and translation are important for the regulation of gene expression. mRNA degradation is often initiated by deadenylation, which leads to decapping and 5'-3' decay. In the budding yeast Saccharomyces cerevisae, decapping ... ...

Abstract	The control of mRNA degradation and translation are important for the regulation of gene expression. mRNA degradation is often initiated by deadenylation, which leads to decapping and 5'-3' decay. In the budding yeast Saccharomyces cerevisae, decapping is promoted by the Dhh1 and Pat1 proteins, which appear to both inhibit translation initiation and promote decapping. To understand the function of these factors, we identified the ribosome binding protein Stm1 as a multicopy suppressor of the temperature sensitivity of the pat1Delta strain. Stm1 loss-of-function alleles and overexpression strains show several genetic interactions with Pat1 and Dhh1 alleles in a manner consistent with Stm1 working upstream of Dhh1 to promote Dhh1 function. Consistent with Stm1 affecting Dhh1 function, stm1Delta strains are defective in the degradation of the EDC1 and COX17 mRNAs, whose decay is strongly affected by the loss of Dhh1. These results identify Stm1 as an additional component of the mRNA degradation machinery and suggest a possible connection of mRNA decapping to ribosome function.
MeSH term(s)	Cytoplasmic Structures/metabolism ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation, Fungal ; Genes, Suppressor ; Half-Life ; Models, Genetic ; Mutation/genetics ; Protein Biosynthesis ; RNA Stability ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Temperature
Chemical Substances	DNA-Binding Proteins ; RNA, Messenger ; Saccharomyces cerevisiae Proteins ; Stm1 protein, S cerevisiae ; DHH1 protein, S cerevisiae (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2008-11-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.108.092601
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