A Dual Origin of the Xist Gene from a Protein-Coding Gene and a Set of Transposable Elements

Elisaphenko, Eugeny A.; Kolesnikov, N. N.; Shevchenko, Alexander I.; Rogozin, Igor B.; Nesterova, Tatyana B.; Brockdorff, Neil; Zakian, Suren M.

doi:10.1371/journal.pone.0002521

Cited by 168 publications

(189 citation statements)

References 27 publications

Supporting

Mentioning

172

Contrasting

Unclassified

Order By: Relevance

“…Unspliced ESTs are also reported as parts of spliced transcripts, in particular those with very long exons such as XIST [37]. In other cases, such as TUG1 [38] we observe predominantly unspliced ESTs that cover nearly the entire primary transcript, even though the genomic location is annotated by the spliced forms.…”

Section: Unspliced Mrnasmentioning

confidence: 79%

Hidden treasures in unspliced EST data

Engelhardt

Stadler

2012

Theory Biosci.

View full text Add to dashboard Cite

Abstract. Several classes of exclusively -or at least predominantly -unspliced non-coding RNAs have been described in the last years, including totally and partially intronic transcripts and long intergenic RNAs. Functionally, they appear to be involved in regulating gene expression, at least in part by associating with the chromatin. Here we systematically analyze the distribution of unspliced ESTs in the human genome. Most appear in clusters overlapping or in the close vicinity of annotated RefSeq genes. Partially Intronic (PIN) unspliced ESTs show complex patterns of overlap with the intron/exon structure of the RefSeq gene. Distinctive patterns of CAGE tags indicate that a large class of unspliced EST clusters forms long extensions of 3'UTRs, at least several hundreds of which probably appear also as independent uaRNAs.

show abstract

Section: Unspliced Mrnasmentioning

confidence: 79%

Hidden treasures in unspliced EST data

Engelhardt

Stadler

2012

Theory Biosci.

View full text Add to dashboard Cite

show abstract

“…Some transcribed pseudogenes have been found to regulate gene expression (often of their ancestral coding genes) by epigenetic or post-transcriptional mechanisms. In fact, Xist is hypothesized to have evolved by the pseudogenization of the protein-coding gene Lnx3 and integration of various transposon-derived repeat elements (Duret et al 2006;Elisaphenko et al 2008).…”

Section: Pseudogenesmentioning

confidence: 99%

Long Noncoding RNAs: Past, Present, and Future

2013

View full text Add to dashboard Cite

Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years as a potentially new and crucial layer of biological regulation. lncRNAs of all kinds have been implicated in a range of developmental processes and diseases, but knowledge of the mechanisms by which they act is still surprisingly limited, and claims that almost the entirety of the mammalian genome is transcribed into functional noncoding transcripts remain controversial. At the same time, a small number of well-studied lncRNAs have given us important clues about the biology of these molecules, and a few key functional and mechanistic themes have begun to emerge, although the robustness of these models and classification schemes remains to be seen. Here, we review the current state of knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions, and mechanisms of action of lncRNAs. We also reflect on how the recent interest in lncRNAs is deeply rooted in biology's longstanding concern with the evolution and function of genomes.T HE past several years have witnessed a steep rise of interest in the study of lncRNAs. Almost on a weekly basis, it seems that a new lncRNA is found to be up-or downregulated in a particular disease, or a new class of noncoding transcripts is uncovered by a transcriptomic study, or a new article heralds a paradigm shift that lncRNAs will bring to our understanding of biology. Without a doubt, the advent of sensitive, high-throughput genomic technologies such as microarrays and next-generation sequencing (NGS) has resulted in an unprecedented ability to detect novel transcripts, the vast majority of which seem not to be derived from annotated protein-coding genes. Despite this explosion of data, however, surprisingly little is known about how lncRNAs function, how many different types of lncRNAs exist, or even whether most of them carry biological significance.In this review, we focus on recently discovered lncRNAs of .200 nt, place these new discoveries in historical context, and outline areas where additional work is needed. The review does not cover "classic" ncRNAs such as ribosomal (r) RNAs, ribozymes, transfer (t)RNAs, small nuclear (sn)RNAs, small nucleolar (sno)RNAs, and telomere-associated RNAs (TERC, TERRA); nor does it cover small ncRNAs such as microRNAs (miRNAs), endogenous small interfering (endo-si)RNAs that participate in RNA interference (RNAi), and Piwi-associated (pi)RNAs. We refer readers to the many

show abstract

“…Rsx expression leads to formation of RNA clouds in the interphase nucleus resembling those produced by Xist RNA. Similar to Xist, Rsx sequence includes multiple copies of simple repeat sequences that may form Has been observed in some species [77].…”

Section: Rsx An Xist-like Molecule In Marsupialsmentioning

confidence: 99%

Advances in understanding chromosome silencing by the long non-coding RNA Xist

Sado

Brockdorff

2013

Phil. Trans. R. Soc. B

Self Cite

View full text Add to dashboard Cite

In female mammals, one of the two X chromosomes becomes genetically silenced to compensate for dosage imbalance of X-linked genes between XX females and XY males. X chromosome inactivation (X-inactivation) is a classical model for epigenetic gene regulation in mammals and has been studied for half a century. In the last two decades, efforts have been focused on the X inactive-specific transcript ( Xist ) locus, discovered to be the master regulator of X-inactivation. The Xist gene produces a non-coding RNA that functions as the primary switch for X-inactivation, coating the X chromosome from which it is transcribed in cis . Significant progress has been made towards understanding how Xist is regulated at the onset of X-inactivation, but our understanding of the molecular basis of silencing mediated by Xist RNA has progressed more slowly. A picture has, however, begun to emerge, and new tools and resources hold out the promise of further advances to come. Here, we provide an overview of the current state of our knowledge, what is known about Xist RNA and how it may trigger chromosome silencing.

show abstract

A Dual Origin of the Xist Gene from a Protein-Coding Gene and a Set of Transposable Elements

Cited by 168 publications

References 27 publications

Hidden treasures in unspliced EST data

Hidden treasures in unspliced EST data

Long Noncoding RNAs: Past, Present, and Future

Advances in understanding chromosome silencing by the long non-coding RNA Xist

Contact Info

Product

Resources

About