The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Epigenetic and experimental approaches influencing non-coding RNAs
Abstract
Epigenetics having sundry ambiences which are robustly linked to non-coding RNAs, precisely small RNAs that are generally imputated in gene expression regulation and helps in directing cytosine methylation and histone modifications of complex organisms. A pivotal peculiarity of epigenetics is that the same genome shows unwonted phenotypes which are situated in different epigenetics states. In last decade, the majority tangled epigenetic phenomena studied encompasses transposon activity and silencing which are directly or indirectly associated in RNA component and are currently epitomize by piRNAs (piwi-interacting RNAs), position effect variegation, X-chromosome inactivation, parental imprinting, and paramutation. Envisagly, there are certain non - coding RNAs are players in epigenetics gene regulation but their mechanism is still underlying. In yeast, plants, and mice, ncRNAs facilitate the inheritance of epigenetic states, effectively transmitting information across generations. This transgenerational epigenetic inheritance underscores the potential of ncRNAs to act as carriers of heritable information, bridging the gap between environmental cues and genetic responses. In conclusion, ncRNAs play a central role in epigenetic regulation and the transfer of genetic information, highlighting their importance in the evolution and complexity of higher organisms. In this review article, ongoing research continues to uncover the multifaceted functions of these molecules, offering deeper insights into the regulatory architectures that underpin life.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“the pre‐conception phase of the ageing process is driven by trans‐ and intergenerational epigenetic factors in response to differing environmental exposures [15].”
From Ignoring the planet: A critical blind spot for research on ageing (2025) · cites this paper as [15]
Citations
Cites
Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
Goodstadt, L., & Ponting, C. P. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020133 · Cited by 154
Research works printed but not linked: 61
- Agrawal, 2003, RNA interference: biology, mechanism, and applications, Microbiol Mol Biol Rev., 67, 657, 10.1128/MMBR.67.4.657-685.2003 · DOI
- Aparicio, 2002, Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes, Science, 297, 1301, 10.1126/science.1072104 · DOI · Paper page
- Bartel, 2004, MicroRNAs: genomics, biogenesis, mechanism, and function, Cell, 116, 281, 10.1016/S0092-8674(04)00045-5 · DOI
- Taft, 2007, The relationship between non-protein-coding DNA and eukaryotic complexity, BioEssays, 29, 288, 10.1002/bies.20544 · DOI
- Benetti, 2008, A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases, Nat Struct Mol Biol., 15, 268, 10.1038/nsmb.1399 · DOI
- Borsani, 2005, Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis, Cell, 123, 1279, 10.1016/j.cell.2005.11.035 · DOI
- Brennecke, 2007, Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila, Cell, 128, 1089, 10.1016/j.cell.2007.01.043 · DOI · Paper page
- Britten, 1969, Gene regulation for higher cells: a theory, Science, 165, 349, 10.1126/science.165.3891.349 · DOI
- Carninci, 2005, The transcriptional landscape of the mammalian genome, Science, 309, 1559, 10.1126/science.1112014 · DOI
- Chu, 2007, Small RNAs: regulators and guardians of the genome, J Cell Physiol., 213, 412, 10.1002/jcp.21230 · DOI
- Clamp, 2007, Distinguishing protein-coding and noncoding genes in the human genome, Proc Natl Acad Sci USA., 104, 19428, 10.1073/pnas.0709013104 · DOI · Paper page
- Costa, 2008, Non-coding RNAs, epigenetics and complexity, Gene, 410, 9, 10.1016/j.gene.2007.12.008 · DOI
- Costa, 2009, Non-coding RNAs and new opportunities for the private sector, Drug Discov Today, 14, 446, 10.1016/j.drudis.2009.01.008 · DOI
- Costa, 2005, Non-coding RNAs: lost in translation?, Gene, 386, 1
- Dieci, 2007, The expanding RNA polymerase III transcriptome, Trends Genet., 23, 614, 10.1016/j.tig.2007.09.001 · DOI
- Farazi, 2008, The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members, Development, 135, 1201, 10.1242/dev.005629 · DOI
- Fischer, 2007, Recovery of learning and memory is associated with chromatin remodelling, Nature, 10, 178, 10.1038/nature05772 · DOI · Paper page
- Grivna, 2006, A novel class of small RNAs in mouse spermatogenic cells, Genes Dev., 20, 1709, 10.1101/gad.1434406 · DOI
- Gunawardane, 2007, A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila, Science, 315, 1587, 10.1126/science.1140494 · DOI
- Mercer, 2009, Long non-coding RNAs: insights into functions, Nat Rev Genet., 10, 155, 10.1038/nrg2521 · DOI · Paper page
- Mochizuki, 2002, Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena, Cell, 110, 689, 10.1016/S0092-8674(02)00909-1 · DOI
- Murrell, 2005, From genome to epigenome, Hum Mol Genet., 12, 3, 10.1093/hmg/ddi110 · DOI
- Henry, 1998, SNAP19 mediates the assembly of a functional core promoter complex (SNAPc) shared by RNA polymerases II and III, Genes Dev., 12, 2664, 10.1101/gad.12.17.2664 · DOI
- Houweling, 2007, A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish, Cell, 129, 69, 10.1016/j.cell.2007.03.026 · DOI
- International Chicken Genome Sequencing Consortium, 2004, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature, 432, 695, 10.1038/nature03154 · DOI · Paper page
- Kable, 1997, RNA editing: getting U into RNA, Trends Biochem. Sci., 22, 162, 10.1016/S0968-0004(97)01041-4 · DOI
- Maden, 1997, Eukaryotic ribosomal RNA: the recent excitement in the nucleotide modification problem, Chromosoma, 105, 391, 10.1007/BF02510475 · DOI
- Mattick, 2001, Non-coding RNAs: the architects of eukaryotic complexity, EMBO Rep., 2, 986, 10.1093/embo-reports/kve230 · DOI
- Mattick, 2005, Small regulatory RNAs in mammals, Hum Mol Genet., 14, R121, 10.1093/hmg/ddi101 · DOI
- Lin, 2007, A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas, Oncogene, 26, 851, 10.1038/sj.onc.1209846 · DOI
- Uhler, 2007, A role for noncoding transcription in activation of the yeast PHO5 gene, Proc Natl Acad Sci USA., 104, 8011, 10.1073/pnas.0702431104 · DOI
- Perez, 2008, Long, abundantly expressed non-coding transcripts are altered in cancer, Hum Mol Genet., 17, 642, 10.1093/hmg/ddm336 · DOI
- Katiyar-Agarwal, 2007, A novel class of bacteria-induced small RNAs in Arabidopsis, Genes Dev., 21, 3123, 10.1101/gad.1595107 · DOI
- Klattenhoff, 2008, Biogenesis and germline functions of piRNAs, Development, 135, 3, 10.1242/dev.006486 · DOI
- Peragine, 2004, SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis, Genes Dev., 18, 2368, 10.1101/gad.1231804 · DOI
- Ponting, 2009, Evolution and functions of long noncoding RNAs, Cell, 136, 629, 10.1016/j.cell.2009.02.006 · DOI · Paper page
- Prasanth, 2007, Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum, Genes Dev., 21, 11, 10.1101/gad.1484207 · DOI
- Klose, 2006, Genomic DNA methylation: the mark and its mediators, Trends Biochem Sci., 31, 89, 10.1016/j.tibs.2005.12.008 · DOI · Paper page
- Liu, 2004, Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena, Proc Natl Acad Sci USA., 101, 1679, 10.1073/pnas.0305421101 · DOI
- Reamon-Buettner, 2007, A new paradigm in toxicology and teratology: altering gene activity in the absence of DNA sequence variation, Reprod Toxicol., 24, 20, 10.1016/j.reprotox.2007.05.002 · DOI
- Saito, 2006, Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome, Genes Dev., 20, 2214, 10.1101/gad.1454806 · DOI
- Seligson, 2005, Global histone modification patterns predict risk of prostate cancer recurrence, Nature, 435, 1262, 10.1038/nature03672 · DOI
- Shamovsky, 2006, Gene control by large noncoding RNAs, Sci STKE, 355, pe40
- Stefani, 2008, Small non-coding RNAs in animal development, Nat Rev Mol Cell Biol., 9, 219, 10.1038/nrm2347 · DOI
- Stuart, 2002, RNA editing: complexity and complications, Mol Microbiol., 45, 591, 10.1046/j.1365-2958.2002.03028.x · DOI
- Szymanski, 2005, A new frontier for molecular medicine: noncoding RNAs, Biochim Biophys Acta., 1756, 65
- Vazquez, 2004, Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs, Mol Cell, 16, 69, 10.1016/j.molcel.2004.09.028 · DOI
- Waterston, 2002, Initial sequencing and comparative analysis of the mouse genome, Nature, 420, 520, 10.1038/nature01262 · DOI · Paper page
- Watanabe, 2006, Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes, Genes Dev., 20, 1732, 10.1101/gad.1425706 · DOI
- Weber, 2007, Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells, Nat Genet., 37, 853, 10.1038/ng1598 · DOI
- Willingham, 2006, TUF love for ‘junk’ DNA, Cell, 125, 1215, 10.1016/j.cell.2006.06.009 · DOI
- Wilusz, 2009, Long noncoding RNAs: functional surprises from the RNA world, Genes Dev., 23, 1494, 10.1101/gad.1800909 · DOI
- Xie, 2008, Diverse small RNA-directed silencing pathways in plants, Biochim Biophys Acta., 1779, 720, 10.1016/j.bbagrm.2008.02.009 · DOI
- Lim, 2010, Computational epigenetics: the new scientific paradigm, Bioinformation, 4, 331, 10.6026/97320630004331 · DOI
- Bock, 2012, Analysing and interpreting DNA methylation data, Nat Rev Genet., 13, 705, 10.1038/nrg3273 · DOI
- Rauluseviciute, 2019, DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis, Clin Epigenetics, 11, 193, 10.1186/s13148-019-0795-x · DOI
- Krueger, 2011, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics, 27, 1571, 10.1093/bioinformatics/btr167 · DOI
- Huang, 2018, BS-Seeker3: ultrafast pipeline for bisulfite sequencing, BMC Bioinforma., 19, 111, 10.1186/s12859-018-2120-7 · DOI
- Hansen, 2012, BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions, Genome Biol., 13, 83, 10.1186/gb-2012-13-10-r83 · DOI
- Nakato, 2020, Methods for ChIP-seq analysis: a practical workflow and advanced applications, Methods, 175, 1
- Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137 · DOI · Paper page
Cited by
Sorted by citations
Ignoring the planet: A critical blind spot for research on ageing
Shiels, P., Neytchev, O., Borland, G., Germushkina, P., Johnson, R., Stenvinkel, P., & Woods, T. (2025) · Journal of Internal Medicine · doi:10.1111/joim.70032 · Cited by 4
Metadata
- Authors
- Vijay, U., Kaur, A., & Polipalli, S. K.
- Affiliations
- SMS Medical College (IN)
- Amrita Vishwa Vidyapeetham (IN)
- Corresponding author
- Urvashi Vijay
- Venue
- Progress in Molecular Biology and Translational Science
- Publisher
- Elsevier
- Published
- 2025
- Volume
- 214
- Pages
- 65-79
- ISSN
- 1877-1173 (ISSN-L)
- OpenAlex
- W4411049620
- Cited by
- 3
- References
- 1
- Citations by year
- 2026: 3
- FWCI
- 6.38
- Type
- book chapter
- Language
- en
- Open access
- closed
- Licence
- Locations
- Progress in molecular biology and translational science (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- non-coding RNA, small RNA, epigenetics, gene expression regulation, cytosine methylation, histone modifications, transposon silencing, piRNA, position effect variegation, X chromosome inactivation, genomic imprinting, paramutation, transgenerational epigenetic inheritance, epigenetic inheritance
- MeSH terms
- Animals, Humans, RNA, Untranslated, Epigenesis, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review