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Article ; Online: Regulatory roles of nucleolus organizer region-derived long non-coding RNAs.

Hao, Qinyu / Prasanth, Kannanganattu V

Mammalian genome : official journal of the International Mammalian Genome Society

2021 Volume 33, Issue 2, Page(s) 402–411

Abstract: The nucleolus is the largest sub-nuclear domain, serving primarily as the place for ribosome biogenesis. A delicately regulated function of the nucleolus is vital to the cell not only for maintaining proper protein synthesis but is also tightly ... ...

Abstract	The nucleolus is the largest sub-nuclear domain, serving primarily as the place for ribosome biogenesis. A delicately regulated function of the nucleolus is vital to the cell not only for maintaining proper protein synthesis but is also tightly associated with responses to different types of cellular stresses. Recently, several long non-coding RNAs (lncRNAs) were found to be part of the regulatory network that modulate nucleolar functions. Several of these lncRNAs are encoded in the ribosomal DNA (rDNA) repeats or are transcribed from the genomic regions that are located near the nucleolus organizer regions (NORs). In this review, we first discuss the current understanding of the sequence of the NORs and variations between different NORs. We then focus on the NOR-derived lncRNAs in mammalian cells and their functions in rRNA transcription and the organization of nucleolar structure under different cellular conditions. The identification of these lncRNAs reveals great potential of the NORs in harboring novel genes involved in the regulation of nucleolar functions.
MeSH term(s)	Animals ; Cell Nucleolus/genetics ; Cell Nucleolus/metabolism ; DNA, Ribosomal/genetics ; DNA, Ribosomal/metabolism ; Mammals/genetics ; Nucleolus Organizer Region/genetics ; Nucleolus Organizer Region/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Transcription, Genetic
Chemical Substances	DNA, Ribosomal ; RNA, Long Noncoding
Language	English
Publishing date	2021-08-26
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	1058547-3
ISSN	1432-1777 ; 0938-8990
ISSN (online)	1432-1777
ISSN	0938-8990
DOI	10.1007/s00335-021-09906-z
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Zs.A 3489: Show issues

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Article ; Online: Cell Phase Identification in a Three-Dimensional Engineered Tumor Model by Infrared Spectroscopic Imaging.

Hsieh, Pei-Hsuan / Phal, Yamuna / Prasanth, Kannanganattu V / Bhargava, Rohit

Analytical chemistry

2022 Volume 95, Issue 6, Page(s) 3349–3357

Abstract: Cell cycle progression plays a vital role in regulating proliferation, metabolism, and apoptosis. Three-dimensional (3D) cell cultures have emerged as an important class ... ...

Abstract	Cell cycle progression plays a vital role in regulating proliferation, metabolism, and apoptosis. Three-dimensional (3D) cell cultures have emerged as an important class of
MeSH term(s)	Humans ; Spectroscopy, Fourier Transform Infrared/methods ; Spectrophotometry, Infrared ; Cell Cycle ; Cell Division ; MCF-7 Cells
Language	English
Publishing date	2022-12-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04554
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Zs.A 4033: Show issues

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Article ; Online: Mechanosensitive changes in the expression of genes in colorectal cancer-associated fibroblasts

Bashar Emon / You Jin Song / M. Saddam H. Joy / Mounisha V. Kovour / Kannanganattu V. Prasanth / M. Taher A. Saif

Scientific Data, Vol 10, Iss 1, Pp 1-

2023 Volume 6

Abstract: Abstract Most solid tumors become stiff with progression of cancer. Cancer Associated Fibroblasts (CAFs), most abundant stromal cells in the tumor microenvironment (TME), are known to mediate such stiffening. While the biochemical crosstalk between CAFs ... ...

Abstract	Abstract Most solid tumors become stiff with progression of cancer. Cancer Associated Fibroblasts (CAFs), most abundant stromal cells in the tumor microenvironment (TME), are known to mediate such stiffening. While the biochemical crosstalk between CAFs and cancer cells have been widely investigated, it is not clear if and how CAFs in stiffer TME promote metastatic progression. To gather insights into the process, we controlled the mechanical stiffness of the substrates and collected gene expression data with human colorectal CAFs. We cultured human primary CAFs on 2D polyacrylamide hydrogels with increasing elastic modulus (E) of 1, 10 and 40 kPa, and performed genome-wide transcriptome analyses in these cells to identify expression levels of ~16000 genes. The high-quality RNAseq results can be an excellent data-source for bioinformatic analysis for identifying novel pathways and biomarkers in cancer development and metastatic progression. With thorough analysis and accurate interpretation, this data may help researchers understand the role of mechanical stiffness of the TME in CAF-cancer cell crosstalk.
Keywords	Science ; Q
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mechanosensitive changes in the expression of genes in colorectal cancer-associated fibroblasts.

Emon, Bashar / Song, You Jin / Joy, M Saddam H / Kovour, Mounisha V / Prasanth, Kannanganattu V / Saif, M Taher A

Scientific data

2023 Volume 10, Issue 1, Page(s) 350

Abstract: Most solid tumors become stiff with progression of cancer. Cancer Associated Fibroblasts (CAFs), most abundant stromal cells in the tumor microenvironment (TME), are known to mediate such stiffening. While the biochemical crosstalk between CAFs and ... ...

Abstract	Most solid tumors become stiff with progression of cancer. Cancer Associated Fibroblasts (CAFs), most abundant stromal cells in the tumor microenvironment (TME), are known to mediate such stiffening. While the biochemical crosstalk between CAFs and cancer cells have been widely investigated, it is not clear if and how CAFs in stiffer TME promote metastatic progression. To gather insights into the process, we controlled the mechanical stiffness of the substrates and collected gene expression data with human colorectal CAFs. We cultured human primary CAFs on 2D polyacrylamide hydrogels with increasing elastic modulus (E) of 1, 10 and 40 kPa, and performed genome-wide transcriptome analyses in these cells to identify expression levels of ~16000 genes. The high-quality RNAseq results can be an excellent data-source for bioinformatic analysis for identifying novel pathways and biomarkers in cancer development and metastatic progression. With thorough analysis and accurate interpretation, this data may help researchers understand the role of mechanical stiffness of the TME in CAF-cancer cell crosstalk.
MeSH term(s)	Humans ; Biomarkers ; Cancer-Associated Fibroblasts/metabolism ; Cancer-Associated Fibroblasts/pathology ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; Fibroblasts/metabolism ; Gene Expression Profiling ; Tumor Microenvironment/genetics
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-06-02
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-023-02233-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Long non-coding RNA Malat1 is essential for fine-tuning bone homeostasis through orchestrating cellular crosstalk and the β-catenin-OPG/Jagged1 pathway.

Qin, Yongli / Shirakawa, Jumpei / Xu, Cheng / Chen, Ruge / Ng, Courtney / Nakano, Shinichi / Elguindy, Mahmoud / Deng, Zhonghao / Prasanth, Kannanganattu V / Eissmann, Moritz F / Nakagawa, Shinichi / Zhao, Baohong

Research square

2023

Abstract: The annotation of lncRNAs is transitioning from original sequence recognition and functional ... ...

Abstract	The annotation of lncRNAs is transitioning from original sequence recognition and functional screening
Language	English
Publishing date	2023-12-28
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3793919/v1
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Article ; Online: One locus with two roles: microRNA-independent functions of microRNA-host-gene locus-encoded long noncoding RNAs.

Sun, Qinyu / Song, You Jin / Prasanth, Kannanganattu V

Wiley interdisciplinary reviews. RNA

2020 Volume 12, Issue 3, Page(s) e1625

Abstract: Long noncoding RNAs (lncRNAs) are RNA transcripts longer than 200 nucleotides that do not code for proteins. LncRNAs play crucial regulatory roles in several biological processes via diverse mechanisms and their aberrant expression is associated with ... ...

Abstract	Long noncoding RNAs (lncRNAs) are RNA transcripts longer than 200 nucleotides that do not code for proteins. LncRNAs play crucial regulatory roles in several biological processes via diverse mechanisms and their aberrant expression is associated with various diseases. LncRNA genes are further subcategorized based on their relative organization in the genome. MicroRNA (miRNA)-host-gene-derived lncRNAs (lnc-MIRHGs) refer to lncRNAs whose genes also harbor miRNAs. There exists crosstalk between the processing of lnc-MIRHGs and the biogenesis of the encoded miRNAs. Although the functions of the encoded miRNAs are usually well understood, whether those lnc-MIRHGs play independent functions are not fully elucidated. Here, we review our current understanding of lnc-MIRHGs, including their biogenesis, function, and mechanism of action, with a focus on discussing the miRNA-independent functions of lnc-MIRHGs, including their involvement in cancer. Our current understanding of lnc-MIRHGs strongly indicates that this class of lncRNAs could play important roles in basic cellular events as well as in diseases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
MeSH term(s)	MicroRNAs/genetics ; RNA, Long Noncoding/genetics
Chemical Substances	MicroRNAs ; RNA, Long Noncoding
Language	English
Publishing date	2020-09-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.1625
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Zs.A 6953: Show issues

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Article ; Online: Easy Stress Relief by EZH2.

Prasanth, Supriya G / Prasanth, Kannanganattu V

Cell

2016 Volume 167, Issue 7, Page(s) 1678–1680

Abstract: While we are beginning to appreciate the cellular roles played by long noncoding RNAs, the function of transcripts emerging from repetitive genomic regions remains enigmatic. In this issue, Zovoilis et al. report that the polycomb protein EZH2, upon heat ...

Abstract	While we are beginning to appreciate the cellular roles played by long noncoding RNAs, the function of transcripts emerging from repetitive genomic regions remains enigmatic. In this issue, Zovoilis et al. report that the polycomb protein EZH2, upon heat shock, facilitates transcription of stress-responsive genes by inducing the degradation of the transcriptional repressor B2 repeat RNA.
MeSH term(s)	Genome ; Heat-Shock Response ; Polycomb Repressive Complex 2 ; Polycomb-Group Proteins ; RNA, Long Noncoding
Chemical Substances	Polycomb-Group Proteins ; RNA, Long Noncoding ; Polycomb Repressive Complex 2 (EC 2.1.1.43)
Language	English
Publishing date	2016--15
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2016.11.051
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 58: Show issues

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Article ; Online: Policing cells under stress: noncoding RNAs capture proteins in nucleolar detention centers.

Prasanth, Kannanganattu V

Molecular cell

2012 Volume 45, Issue 2, Page(s) 141–142

Abstract: In this issue of Molecular Cell, Audas et al. (2012) demonstrate that a class of stress-induced noncoding RNAs immobilizes proteins in the nucleolus in response to a specific stimulus. ...

Abstract	In this issue of Molecular Cell, Audas et al. (2012) demonstrate that a class of stress-induced noncoding RNAs immobilizes proteins in the nucleolus in response to a specific stimulus.
Language	English
Publishing date	2012-01-28
Publishing country	United States
Document type	Comment ; Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2012.01.005
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Zs.A 5055: Show issues

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Article ; Online: Cell Phase Identification in a Three-Dimensional Engineered Tumor Model by Infrared Spectroscopic Imaging

Hsieh, Pei-Hsuan / Phal, Yamuna / Prasanth, Kannanganattu V. / Bhargava, Rohit

Analytical Chemistry. 2022 Dec. 27, v. 95, no. 6 p.3349-3357

2022

Abstract: Cell cycle progression plays a vital role in regulating proliferation, metabolism, and apoptosis. Three-dimensional (3D) cell cultures have emerged as an important class of in vitro disease models, and incorporating the variation occurring from cell ... ...

Abstract	Cell cycle progression plays a vital role in regulating proliferation, metabolism, and apoptosis. Three-dimensional (3D) cell cultures have emerged as an important class of in vitro disease models, and incorporating the variation occurring from cell cycle progression in these systems is critical. Here, we report the use of Fourier transform infrared (FT-IR) spectroscopic imaging to identify subtle biochemical changes within cells, indicative of the G1/S and G2/M phases of the cell cycle. Following previous studies, we first synchronized samples from two-dimensional (2D) cell cultures, confirmed their states by flow cytometry and DNA quantification, and recorded spectra. We determined two critical wavenumbers (1059 and 1219 cm–¹) as spectral indicators of the cell cycle for a set of isogenic breast cancer cell lines (MCF10AT series). These two simple spectral markers were then applied to distinguish cell cycle stages in a 3D cell culture model using four cell lines that represent the main stages of cancer progression from normal cells to metastatic disease. Temporal dependence of spectral biomarkers during acini maturation validated the hypothesis that the cells are more proliferative in the early stages of acini development; later stages of the culture showed stability in the overall composition but unique spatial differences in cells in the two phases. Altogether, this study presents a computational and quantitative approach for cell phase analysis in tissue-like 3D structures without any biomarker staining and provides a means to characterize the impact of the cell cycle on 3D biological systems and disease diagnostic studies using IR imaging.
Keywords	DNA ; Fourier transform infrared spectroscopy ; analytical chemistry ; apoptosis ; biomarkers ; breast neoplasms ; cell culture ; cell cycle ; flow cytometry ; metabolism ; metastasis ; models ; neoplasm cells ; neoplasm progression ; quantitative analysis
Language	English
Dates of publication	2022-1227
Size	p. 3349-3357.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04554
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: DNA Damage-Induced, S-Phase Specific Phosphorylation of Orc6 is Critical for the Maintenance of Genome Stability.

Lin, Yo-Chuen / Liu, Dazhen / Chakraborty, Arindam / Macias, Virgilia / Brister, Eileen / Sonalkar, Jay / Shen, Linyuan / Mitra, Jaba / Ha, Taekjip / Kajdacsy-Balla, Andre / Prasanth, Kannanganattu V / Prasanth, Supriya G

Molecular and cellular biology

2023 Volume 43, Issue 4, Page(s) 143–156

Abstract: The smallest subunit of the human Origin Recognition Complex, hOrc6, is required for DNA replication progression and plays an important role in mismatch repair (MMR) during S-phase. However, the molecular details of how hOrc6 regulates DNA replication ... ...

Abstract	The smallest subunit of the human Origin Recognition Complex, hOrc6, is required for DNA replication progression and plays an important role in mismatch repair (MMR) during S-phase. However, the molecular details of how hOrc6 regulates DNA replication and DNA damage response remain to be elucidated. Orc6 levels are elevated upon specific types of genotoxic stress, and it is phosphorylated at Thr229, predominantly during S-phase, in response to oxidative stress. Many repair pathways, including MMR, mediate oxidative DNA damage repair. Defects in MMR are linked to Lynch syndrome, predisposing patients to many cancers, including colorectal cancer. Orc6 levels are known to be elevated in colorectal cancers. Interestingly, tumor cells show reduced hOrc6-Thr229 phosphorylation compared to adjacent normal mucosa. Further, elevated expression of wild-type and the phospho-dead forms of Orc6 results in increased tumorigenicity, implying that in the absence of this "checkpoint" signal, cells proliferate unabated. Based on these results, we propose that DNA-damage-induced hOrc6-pThr229 phosphorylation during S-phase facilitates ATR signaling in the S-phase, halts fork progression, and enables assembly of repair factors to mediate efficient repair to prevent tumorigenesis. Our study provides novel insights into how hOrc6 regulates genome stability.
MeSH term(s)	Humans ; Phosphorylation ; Origin Recognition Complex/genetics ; Origin Recognition Complex/metabolism ; S Phase ; DNA Replication ; Genomic Instability ; DNA Damage
Chemical Substances	Origin Recognition Complex ; ORC6 protein, human
Language	English
Publishing date	2023-04-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1080/10985549.2023.2196204
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