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Article: Long Non-Coding RNAs: Tools for Understanding and Targeting Cancer Pathways.

Pandey, Gaurav Kumar / Kanduri, Chandrasekhar

2022 Volume 14, Issue 19

Abstract: The regulatory nature of long non-coding RNAs (lncRNAs) has been well established in various processes of cellular growth, development, and differentiation. Therefore, it is vital to examine their contribution to cancer development. There are ample ... ...

Abstract	The regulatory nature of long non-coding RNAs (lncRNAs) has been well established in various processes of cellular growth, development, and differentiation. Therefore, it is vital to examine their contribution to cancer development. There are ample examples of lncRNAs whose cellular levels are significantly associated with clinical outcomes. However, whether these non-coding molecules can work as either key drivers or barriers to cancer development remains unknown. The current review aims to discuss some well-characterised lncRNAs in the process of oncogenesis and extrapolate the extent of their decisive contribution to tumour development. We ask if these lncRNAs can independently initiate neoplastic lesions or they always need the modulation of well characterized oncogenes or tumour suppressors to exert their functional properties. Finally, we discuss the emerging genetic approaches and appropriate animal and humanised models that can significantly contribute to the functional dissection of lncRNAs in cancer development and progression.
Language	English
Publishing date	2022-09-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers14194760
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Article: Long noncoding RNAs: Lessons from genomic imprinting.

Kanduri, Chandrasekhar

Biochimica et biophysica acta

2016 Volume 1859, Issue 1, Page(s) 102–111

Abstract: Genomic imprinting has been a great resource for studying transcriptional and post-transcriptional-based gene regulation by long noncoding RNAs (lncRNAs). In this article, I overview the functional role of intergenic lncRNAs (H19, IPW, and MEG3), ... ...

Abstract	Genomic imprinting has been a great resource for studying transcriptional and post-transcriptional-based gene regulation by long noncoding RNAs (lncRNAs). In this article, I overview the functional role of intergenic lncRNAs (H19, IPW, and MEG3), antisense lncRNAs (Kcnq1ot1, Airn, Nespas, Ube3a-ATS), and enhancer lncRNAs (IG-DMR eRNAs) to understand the diverse mechanisms being employed by them in cis and/or trans to regulate the parent-of-origin-specific expression of target genes. Recent evidence suggests that some of the lncRNAs regulate imprinting by promoting intra-chromosomal higher-order chromatin compartmentalization, affecting replication timing and subnuclear positioning. Whereas others act via transcriptional occlusion or transcriptional collision-based mechanisms. By establishing genomic imprinting of target genes, the lncRNAs play a critical role in important biological functions, such as placental and embryonic growth, pluripotency maintenance, cell differentiation, and neural-related functions such as synaptic development and plasticity. An emerging consensus from the recent evidence is that the imprinted lncRNAs fine-tune gene expression of the protein-coding genes to maintain their dosage in cell. Hence, lncRNAs from imprinted clusters offer insights into their mode of action, and these mechanisms have been the basis for uncovering the mode of action of lncRNAs in several other biological contexts. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
MeSH term(s)	Cell Differentiation/genetics ; Chromatin/genetics ; DNA Replication/genetics ; Gene Expression Regulation, Developmental ; Genomic Imprinting/genetics ; Humans ; Neuronal Plasticity/genetics ; RNA, Long Noncoding/classification ; RNA, Long Noncoding/genetics
Chemical Substances	Chromatin ; H19 long non-coding RNA ; RNA, Long Noncoding
Language	English
Publishing date	2016-01
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.2015.05.006
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Article ; Online: Understanding Long Noncoding RNA and Chromatin Interactions: What We Know So Far.

Mishra, Kankadeb / Kanduri, Chandrasekhar

Non-coding RNA

2019 Volume 5, Issue 4

Abstract: With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their ...

Abstract	With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their genome-wide chromatin binding regions and mode of action. Evidence from these new technologies emphasize that chromatin targeting of lncRNAs is a prominent mechanism and that these chromatin targeted lncRNAs exert their functionality by fine tuning chromatin architecture resulting in an altered transcriptional readout. Currently, there are no unifying principles that define chromatin association of lncRNAs, however, evidence from a few chromatin-associated lncRNAs show presence of a short common sequence for chromatin targeting. In this article, we review how technological advancements contributed in characterizing chromatin associated lncRNAs, and discuss the potential mechanisms by which chromatin associated lncRNAs execute their functions.
Language	English
Publishing date	2019-12-03
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2813993-8
ISSN	2311-553X ; 2311-553X
ISSN (online)	2311-553X
ISSN	2311-553X
DOI	10.3390/ncrna5040054
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Article: LncRNAs join hands together to regulate neuroblastoma progression.

Mondal, Tanmoy / Kanduri, Chandrasekhar

Molecular & cellular oncology

2018 Volume 6, Issue 1, Page(s) 1553697

Abstract: Trait associated single nucleotide polymorphisms often overlap with noncoding transcripts but their contribution to disease phenotype is poorly investigated. Our study on neuroblastoma risk associated 6p22.3 locus derived long noncoding RNAs (lncRNAs) ... ...

Abstract	Trait associated single nucleotide polymorphisms often overlap with noncoding transcripts but their contribution to disease phenotype is poorly investigated. Our study on neuroblastoma risk associated 6p22.3 locus derived long noncoding RNAs (lncRNAs) demonstrates that functional co-operation between sense-antisense
Language	English
Publishing date	2018-12-17
Publishing country	United States
Document type	Journal Article
ISSN	2372-3556
ISSN	2372-3556
DOI	10.1080/23723556.2018.1553697
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Article ; Online: Sperm Originated Chromatin Imprints and LincRNAs in Organismal Development and Cancer.

Subhash, Santhilal / Kanduri, Meena / Kanduri, Chandrasekhar

iScience

2020 Volume 23, Issue 6, Page(s) 101165

Abstract: Importance of sperm-derived transcripts and chromatin imprints in organismal development is poorly investigated. Here using an integrative approach, we show that human sperm transcripts are equally important as oocyte. Sperm-specific and sperm-oocyte ... ...

Abstract	Importance of sperm-derived transcripts and chromatin imprints in organismal development is poorly investigated. Here using an integrative approach, we show that human sperm transcripts are equally important as oocyte. Sperm-specific and sperm-oocyte common transcripts carry distinct chromatin structures at their promoters correlating with corresponding transcript levels in sperm. Interestingly, sperm-specific H3K4me3 patterns at the lincRNA promoters are not maintained in the germ layers and somatic tissues. However, bivalent chromatin at the sperm-specific protein-coding gene promoters is maintained throughout the development. Sperm-specific transcripts reach their peak expression during zygotic genome activation, whereas sperm-oocyte common transcripts are present during early preimplantation development but decline at the onset of zygotic genome activation. Additionally, there is an inverse correlation between sperm-specific and sperm-oocyte lincRNAs throughout the development. Sperm-lincRNAs also show aberrant activation in tumors. Overall, our observations indicate that sperm transcripts carrying chromatin imprints may play an important role in human development and cancer.
Language	English
Publishing date	2020-05-15
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2020.101165
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Article ; Online: In Vivo Administration of Therapeutic Antisense Oligonucleotides.

Statello, Luisa / Ali, Mohamad Moustafa / Kanduri, Chandrasekhar

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2254, Page(s) 273–282

Abstract: With the rapid revolution in RNA/DNA sequencing technologies, it is evident that mammalian genomes express tens of thousands of long noncoding RNAs (lncRNAs). Since a large majority of lncRNAs have been functionally implicated in cancer development and ... ...

Abstract	With the rapid revolution in RNA/DNA sequencing technologies, it is evident that mammalian genomes express tens of thousands of long noncoding RNAs (lncRNAs). Since a large majority of lncRNAs have been functionally implicated in cancer development and progression, there is an increasing appreciation for the use of antisense oligonucleotide (ASO)-based therapies targeting lncRNAs in several cancers. Despite their great potential in therapeutic applications, their use is still limited due to cellular toxicity and shortcomings in achieving required stability in biological fluids and tissue uptake. To overcome these limitations, major changes in ASO chemistry have been introduced to generate second and third generation ASOs, including locked nucleic acids (LNA) technology. Here we describe two different LNA-ASO delivery approaches, a peritumoral administration and a systemic delivery in xenograft models of lung adenocarcinoma, that significantly reduced tumor growth without inducing toxicity.
MeSH term(s)	A549 Cells ; Adenocarcinoma of Lung/genetics ; Adenocarcinoma of Lung/therapy ; Animals ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Lung Neoplasms/genetics ; Lung Neoplasms/therapy ; Mice ; Oligonucleotides, Antisense/administration & dosage ; Oligonucleotides, Antisense/pharmacology ; Pilot Projects ; RNA, Long Noncoding/genetics ; Xenograft Model Antitumor Assays
Chemical Substances	Oligonucleotides, Antisense ; RNA, Long Noncoding
Language	English
Publishing date	2020-12-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1158-6_17
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Article: Long noncoding RNA and epigenomics.

Kanduri, Chandrasekhar

Advances in experimental medicine and biology

2011 Volume 722, Page(s) 174–195

Abstract: Accumulating evidence over the last decade has presented us with the intriguing observation that the majority of eukaryotic genomes are pervasively transcribed to encode a complex network of small and long noncoding RNAs. Long noncoding RNAs are of ... ...

Abstract	Accumulating evidence over the last decade has presented us with the intriguing observation that the majority of eukaryotic genomes are pervasively transcribed to encode a complex network of small and long noncoding RNAs. Long noncoding RNAs are of particular interest, as they were once thought to be restricted to housekeeping functions and are now linked to a wide variety of biological functions related to physiology, embryology and development. Emerging evidence indicates that a subset of long noncoding RNAs mediate their biological functions by using chromatin as a substrate, to index the genetic information encoded in the genome. This chapter will discuss how noncoding RNAs and the processes underlying their transcription mediate transcriptional regulation, by epigenetically regulating the structure of chromatin in various biological contexts.
MeSH term(s)	Animals ; Centromere/genetics ; Chromatin/genetics ; Drosophila melanogaster/genetics ; Epigenesis, Genetic/genetics ; Epigenomics ; Humans ; Mice ; MicroRNAs/genetics ; Models, Genetic ; RNA, Small Interfering/genetics ; RNA, Small Nucleolar/genetics ; RNA, Untranslated/genetics ; Schizosaccharomyces/genetics
Chemical Substances	Chromatin ; MicroRNAs ; RNA, Small Interfering ; RNA, Small Nucleolar ; RNA, Untranslated
Language	English
Publishing date	2011
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-1-4614-0332-6_11
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Article ; Online: Kcnq1ot1: a chromatin regulatory RNA.

Kanduri, Chandrasekhar

Seminars in cell & developmental biology

2011 Volume 22, Issue 4, Page(s) 343–350

Abstract: There is a growing interest for noncoding RNA (ncRNA)-mediated epigenetic regulation of transcription in diverse biological functions. Recent evidence suggests that a subset of long ncRNA epigenetically regulate the transcription of multiple genes in ... ...

Abstract	There is a growing interest for noncoding RNA (ncRNA)-mediated epigenetic regulation of transcription in diverse biological functions. Recent evidence suggests that a subset of long ncRNA epigenetically regulate the transcription of multiple genes in chromosomal domains via interaction with chromatin. Kcnq1ot1 is one such long chromatin-interacting ncRNA that silences multiple genes in the Kcnq1 domain by establishing a repressive higher order chromatin structure. This is done by the recruitment of chromatin and DNA-modifying proteins. This review looks at recent evidence supporting the notion that Kcnq1ot1-mediated silencing is a multilayered pathway. Comparing the mode of action of Kcnq1ot1 with other well-investigated chromatin regulatory long ncRNAs, such as Xist, HOTAIR and Airn, revealed that chromatin regulatory ncRNAs share common epigenetic pathways in the silencing of multiple genes.
MeSH term(s)	Animals ; Chromatin/metabolism ; DNA Methylation ; Gene Silencing ; Humans ; KCNQ1 Potassium Channel/genetics ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism
Chemical Substances	Chromatin ; KCNQ1 Potassium Channel ; RNA, Untranslated
Language	English
Publishing date	2011-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2011.02.020
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Article ; Online: Labeling and Purification of Temporally Expressed RNAs During the S-Phase of the Cell Cycle in Living Cells.

Meryet-Figuiere, Matthieu / Ali, Mohamad Moustafa / Subhash, Santhilal / Kanduri, Chandrasekhar

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2254, Page(s) 239–249

Abstract: From high-throughput DNA and RNA sequencing technologies, it is evident that more than two-thirds of the mammalian genome is transcribed and nearly 98% of the transcriptional output in humans constitute noncoding RNA, comprising tens of thousands of ... ...

Abstract	From high-throughput DNA and RNA sequencing technologies, it is evident that more than two-thirds of the mammalian genome is transcribed and nearly 98% of the transcriptional output in humans constitute noncoding RNA, comprising tens of thousands of small and long noncoding RNAs. These observations have put the study of RNA expression levels at the center of molecular biology research. The transcriptional output of cells changes temporally throughout different cell cycle phases, or in response to a large panel of stimuli. In such instances, the measure of induced RNA transcripts might be obscured by the presence of steady-state RNA levels in the total transcriptome. With this protocol, we provide a method for labeling and purification of the nascent RNAs transcribed over short periods of time in cultured cells. The supplementation of cell culture medium with a chemically modified analog of uridine, ethynyl-uridine, allows for the subsequent biotinylation of ethynyl-uridine residues with a click-chemistry reaction. The labeled RNA is then purified on streptavidin beads and eluted. The purified RNA is suitable for use in RT-qPCR assays as well as in deep sequencing applications.
MeSH term(s)	Cell Culture Techniques/methods ; Cell Cycle ; Click Chemistry ; Culture Media/chemistry ; Gene Expression Profiling/methods ; HeLa Cells ; High-Throughput Nucleotide Sequencing ; Humans ; RNA/chemistry ; RNA/isolation & purification ; S Phase ; Staining and Labeling ; Uridine/analogs & derivatives
Chemical Substances	Culture Media ; RNA (63231-63-0) ; Uridine (WHI7HQ7H85)
Language	English
Publishing date	2020-12-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1158-6_14
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Article ; Online: GeneSCF: a real-time based functional enrichment tool with support for multiple organisms.

Subhash, Santhilal / Kanduri, Chandrasekhar

BMC bioinformatics

2016 Volume 17, Issue 1, Page(s) 365

Abstract: Background: High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significance ...

Abstract	Background: High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significance of the affected genes from these high-throughput studies. However, currently available functional enrichment tools need to be updated frequently to adapt to new entries from the functional database repositories. Hence there is a need for a simplified tool that can perform functional enrichment analysis by using updated information directly from the source databases such as KEGG, Reactome or Gene Ontology etc. Results: In this study, we focused on designing a command-line tool called GeneSCF (Gene Set Clustering based on Functional annotations), that can predict the functionally relevant biological information for a set of genes in a real-time updated manner. It is designed to handle information from more than 4000 organisms from freely available prominent functional databases like KEGG, Reactome and Gene Ontology. We successfully employed our tool on two of published datasets to predict the biologically relevant functional information. The core features of this tool were tested on Linux machines without the need for installation of more dependencies. Conclusions: GeneSCF is more reliable compared to other enrichment tools because of its ability to use reference functional databases in real-time to perform enrichment analysis. It is an easy-to-integrate tool with other pipelines available for downstream analysis of high-throughput data. More importantly, GeneSCF can run multiple gene lists simultaneously on different organisms thereby saving time for the users. Since the tool is designed to be ready-to-use, there is no need for any complex compilation and installation procedures.
MeSH term(s)	Databases, Factual/standards ; Databases, Factual/utilization ; Gene Ontology ; Humans ; Metabolomics/methods ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods
Language	English
Publishing date	2016-09-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-016-1250-z
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