DOCSLIB.ORG

Biological Functions of Natural Antisense Transcripts Wojciech Rosikiewicz* and Izabela Makałowska

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Biological Functions of Natural Antisense Transcripts Wojciech Rosikiewicz* and Izabela Makałowska Vol. 63, No 4/2016 665–673 https://doi.org/10.18388/abp.2016_1350 Review Biological functions of natural antisense transcripts Wojciech Rosikiewicz* and Izabela Makałowska Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland Natural antisense transcripts (NATs) are RNA mol- plementary between the sense and antisense RNAs, un- ecules that originate from opposite DNA strands of the like trans-NATs, where transcripts originate from differ- same genomic locus (cis-NAT) or unlinked genomic loci ent genomic loci (Fig. 1D) (Vanhée-Brossollet & Vaque- (trans-NAT). NATs may play various regulatory functions ro, 1998). at the transcriptional level via transcriptional interfer- Almost half of the century has passed since the first ence. NATs may also regulate gene expression levels natural antisense RNAs were found within the b2 re- post-transcriptionally via induction of epigenetic chang- gion of coliphage λ (Bovre & Szybalski, 1969). Bovre es or double-stranded RNA formation, which may lead and Szybalski concluded that double-stranded RNA to endogenous RNA interference, RNA editing or RNA (dsRNA) may be produced from overlapping transcripts masking. The true biological significance of the natural under some conditions. They also suggested that RNA antisense transcripts remains controversial despite many polymerases transcribing opposite strands in the b2 re- years of research. Here, we summarize the current state gion may collide with each other, which would lead to of knowledge and discuss the sense-antisense overlap premature transcription termination (Bovre & Szybalski regulatory mechanisms and their potential. 1969). Today this is known as polymerase collision, one of the transcriptional interference scenarios (Shearwin et Key words: Natural antisense transcripts, antisense transcription, ex- al., 2005). The golden age of natural antisense transcripts pression level regulation was far ahead despite this early discovery. Only 11 pairs Received: 03 June, 2016; revised: 24 June, 2016; accepted: 25 June, of protein-coding genes with non-protein coding natu- 2016; available on-line: 21 October, 2016 ral antisense counterparts were described until the late 1980s, all in viral genomes (Inouye, 1988). These stud- ies consolidated the hypotheses that this type of genom- INTRODUCTION ic architecture was rather rare and probably limited to bacterial and viral genomes (Barrell et al., 1976; Sanger et Natural antisense transcripts (NATs) are separated al., 1977; Szekely, 1977). However, the first discoveries into two main categories, cis or trans, depending on of overlapping genes in eukaryotic genomes were pub- their genomic origin. The most popular definition of lished in 1986. Henikoff and co-workers found that the cis-NATs describes these molecules as RNA sequences pupal cuticle protein (Pcp) gene of Drosophila melanogaster was embedded on the opposite DNA strand of the Gart gene within its first intron (Henikoff et al., 1986). Further discoveries in fruit fly (Spencer et al., 1986) and mouse (Williams & Fried, 1986) were identified in the same year. The first overlapping pairs were found in humans and yeast three years later (van Duin et al., 1989). Comprehensive discoveries of natural antisense transcripts began to emerge at the beginning of the 21st century in vari- ous species, including plants (Mol et al., 1990; Quesada et al., 1999; Osato et al., 2003; Wang et al., 2006), fungi (Steigele Figure 1. Types of natural antisense transcript overlap. & Nieselt, 2005, David et al., 2006), ver- (A) Head-to-head overlap in cis; (B) Tail-to-tail overlap in cis; (C) Embedded over- tebrates (Lehrer et al., 2002; Shendure & lap in cis; (D) Overlap in trans, green and blue arrows represent transcripts origi- nated from different genomic loci, and forming double-stranded RNA. Full or Church, 2002; Zhou & Blumberg, 2003, partial complementarity between transcripts is indicated by a regularly spaced or Veeramachaneni et al., 2005; Ge et al., disrupted “ladder” of grey vertical lines within the overlap region of cis and trans 2008) and invertebrates (Misener & Walk- overlapping transcripts, respectively. er, 2000; Lee et al., 2005). Antisense tran- that originate from the opposite DNA strand of the *e-mail: [email protected] same genomic locus, such that they physically share some Abbreviations: NAT, natural antisense transcript; cis-NAT, natural genetic sequence. The overlap may be complete (Fig. antisense transcripts originating from the opposite DNA strands 1C) or partial (Fig. 1A, B), and it may also be described of the same genomic locus; trans-NAT, natural antisense transcripts as head-to-head (Fig. 1A), tail-to-tail (Fig. 1B) or embed- originating from different genomicloci; dsRNA, double-stranded RNA; TI, transcriptional interference; RNAPII, RNA polymerase II; ded (Fig. 1C) (Makalowska et al., 2005). The sequences RNAi, RNA interference of cis-NATs within the overlap region are perfectly com- 666 W. Rosikiewicz and I. Makałowska 2016 scription is now considered a widespread phenomenon of double-stranded RNA, which leads to RNA masking, that concerns up to 30% of human and mouse genom- RNA interference or RNA editing (Faghihi and Wahlest- es (Yelin et al., 2003; Chen et al., 2004; Katayama et al., edt 2009, Lu et al., 2012, Celton et al., 2014). Expression 2005; Zhang et al., 2006). level regulation in cis, described in sections 1 and 2, may Natural antisense transcripts were studied using vari- occur at the transcriptional and post-transcriptional lev- ous approaches, including in silico analyses of the ex- els. In contrast, regulation in trans, discussed in section 3, pressed sequence tags (Shendure & Church, 2002, Chen may act only post-transcriptionally (Vanhée-Brossollet & et al., 2004), large-scale sequencing of full-length comple- Vaquero, 1998). mentary DNAs (Osato et al., 2003; Wang et al., 2005), and tiling arrays (Li et al., 2006; Matsui et al., 2008). Cur- TRANSCRIPTIONAL LEVEL OF REGULATION rent approaches are often based on next-generation se- quencing technologies, such as RNA sequencing (RNA- Seq), single-strand RNA sequencing (ssRNA-Seq) or Transcriptional interference chromatin immunoprecipitation-sequencing (ChIP-Seq), which allowed for the discoveries of natural antisense Natural antisense transcripts may regulate expression transcripts across species on a large scale (Lu et al., 2012; at the level of transcription via transcriptional interfer- Conley & Jordan, 2012; Li et al., 2013; Luo et al., 2013). ence (TI). This term describes a down-regulatory in- fluence of the two ongoing transcription processes in BIOLOGICAL FUNCTIONS OF NATURAL ANTISENSE a relatively close proximity (Shearwin et al., 2005). TI TRANSCRIPTS may result in transcriptional downturn, transcriptional inhibition or early transcription termination. Four main mechanisms of transcriptional interference were pro- The biological significance of natural antisense tran- posed. The first mechanism, promoter competition, is scripts remains controversial despite many years of re- a mechanism in which promoter regions overlap, and search. Some groups describe natural antisense tran- transcription may start only at one of them at a time scripts as transcriptional noise with the potential to ac- (Fig. 2A). The second mechanism is called “sitting duck quire a secondary function. Other groups posit that this interference”, and it describes a situation in which RNA latent regulatory potential is underestimated and should polymerase II (RNAPII) progresses too slowly to the be considered as another level of gene expression regu- elongation phase, and it is dislodged by another RNA lation. The overlap between natural sense and antisense polymerase II (Fig. 2B). The third scenario, occlusion, transcripts may regulate expression at the transcriptional involves the temporary blocking of transcription initia- level (via transcriptional interference) and/or post-tran- tion at a particular promoter region by the ongoing elon- scriptional level. Regulation may be achieved via modula- gation of RNAPII originating from a different promoter tion of chromatin changes by NATs or the formation (Fig. 2C). The last mechanism, polymerase collision, occurs when two RNAPIIs, which are transcribing genes in opposite directions, block each other’s passage and collide in a head- to-head manner (Fig. 2D). Shearwin et al., thoroughly dis- cussed these mechanisms in a review (Shearwin et al., 2005). Transcriptional interference was intensively studied in re- cent years. A transcriptional collision model was inferred from human and mouse ge- nomes analyses, which ob- served lower expression levels of sense-antisense transcripts in longer overlapping regions (Shearwin et al., 2005; Osato et al., 2007). RNAPII colli- sions were described in yeast in in vitro and in vivo models. RNAPIIs were temporary sus- pended during transcriptional collision events, but the elon- gation complexes were stable, which extended the half-life of the RNAPII involved in this process (Hobson et al., 2012). Notably, the RNAPII Figure 2. Mechanisms of transcriptional interference. collision was also linked with (A) Promoter competition; (B) Sitting duck interference; (C) Occlusion; (D) Polymerase colli- the “off-targeting” of the ac- sion; RNAPII – RNA polymerase II; Blue/green boxes with arrows indicate the transcription direction and promoter regions of genes A and B, respectively. Arrows next to RNAPIIs in- tivation-induced
Load more

Recommended publications
  • Long Non‑Coding Rnas XIST and MALAT1 Hijack the PD‑L1 Regulatory Signaling Pathway in Breast Cancer Subtypes
    ONCOLOGY LETTERS 22: 593, 2021 Long non‑coding RNAs XIST and MALAT1 hijack the PD‑L1 regulatory signaling pathway in breast cancer subtypes AMANY SAMIR1, REDA ABDEL TAWAB2 and HEND M. EL TAYEBI1 1Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, German University in Cairo, Cairo 11835; 2Department of General Surgery, Ain Shams University, Cairo 11772, Egypt Received July 18, 2020; Accepted January 14, 2021 DOI: 10.3892/ol.2021.12854 Abstract. Long non‑coding RNAs (lncRNAs) have attracted presence of lncRNAs. Therefore, the results of the present widespread attention as potential biological and patho‑ study indicated that although miR‑182‑5p exhibited an onco‑ logical regulators. lncRNAs are involved in several biological genic effect, XIST exerted a dominant effect on the regulation processes in cancer. Triple negative breast cancer (TNBC) is of the PD‑L1 signaling pathway via the inhibition of the onco‑ characterized by strong heterogeneity and aggressiveness. At genic function of MALAT1. present, the implication of microRNAs (miRs) and lncRNAs in immunotherapy has been poorly studied. Nevertheless, Introduction the blockade of immune checkpoints, particularly that of the programmed cell‑death protein‑1/programmed cell‑death In the context of tumor biology, the six hallmarks of cancer ligand‑1 (PD‑L1) axis, is considered as a principle approach in have been proposed to be associated with progressively breast cancer (BC) therapy. The present study aimed to inves‑ growing tumors and to be responsible for the complexity of tigate the interaction between immune‑modulatory upstream neoplastic diseases, and these are limitless replicative poten‑ signaling pathways of the PD‑L1 transcript that could enhance tial, evading apoptosis, self‑sufficiency in growth signals, personalized targeted therapy.
    [Show full text]
  • Biological Functions of Natural Antisense Transcripts Andreas Werner
    Werner BMC Biology 2013, 11:31 http://www.biomedcentral.com/1741-7007/11/31 COMMENTARY Open Access Biological functions of natural antisense transcripts Andreas Werner Abstract The most common meaning of the term 'antisense tran- script' refers to a protein coding sense transcript and a In theory, the human genome is large enough to fully processed (capped, polyadenylated) antisense RNA keep its roughly 20,000 genes well separated. In with complementarity in exonic regions (Figure 1). The practice, genes are clustered; even more puzzling, in key issue of whether the antisense transcripts act as ex- many cases both DNA strands of a protein coding quisitely specific gene regulators or are simply transcrip- gene are transcribed. The resulting natural antisense tional waste that a cell has learned to live with is still a transcripts can be a blessing and curse, as many matter of controversy [2]. However, a study published in appreciate, or simply transcriptional trash, as others BMC Genomics reports conservation of natural antisense believe. Widespread evolutionary conservation, as transcripts at a large scale between human, rat and mouse, recently demonstrated, is a good indicator for which strongly suggests that there is biological sense to potential biological functions of natural antisense having antisense transcripts [3]. transcripts. See research article: http://www.biomedcentral.com/ Regulatory antisense transcripts 1471-2164/14/243 The most convincing way to demonstrate the biologi- cal significance of an antisense transcript is to interfere with its expression and demonstrate phenotypic conse- By the mid-1980s antisense transcription in mammalian quences or altered expression levels of the sense tran- genomes had already been described by a few isolated script.
    [Show full text]
  • Thoughts About SLC16A2, TSIX and XIST Gene Like Sites in the Human Genome and a Potential Role in Cellular Chromosome Counting Martina Rinčić1, Ivan Y
    Rinčić et al. Molecular Cytogenetics (2016) 9:56 DOI 10.1186/s13039-016-0271-7 HYPOTHESIS Open Access Thoughts about SLC16A2, TSIX and XIST gene like sites in the human genome and a potential role in cellular chromosome counting Martina Rinčić1, Ivan Y. Iourov2,3,4 and Thomas Liehr5* Abstract Background: Chromosome counting is a process in which cells determine somehow their intrinsic chromosome number(s). The best-studied cellular mechanism that involves chromosome counting is ‘chromosome-kissing’ and X-chromosome inactivation (XCI) mechanism. It is necessary for the well-known dosage compensation between the genders in mammals to balance the number of active X-chromosomes (Xa) with regard to diploid set of autosomes. At the onset of XCI, two X-chromosomes are coming in close proximity and pair physically by a specific segment denominated X-pairing region (Xpr) that involves the SLC16A2 gene. Results: An Ensembl BLAST search for human and mouse SLC16A2/Slc16a2 homologues revealed, that highly similar sequences can be found at almost each chromosome in the corresponding genomes. Additionally, a BLAST search for SLC16A2/TSIX/XIST (genes responsible for XCI) reveled that “SLC16A2/TSIX/XIST like sequences” cover equally all chromosomes, too. With respect to this we provide following hypotheses. Hypotheses: If a single genomic region containing the SLC16A2 gene on X-chromosome is responsible for maintaining “balanced” active copy numbers, it is possible that similar sequences or gene/s have the same function on other chromosomes (autosomes). SLC16A2 like sequences on autosomes could encompass evolutionary older, but functionally active key regions for chromosome counting in early embryogenesis.
    [Show full text]
  • Small Rnas and the Regulation of Cis-Natural Antisense Transcripts in Arabidopsis
    UC Riverside UC Riverside Previously Published Works Title Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis Permalink https://escholarship.org/uc/item/66p3c9bz Journal BMC Molecular Biology, 9 ISSN 1471-2199 Authors Jin, Hailing Vacic, Vladimir Girke, Thomas et al. Publication Date 2008 Peer reviewed eScholarship.org Powered by the California Digital Library University of California BMC Molecular Biology BioMed Central Research article Open Access Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis Hailing Jin*1, Vladimir Vacic2, Thomas Girke3, Stefano Lonardi4 and Jian- Kang Zhu*3 Address: 1Departments of Plant Pathology & Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA, 2Computer Science and Engineering, University of California, Riverside, CA 92521, USA, 3Botany and Plant Sciences, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA and 4Computer Science and Engineering, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA Email: Hailing Jin* - [email protected]; Vladimir Vacic - [email protected]; Thomas Girke - [email protected]; Stefano Lonardi - [email protected]; Jian-Kang Zhu* - [email protected] * Corresponding authors Published: 14 January 2008 Received: 30 May 2007 Accepted: 14 January 2008 BMC Molecular Biology 2008, 9:6 doi:10.1186/1471-2199-9-6 This article is available from: http://www.biomedcentral.com/1471-2199/9/6 © 2008 Jin et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    [Show full text]
  • Antisense Transcription Licenses Nascent Transcripts to Mediate Transcriptional Gene Silencing
    Downloaded from genesdev.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Antisense transcription licenses nascent transcripts to mediate transcriptional gene silencing Yunkun Dang,1,4 Jiasen Cheng,2,4 Xianyun Sun,3 Zhipeng Zhou,1 and Yi Liu1 1Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 2State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; 3State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Beijing 100080, China In eukaryotes, antisense transcription can regulate sense transcription by induction of epigenetic modifications. We showed previously that antisense transcription triggers Dicer-independent siRNA (disiRNA) production and dis- iRNA locus DNA methylation (DLDM) in Neurospora crassa. Here we show that the conserved exonuclease ERI-1 (enhanced RNAi-1) is a critical component in this process. Antisense transcription and ERI-1 binding to target RNAs are necessary and sufficient to trigger DLDM. Convergent transcription causes stalling of RNA polymerase II during transcription, which permits ERI-1 to bind nascent RNAs in the nucleus and recruit a histone methyltransferase complex that catalyzes chromatin modifications. Furthermore, we show that, in the cytoplasm, ERI-1 targets hundreds of transcripts from loci without antisense transcription to regulate RNA stability. Together, our results demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism. [Keywords: DNA methylation; Neurospora; antisense transcription; gene silencing; small RNA] Supplemental material is available for this article.
    [Show full text]
  • The Epigenetics of Non-Coding RNA
    CHAPTER 4 The Epigenetics of Non-coding RNA Lesley J. Collins1, Barbara Schönfeld2,3, and Xiaowei Sylvia Chen4 1Massey Genome Service, Massey University, Palmerston North, New Zealand 2Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand 3Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand 4Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand INTRODUCTION Non-protein-coding RNAs (ncRNAs) are RNAs that are transcribed from DNA but are not translated into proteins. Many are functional and are involved in the processing and regulation of other RNAs such as mRNA, tRNA, and rRNA. Processing-type ncRNAs include small nuclear RNAs (snRNAs) involved in splicing, small nucleolar RNAs (snoRNAs) that 49 modify nucleotides in rRNAs and other RNAs, and RNase P that cleaves pre-tRNAs. Other small ncRNAs such as microRNAs (miRNAs) and short interfering RNAs (siRNAs) are involved in the regulation of target mRNAs and chromatin. Although many of these latter ncRNA classes are grouped under the term RNA interference (RNAi), it has become clear that there are many different ways that ncRNAs can interact with genes to up-regulate or down-regulate expression, to silence translation, or guide methylation [1–3]. Adding to these classes are long ncRNAs (typically 200 nt) that have also been implicated in gene regulation [4]. All of these ncRNAs form a network of processes, the RNA-infrastructure [2] that spans the cell not only spatially as RNAs move across the cell, but also temporally as the RNAs regulate gene processes during the cell cycle. Thus, the regulation of RNA processes may not only be transcriptional or translational, but also from their biogenesis and processing pathways [2].
    [Show full text]
  • Transcriptional Interferences in Cis Natural Antisense Transcripts of Humans and Mice
    Copyright Ó 2007 by the Genetics Society of America DOI: 10.1534/genetics.106.069484 Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice Naoki Osato, Yoshiyuki Suzuki, Kazuho Ikeo and Takashi Gojobori1 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411-8540, Japan Manuscript received December 9, 2006 Accepted for publication March 21, 2007 ABSTRACT For a significant fraction of mRNAs, their expression is regulated by other RNAs, including cis natural antisense transcripts (cis -NATs) that are complementary mRNAs transcribed from opposite strands of DNA at the same genomic locus. The regulatory mechanism of mRNA expression by cis -NATs is unknown, although a few possible explanations have been proposed. To understand this regulatory mechanism, we conducted a large-scale analysis of the currently available data and examined how the overlapping arrange- ments of cis -NATs affect their expression level. Here, we show that for both human and mouse the expression level of cis -NATs decreases as the length of the overlapping region increases. In particular, the proportions of the highly expressed cis -NATs in all cis -NATs examined were 36 and 47% for human and mouse, respectively, when the overlapping region was ,200 bp. However, both proportions decreased to virtually zero when the overlapping regions were .2000 bp in length. Moreover, the distribution of the expression level of cis -NATs changes according to different types of the overlapping pattern of cis -NATs in the genome. These results are consistent with the transcriptional collision model for the regulatory mechanism of gene expression by cis -NATs.
    [Show full text]
  • Strand-Specific RNA-Seq Reveals Widespread Occurrence of Novel Cis
    Lu et al. BMC Genomics 2012, 13:721 http://www.biomedcentral.com/1471-2164/13/721 RESEARCH ARTICLE Open Access Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice Tingting Lu1*, Chuanrang Zhu1, Guojun Lu1, Yunli Guo1, Yan Zhou1, Zhiyong Zhang2, Yan Zhao1, Wenjun Li1, Ying Lu1, Weihua Tang2, Qi Feng1 and Bin Han1* Abstract Background: Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs), which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice. However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs. Results: We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq) to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa). Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set), 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified. Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data and small RNA data.
    [Show full text]
  • XIST RNA and the Mechanism of X Chromosome Inactivation, Kathrin Plath, Susanna Mlynarczyk-Evans, Dmitri A
    10 Sep 2002 21:18 AR AR174-GE36-10.tex AR174-GE36-10.SGM LaTeX2e(2002/01/18) P1: IBC 10.1146/annurev.genet.36.042902.092433 Annu. Rev. Genet. 2002. 36:233–78 doi: 10.1146/annurev.genet.36.042902.092433 Copyright c 2002 by Annual Reviews. All rights reserved XIST RNA AND THE MECHANISM OF XCHROMOSOME INACTIVATION Kathrin Plath, Susanna Mlynarczyk-Evans, Dmitri A. Nusinow, and Barbara Panning Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94143; e-mail: [email protected], [email protected], [email protected], [email protected] Key Words dosage compensation, imprinting, Tsix RNA, facultative heterochromatin, differentiation ■ Abstract Dosage compensation in mammals is achieved by the transcriptional inactivation of one X chromosome in female cells. From the time X chromosome inac- tivation was initially described, it was clear that several mechanisms must be precisely integrated to achieve correct regulation of this complex process. X-inactivation ap- pears to be triggered upon differentiation, suggesting its regulation by developmental cues. Whereas any number of X chromosomes greater than one is silenced, only one X chromosome remains active. Silencing on the inactive X chromosome coincides with the acquisition of a multitude of chromatin modifications, resulting in the formation of extraordinarily stable facultative heterochromatin that is faithfully propagated through subsequent cell divisions. The integration of all these processes requires a region of the X chromosome known as the X-inactivation center, which contains the Xist gene and its cis-regulatory elements. Xist encodes an RNA molecule that plays critical roles in the choice of which X chromosome remains active, and in the initial spread and es- tablishment of silencing on the inactive X chromosome.
    [Show full text]
  • Dosage Compensation in Mammals: Fine-Tuning the Expression of the X Chromosome
    Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Dosage compensation in mammals: fine-tuning the expression of the X chromosome Edith Heard1,3 and Christine M. Disteche2,4 1CNRS UMR218, Curie Institute, 75248 Paris, Cedex 05, France; 2Department of Pathology and Department of Medicine, University of Washington, Seattle, Washington 98195, USA Mammalian females have two X chromosomes and somes. In eutherians, X-chromosome inactivation (XCI) males have only one. This has led to the evolution of affects the paternal or maternal X chromosome ran- special mechanisms of dosage compensation. The inac- domly during early development, and the inactive state tivation of one X chromosome in females equalizes gene is then stably inherited, giving rise to adults that are expression between the sexes. This process of X-chromo- mosaics for two cell types, expressing one or the other X some inactivation (XCI) is a remarkable example of long- chromosome. The initiation of X inactivation is con- range, monoallelic gene silencing and facultative hetero- trolled by the X-inactivation center (Xic), which pro- chromatin formation, and the questions surrounding it duces the noncoding Xist transcript responsible for trig- have fascinated biologists for decades. How does the in- gering silencing in cis. In marsupials and in the extraem- activation of more than a thousand genes on one X chro- bryonic tissues of some placental mammals such as mosome take place while the other X chromosome, rodents, XCI is imprinted, with the paternal X chromo- present in the same nucleus, remains genetically active? some (Xp) being inactivated.
    [Show full text]
  • Xist/Tsix Expression Dynamics During Mouse Peri-Implantation
    www.nature.com/scientificreports OPEN Xist/Tsix expression dynamics during mouse peri-implantation development revealed by whole- Received: 20 June 2018 Accepted: 11 December 2018 mount 3D RNA-FISH Published: xx xx xxxx Hirosuke Shiura1,2,3 & Kuniya Abe1,4 During peri-implantation development in mice, X chromosome inactivation (XCI) status changes dynamically. Here, we examined the expression of Xist and its antisense partner, Tsix, via whole- mount 3D RNA-FISH using strand-specifc probes and evaluated XCI status. The results indicate that Xist expression disappears completely by embryonic day (E) 4.5 without Tsix activation in the ICM and that Xist re-expression occurs at E4.75 in some cells, suggesting that random XCI is already initiated in these cells. Intriguingly, epiblast cells exhibiting biallelic Xist expression were observed frequently (~15%) at E5.25 and E5.5. Immunostaining analysis of epigenetic modifcations suggests that global change in epigenomic status occurs concomitantly with the transition from imprinted to random XCI. However, global upregulation of H3K27me3 modifcations initiated earlier than other modifcations, occurring specifcally in ICM during progression of Xist erasure. Although both Xist expression and imprinted XCI are thought to be stable in the primitive endoderm/visceral endoderm and trophectoderm/extraembryonic ectoderm lineages, transient loss of Xist clouds was noted only in a subset of extraembryonic ectodermal cells, suggesting distinct features of Xist regulation among the three diferent embryonic tissue layers. These results will serve as a basis for future functional studies of XCI regulation in vivo. In female mammals, one of the two X chromosomes is inactivated for gene dosage compensation between XX females and XY males1.
    [Show full text]
  • Molecular Coupling of Tsix Regulation and Pluripotency
    LETTER doi:10.1038/nature09496 Molecular coupling of Tsix regulation and pluripotency Pablo Navarro1,2, Andrew Oldfield1,3, Julie Legoupi1, Nicola Festuccia2, Agne`s Dubois1, Mikael Attia1, Jon Schoorlemmer4, Claire Rougeulle1,3, Ian Chambers2 & Philip Avner1 The reprogramming of X-chromosome inactivation during the Nanog, at DXPas34 (ref. 17) and at Xite18 two enhancers of Tsix19.Oct4 acquisition of pluripotency in vivo and in vitro1 is accompanied by and Sox2, by simultaneously controlling Xist and Tsix, could be acting at the repression of Xist2, the trigger of X-inactivation3, and the upre- the top of the X-inactivation regulatory hierarchy in pluripotent cells. gulation of its antisense counterpart Tsix4. We have shown that key Uncertainties, however, surround this hypothesis because (1) the factors supporting pluripotency—Nanog, Oct4 and Sox2—bind reported binding of Oct4 and Sox2 to DXPas34,thestrongembry- within Xist intron 1 in undifferentiated embryonic stem cells (ESC) onic-stem-specific enhancer of Tsix, is not reproducible (Supplemen- to repress Xist transcription5. However, the relationship between tary Fig. 1), (2) binding levels at Xite are very low (Supplementary Fig. 1) transcription factors of the pluripotency network and Tsix regulation and (3) Xite is a weak enhancer of Tsix18. It appears likely that Oct4 and has remained unclear5,6. Here we show that Tsix upregulation in Sox2 play a minor role, if any, in the establishment of Tsix transcription embryonic stem cells depends on the recruitment of the pluripotent in undifferentiated ESC. In agreement, Tsix remains unaffected after marker Rex1, and of the reprogramming-associated factors Klf4 and 24 h of Oct4 knockdown, whereas Xist upregulation is already estab- c-Myc, by the DXPas34 minisatellite associated with the Tsix pro- lished (Supplementary Fig.
    [Show full text]