101
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Lakhotia SC. From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:75-118. [PMID: 28815537 DOI: 10.1007/978-981-10-5203-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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102
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Chen L, Dzakah EE, Shan G. Targetable long non-coding RNAs in cancer treatments. Cancer Lett 2018; 418:119-124. [PMID: 29341880 DOI: 10.1016/j.canlet.2018.01.042] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/25/2017] [Accepted: 01/09/2018] [Indexed: 02/09/2023]
Abstract
Aberrant expression of many long non-coding RNAs has been observed in various types of cancer, implicating their crucial roles in tumorigenesis and cancer progression. Emerging knowledge with regard to the critical physiological and pathological roles of long non-coding RNAs in cancers makes them potential targets in cancer treatments. In this review, we present a summary of the relatively well studied long non-coding RNAs that are involved in oncogenesis and outline their functions and functional mechanisms. Recent findings that may be utilized in therapeutic intervention are also highlighted. With the fast development in nucleic acid-based therapeutic reagents that can target disease associated RNAs, lncRNAs should be explored as potential targets in cancer treatments.
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Affiliation(s)
- Liang Chen
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China.
| | - Emmanuel Enoch Dzakah
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China
| | - Ge Shan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province 230027, China.
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103
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Xu J, Peng X, Chen Y, Zhang Y, Ma Q, Liang L, Carter AC, Lu X, Wu CI. Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity. eLife 2017; 6. [PMID: 29251591 PMCID: PMC5734875 DOI: 10.7554/elife.28070] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/28/2017] [Indexed: 01/06/2023] Open
Abstract
Cells of multi-cellular organisms evolve toward uni-cellularity in the form of cancer and, if humans intervene, continue to evolve in cell culture. During this process, gene dosage relationships may evolve in novel ways to cope with the new environment and may regress back to the ancestral uni-cellular state. In this context, the evolution of sex chromosomes vis-a-vis autosomes is of particular interest. Here, we report the chromosomal evolution in ~ 600 cancer cell lines. Many of them jettisoned either Y or the inactive X; thus, free-living male and female cells converge by becoming ‘de-sexualized’. Surprisingly, the active X often doubled, accompanied by the addition of one haploid complement of autosomes, leading to an X:A ratio of 2:3 from the extant ratio of 1:2. Theoretical modeling of the frequency distribution of X:A karyotypes suggests that the 2:3 ratio confers a higher fitness and may reflect aspects of sex chromosome evolution. Multicellular life relies on a group of cells working together for a common interest. To study these cells, researchers take them out of the organism and grow them in the laboratory. Instead of growing as part of organs and tissues, the cells normally have a free-living lifestyle. Because multicellular life evolved from single-celled organisms, laboratory-grown cells can be considered as life forms that are evolving backward from a multicellular to a single-celled existence. Normally, the cells that make up most of the tissues in the human body have 22 pairs of chromosomes known as autosomes and a pair of sex chromosomes. The cells of women have two X sex chromosomes, one of which is inactive, while those of men have one X and one Y chromosome. However, free-living single cells do not need to distinguish between male and female cells. Xu, Peng, Chen et al. have now studied the chromosomes of cancer cells taken from over 600 people and grown in the laboratory. As the cells evolved in response to their free-living lifestyle, they became ‘de-sexualized’; male cells lost their Y chromosome, while female cells abandoned their inactive X chromosome. The cells then evolved toward a new state in which they possessed two active X chromosomes and three sets of autosomes. This new configuration suggests that the current X chromosome to autosome ratio may not be optimal for fitness and hence sheds some light on how mammalian sex chromosomes evolved. It is currently thought that as cancerous tumors grow, their cells evolve to favor their own interests over the common interests of the rest of the organism. In this way, they develop characteristics more like those of single cells. Further research is therefore needed to investigate whether changes occur to the chromosomes of cancer cells growing within the body, and whether this gives them an advantage over normal cells.
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Affiliation(s)
- Jin Xu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinxin Peng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yuxin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuezheng Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qin Ma
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liang Liang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, United States
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Chung-I Wu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Department of Ecology and Evolution, University of Chicago, Chicago, United States
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104
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AGTR2 and sprint/power performance: a case-control replication study for rs11091046 polymorphism in two ethnicities. Biol Sport 2017; 35:105-109. [PMID: 30455538 PMCID: PMC6234304 DOI: 10.5114/biolsport.2018.71599] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/19/2017] [Accepted: 10/26/2017] [Indexed: 01/12/2023] Open
Abstract
We aimed to replicate, in a specific athletic event cohort (only track and field) and in two different ethnicities (Japanese and East European, i.e. Russian and Polish), original findings showing the association of the angiotensin-II receptor type-2 gene (AGTR2) rs11091046 A>C polymorphism with athlete status. We compared genotypic frequencies of the AGTR2 rs11091046 polymorphism among 282 track and field sprint/power athletes (200 men and 82 women), including several national record holders and Olympic medallists (214 Japanese, 68 Russian and Polish), and 2024 control subjects (842 men and 1182 women) (804 Japanese, 1220 Russian and Polish). In men, a meta-analysis from the two combined cohorts showed a significantly higher frequency of the C allele in athletes than in controls (odds ratio: 1.62, P=0.008, heterogeneity index I2=0%). With regard to respective cohorts, C allele frequency was higher in Japanese male athletes than in controls (67.7% vs. 55.9%, P=0.022), but not in Russian/Polish male athletes (61.9% vs. 51.0%, P=0.172). In women, no significant results were obtained by meta-analysis for the two cohorts combination (P=0.850). The AC genotype frequency was significantly higher in Russian/Polish women athletes than in controls (69.2% vs. 42.1%, P=0.022), but not in Japanese women athletes (P=0.226). Our results, in contrast to previous findings, suggested by meta-analysis that the C allele of the AGTR2 rs11091046 polymorphism is associated with sprint/power track and field athlete status in men, but not in women.
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105
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Luo Y, Wang C, Yong P, Ye P, Liu Z, Fu Z, Lu F, Xiang W, Tan W, Xiao J. Decreased expression of the long non-coding RNA SLC7A11-AS1 predicts poor prognosis and promotes tumor growth in gastric cancer. Oncotarget 2017; 8:112530-112549. [PMID: 29348845 PMCID: PMC5762530 DOI: 10.18632/oncotarget.22486] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 09/30/2017] [Indexed: 12/26/2022] Open
Abstract
Many lncRNA and mRNA sense-antisense transcripts have been systematically identified in malignant cells. However, the molecular mechanisms of most lncRNA-mRNA pairs in gastric cancer remain largely unknown. We found the gastric cancer-associated lncRNA SLC7A11-AS1 and coding transcript mRNA SLC7A11 in human gastric cancer specimens by microarray. SLC7A11-AS1, antisense to SLC7A11, is significantly down-regulated in gastric cancer and could promote tumor growth in vitro and in vivo. The effects of SLC7A11-AS1 depend on the regulation of SLC7A11 via the ASK1-p38MAPK/JNK signaling pathway. These findings suggest that decreased expression of SLC7A11-AS1 contributes to the progression of gastric cancer and may be a novel diagnostic biomarker and effective therapeutic target in gastric cancer patients.
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Affiliation(s)
- Yajun Luo
- The Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Cheng Wang
- The Department of Pediatric Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Peng Yong
- The Department of HPB Surgery, Nanchong Central Hospital, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Pengcheng Ye
- The Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Zilin Liu
- The Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Zhiming Fu
- The Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Fei Lu
- The Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Wanping Xiang
- The Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Wang Tan
- The Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Jiangwei Xiao
- The Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China.,The Department of General Surgery, Chengdu First People's Hospital, Chengdu, Sichuan, People's Republic of China
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106
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Röpke A, Tüttelmann F. MECHANISMS IN ENDOCRINOLOGY: Aberrations of the X chromosome as cause of male infertility. Eur J Endocrinol 2017; 177:R249-R259. [PMID: 28611019 DOI: 10.1530/eje-17-0246] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/22/2017] [Accepted: 06/13/2017] [Indexed: 11/08/2022]
Abstract
Male infertility is most commonly caused by spermatogenetic failure, clinically noted as oligo- or a-zoospermia. Today, in approximately 20% of azoospermic patients, a causal genetic defect can be identified. The most frequent genetic causes of azoospermia (or severe oligozoospermia) are Klinefelter syndrome (47,XXY), structural chromosomal abnormalities and Y-chromosomal microdeletions. Consistent with Ohno's law, the human X chromosome is the most stable of all the chromosomes, but contrary to Ohno's law, the X chromosome is loaded with regions of acquired, rapidly evolving genes, which are of special interest because they are predominantly expressed in the testis. Therefore, it is not surprising that the X chromosome, considered as the female counterpart of the male-associated Y chromosome, may actually play an essential role in male infertility and sperm production. This is supported by the recent description of a significantly increased copy number variation (CNV) burden on both sex chromosomes in infertile men and point mutations in X-chromosomal genes responsible for male infertility. Thus, the X chromosome seems to be frequently affected in infertile male patients. Four principal X-chromosomal aberrations have been identified so far: (1) aneuploidy of the X chromosome as found in Klinefelter syndrome (47,XXY or mosaicism for additional X chromosomes). (2) Translocations involving the X chromosome, e.g. nonsyndromic 46,XX testicular disorders of sex development (XX-male syndrome) or X-autosome translocations. (3) CNVs affecting the X chromosome. (4) Point mutations disrupting X-chromosomal genes. All these are reviewed herein and assessed concerning their importance for the clinical routine diagnostic workup of the infertile male as well as their potential to shape research on spermatogenic failure in the next years.
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107
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Andersen RE, Lim DA. Forging our understanding of lncRNAs in the brain. Cell Tissue Res 2017; 371:55-71. [PMID: 29079882 DOI: 10.1007/s00441-017-2711-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022]
Abstract
During both development and adulthood, the human brain expresses many thousands of long noncoding RNAs (lncRNAs), and aberrant lncRNA expression has been associated with a wide range of neurological diseases. Although the biological significance of most lncRNAs remains to be discovered, it is now clear that certain lncRNAs carry out important functions in neurodevelopment, neural cell function, and perhaps even diseases of the human brain. Given the relatively inclusive definition of lncRNAs-transcripts longer than 200 nucleotides with essentially no protein coding potential-this class of noncoding transcript is both large and very diverse. Furthermore, emerging data indicate that lncRNA genes can act via multiple, non-mutually exclusive molecular mechanisms, and specific functions are difficult to predict from lncRNA expression or sequence alone. Thus, the different experimental approaches used to explore the role of a lncRNA might each shed light upon distinct facets of its overall molecular mechanism, and combining multiple approaches may be necessary to fully illuminate the function of any particular lncRNA. To understand how lncRNAs affect brain development and neurological disease, in vivo studies of lncRNA function are required. Thus, in this review, we focus our discussion upon a small set of neural lncRNAs that have been experimentally manipulated in mice. Together, these examples illustrate how studies of individual lncRNAs using multiple experimental approaches can help reveal the richness and complexity of lncRNA function in both neurodevelopment and diseases of the brain.
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Affiliation(s)
- Rebecca E Andersen
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA.,Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA. .,San Francisco Veterans Affairs Medical Center, San Francisco, CA, 94121, USA.
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108
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Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward. Vaccines (Basel) 2017; 5:vaccines5040037. [PMID: 29053596 PMCID: PMC5748604 DOI: 10.3390/vaccines5040037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/12/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022] Open
Abstract
Research over the past decade has clearly shown that long non-coding RNAs (lncRNAs) are functional. Many lncRNAs can be related to immunity and the host response to viral infection, but their specific functions remain largely elusive. The vast majority of lncRNAs are annotated with extremely limited knowledge and tend to be expressed at low levels, making ad hoc experimentation difficult. Changes to lncRNA expression during infection can be systematically profiled using deep sequencing; however, this often produces an intractable number of candidate lncRNAs, leaving no clear path forward. For these reasons, it is especially important to prioritize lncRNAs into high-confidence “hits” by utilizing multiple methodologies. Large scale perturbation studies may be used to screen lncRNAs involved in phenotypes of interest, such as resistance to viral infection. Single cell transcriptome sequencing quantifies cell-type specific lncRNAs that are less abundant in a mixture. When coupled with iterative experimental validations, new computational strategies for efficiently integrating orthogonal high-throughput data will likely be the driver for elucidating the functional role of lncRNAs during viral infection. This review highlights new high-throughput technologies and discusses the potential for integrative computational analysis to streamline the identification of infection-related lncRNAs and unveil novel targets for antiviral therapeutics.
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109
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Bank vole immunoheterogeneity may limit Nephropatia Epidemica emergence in a French non-endemic region. Parasitology 2017; 145:393-407. [PMID: 28931451 DOI: 10.1017/s0031182017001548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ecoevolutionary processes affecting hosts, vectors and pathogens are important drivers of zoonotic disease emergence. In this study, we focused on nephropathia epidemica (NE), which is caused by Puumala hantavirus (PUUV) whose natural reservoir is the bank vole, Myodes glareolus. We questioned the possibility of NE emergence in a French region that is considered to be NE-free but that is adjacent to a NE-endemic region. We first confirmed the epidemiology of these two regions and we demonstrated the absence of spatial barriers that could have limited dispersal, and consequently, the spread of PUUV into the NE-free region. We next tested whether regional immunoheterogeneity could impact PUUV chances to circulate and persist in the NE-free region. We showed that bank voles from the NE-free region were sensitive to experimental PUUV infection. We observed high levels of immunoheterogeneity between individuals and also between regions. Antiviral gene expression (Tnf and Mx2) reached higher levels in bank voles from the NE-free region. During experimental infections, anti-PUUV antibody production was higher in bank voles from the NE-endemic region. These results indicated a lower susceptibility to PUUV for bank voles from this NE-free region, which might limit PUUV persistence and therefore, the risk of NE.
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110
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Ren J, Du X, Zeng T, Chen L, Shen J, Lu L, Hu J. Divergently expressed gene identification and interaction prediction of long noncoding RNA and mRNA involved in duck reproduction. Anim Reprod Sci 2017; 185:8-17. [PMID: 28886878 DOI: 10.1016/j.anireprosci.2017.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 01/21/2023]
Abstract
Long noncoding RNAs (lncRNAs) and divergently expressed genes exist widely in different tissues of mammals and birds, in which they are involved in various biological processes. However, there is limited information on their role in the regulation of normal biological processes during differentiation, development, and reproduction in birds. In this study, whole transcriptome strand-specific RNA sequencing of the ovary from young ducks (60days), first-laying ducks (160days), and old ducks, i.e., ducks that stopped laying eggs (490days) was performed. The lncRNAs and mRNAs from these ducks were systematically analyzed and identified by duck genome sequencing in the three study groups. The transcriptome from the duck ovary comprised 15,011 protein-coding genes and 2905 lncRNAs; all the lncRNAs were identified as novel long noncoding transcripts. The comparison of transcriptome data from different study groups identified 2240 divergent transcription genes and 135 divergently expressed lncRNAs, which differed among the groups; most of them were significantly downregulated with age. Among the divergent genes, 38 genes were related to the reproductive process and 6 genes were upregulated. Further prediction analysis revealed that 52 lncRNAs were closely correlated with divergent reproductive mRNAs. More importantly, 6 remarkable lncRNAs were correlated significantly with the conversion of the ovary in different phases. Our results aid in the understanding of the divergent transcriptome of duck ovary in different phases and the underlying mechanisms that drive the specificity of protein-coding genes and lncRNAs in duck ovary.
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Affiliation(s)
- Jindong Ren
- College of Animal Science and Technology, Northwest A & F University, No. 21 Xinong Road, Yangling, Shaanxi 712100, PR China; Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Xue Du
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Tao Zeng
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Li Chen
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Junda Shen
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Lizhi Lu
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Jianhong Hu
- College of Animal Science and Technology, Northwest A & F University, No. 21 Xinong Road, Yangling, Shaanxi 712100, PR China.
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111
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Functions of long non-coding RNAs in human disease and their conservation in Drosophila development. Biochem Soc Trans 2017; 45:895-904. [PMID: 28673935 DOI: 10.1042/bst20160428] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/18/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023]
Abstract
Genomic analysis has found that the transcriptome in both humans and Drosophila melanogaster features large numbers of long non-coding RNA transcripts (lncRNAs). This recently discovered class of RNAs regulates gene expression in diverse ways and has been involved in a large variety of important biological functions. Importantly, an increasing number of lncRNAs have also been associated with a range of human diseases, including cancer. Comparative analyses of their functions among these organisms suggest that some of their modes of action appear to be conserved. This highlights the importance of model organisms such as Drosophila, which shares many gene regulatory networks with humans, in understanding lncRNA function and its possible impact in human health. This review discusses some known functions and mechanisms of action of lncRNAs and their implication in human diseases, together with their functional conservation and relevance in Drosophila development.
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112
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Wan P, Su W, Zhuo Y. Precise long non-coding RNA modulation in visual maintenance and impairment. J Med Genet 2017; 54:450-459. [PMID: 28003323 PMCID: PMC5502309 DOI: 10.1136/jmedgenet-2016-104266] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/27/2016] [Accepted: 11/28/2016] [Indexed: 12/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) are remarkably powerful, flexible and pervasive cellular regulators. With the help of cheaper RNA-seq, high-throughput screening of lncRNAs has become widely applied and has identified large numbers of specific lncRNAs in various physiological or pathological processes. Vision is known to be a complex and vital perception that comprises 80% of the sensory information we receive. A consensus has been reached that normal visual maintenance and impairment are primarily driven by gene regulation. Recently, it has become understood that lncRNAs are key regulators in most biological processes, including cell proliferation, apoptosis, differentiation, immune responses, oxidative stress and inflammation. Our review is intended to provide insight towards a comprehensive view of the precise modulation of lncRNAs in visual maintenance and impairment. We also highlight the challenges and future directions in conducting lncRNA studies, particularly in patients whose lncRNAs may hold expanded promise for diagnostic, prognostic and therapeutic applications.
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Affiliation(s)
- Peixing Wan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
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113
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Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. Cell Stem Cell 2017; 20:858-873.e4. [DOI: 10.1016/j.stem.2017.03.007] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 11/15/2022]
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114
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Eggert F, Kulikov K, Domnick C, Leifels P, Kath-Schorr S. Iluminated by foreign letters - Strategies for site-specific cyclopropene modification of large functional RNAs via in vitro transcription. Methods 2017; 120:17-27. [PMID: 28454775 DOI: 10.1016/j.ymeth.2017.04.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/18/2017] [Accepted: 04/23/2017] [Indexed: 10/19/2022] Open
Abstract
The synthesis of sequence-specifically modified long RNA molecules, which cannot entirely be prepared via solid phase synthesis methods is experimentally challenging. We are using a new approach based on an expanded genetic alphabet preparing site-specifically modified RNA molecules via standard in vitro transcription. In this report, the site-specific labeling of functional RNAs, in particular ribozymes and a long non-coding RNA with cyclopropene moieties, is presented. We provide detailed instructions for RNA labeling via in vitro transcription and include required analytical methods to verify production and identity of the transcript. We further present post-transcriptional inverse electron demand Diels-Alder cycloaddition reactions on the cyclopropene-modified sequences and discuss applications of the genetic alphabet expansion transcription for in vitro preparation of labeled functional RNAs with complex foldings. In detail, the glmS and CPEB3 ribozymes were site-specifically decorated with methyl cyclopropene moieties using the unnatural TPT3CP triphosphate and were proven to be still functional. In addition, the structurally complex A region of the Xist lncRNA (401nt) was site-specifically modified with methyl cyclopropene and detected by fluorescence after cycloaddition reaction with a tetrazine-BODIPY conjugate.
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Affiliation(s)
- Frank Eggert
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Katharina Kulikov
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Christof Domnick
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Philipp Leifels
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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115
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Aldrich JC, Ferree PM. Genome Silencing and Elimination: Insights from a "Selfish" B Chromosome. Front Genet 2017; 8:50. [PMID: 28487723 PMCID: PMC5403880 DOI: 10.3389/fgene.2017.00050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/10/2017] [Indexed: 02/04/2023] Open
Abstract
B chromosomes are non-essential components of numerous plant and animal genomes. Because many of these "extra" chromosomes enhance their own transmission in ways that are detrimental to the rest of the genome, they can be thought of as genome parasites. An extreme example is a paternally inherited B chromosome known as paternal sex ratio (PSR), which is found in natural populations of the jewel wasp Nasonia vitripennis. In order to ensure its own propagation, PSR severely biases the wasp sex ratio by converting diploid female-destined embryos into transmitting haploid males. This action occurs at the expense of the other paternally inherited chromosomes, which fail to resolve during the first round of division and are thus eliminated. Recent work has revealed that paternal genome elimination by PSR occurs through the disruption of a number of specific histone post-translational modifications, suggesting a central role for chromatin regulation in this phenomenon. In this review, we describe these recent advances in the light of older ones and in the context of what is currently understood about the molecular mechanisms of targeted genome silencing and elimination in other systems.
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Affiliation(s)
| | - Patrick M. Ferree
- W.M. Keck Science Department, Claremont McKenna College, Pitzer College and Scripps College, ClaremontCA, USA
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116
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Ayana R, Singh S, Pati S. Decoding Crucial LncRNAs Implicated in Neurogenesis and Neurological Disorders. Stem Cells Dev 2017; 26:541-553. [PMID: 28095733 DOI: 10.1089/scd.2016.0290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Unraveling transcriptional heterogeneity and the labyrinthine nature of neurodevelopment can probe insights into neuropsychiatric disorders. It is noteworthy that adult neurogenesis is restricted to the subventricular and subgranular zones of the brain. Recent studies suggest long non-coding RNAs (lncRNAs) as an avant-garde class of regulators implicated in neurodevelopment. But, paucity exists in the knowledge regarding lncRNAs in neurogenesis and their associations with neurodevelopmental defects. To address this, we extensively reviewed the existing literature databases as well as performed relevant in-silico analysis. We utilized Allen Brain Atlas (ABA) differential search module and generated a catalogue of ∼30,000 transcripts specific to the neurogenic zones, including coding and non-coding transcripts. To explore the existing lncRNAs reported in neurogenesis, we performed extensive literature mining and identified 392 lncRNAs. These degenerate lncRNAs were mapped onto the ABA transcript list leading to detection of 20 lncRNAs specific to neurogenic zones (Dentate gyrus/Lateral ventricle), among which 10 showed associations to several neurodevelopmental disorders following in-silico mapping onto brain disease databases like Simons Foundation Autism Research Initiative, AutDB, and lncRNADisease. Notably, using ABA correlation module, we could establish lncRNA-to-mRNA coexpression networks for the above 10 candidate lncRNAs. Finally, pathway prediction revealed physical, biochemical, or regulatory interactions for nine lncRNAs. In addition, ABA differential search also revealed 54 novel significant lncRNAs from the null set (∼30,000). Conclusively, this review represents an updated catalogue of lncRNAs in neurogenesis and neurological diseases, and overviews the field of OMICs-based data analysis for understanding lncRNome-based regulation in neurodevelopment.
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Affiliation(s)
- R Ayana
- 1 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University , Greater Noida, Uttar Pradesh, India
| | - Shailja Singh
- 1 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University , Greater Noida, Uttar Pradesh, India .,2 Special Center for Molecular Medicine, Jawaharlal Nehru University , Delhi, India
| | - Soumya Pati
- 1 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University , Greater Noida, Uttar Pradesh, India
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117
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Aldrich JC, Leibholz A, Cheema MS, Ausiό J, Ferree PM. A 'selfish' B chromosome induces genome elimination by disrupting the histone code in the jewel wasp Nasonia vitripennis. Sci Rep 2017; 7:42551. [PMID: 28211924 PMCID: PMC5304203 DOI: 10.1038/srep42551] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/10/2017] [Indexed: 01/04/2023] Open
Abstract
Intragenomic conflict describes a phenomenon in which genetic elements act ‘selfishly’ to gain a transmission advantage at the expense of the whole genome. A non-essential, selfish B chromosome known as Paternal Sex Ratio (PSR) induces complete elimination of the sperm-derived hereditary material in the jewel wasp Nasonia vitripennis. PSR prevents the paternal chromatin from forming chromosomes during the first embryonic mitosis, leading to its loss. Although paternally transmitted, PSR evades self-elimination in order to be inherited. We examined important post-translational modifications to the DNA packaging histones on the normal genome and the PSR chromosome in the fertilized embryo. Three histone marks – H3K9me2,3, H3K27me1, and H4K20me1 – became abnormally enriched and spread to ectopic positions on the sperm’s chromatin before entry into mitosis. In contrast, other histone marks and DNA methylation were not affected by PSR, suggesting that its effect on the paternal genome is specific to a subset of histone marks. Contrary to the paternally derived genome, the PSR chromosome was visibly devoid of the H3K27me1 and H4K20me1 marks. These findings strongly suggest that PSR causes paternal genome elimination by disrupting at least three histone marks following fertilization, while PSR avoids self-elimination by evading two of these marks.
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Affiliation(s)
- John C Aldrich
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - Alexandra Leibholz
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada
| | - Juan Ausiό
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada
| | - Patrick M Ferree
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
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118
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Bonomi M, Rochira V, Pasquali D, Balercia G, Jannini EA, Ferlin A. Klinefelter syndrome (KS): genetics, clinical phenotype and hypogonadism. J Endocrinol Invest 2017; 40:123-134. [PMID: 27644703 PMCID: PMC5269463 DOI: 10.1007/s40618-016-0541-6] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/25/2016] [Indexed: 01/29/2023]
Abstract
Klinefelter Syndrome (KS) is characterized by an extreme heterogeneity in its clinical and genetic presentation. The relationship between clinical phenotype and genetic background has been partially disclosed; nevertheless, physicians are aware that several aspects concerning this issue are far to be fully understood. By improving our knowledge on the role of some genetic aspects as well as on the KS, patients' interindividual differences in terms of health status will result in a better management of this chromosomal disease. The aim of this review is to provide an update on both genetic and clinical phenotype and their interrelationships.
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Affiliation(s)
- M Bonomi
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Division of Endocrine and Metabolic Diseases & Laboratory of Endocrine and Metabolic Research, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - V Rochira
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via P. Giardini 1355, 41126, Modena, Italy.
- Azienda USL of Modena, NOCSAE, Via P. Giardini 1355, 41126, Modena, Italy.
| | - D Pasquali
- Department of Cardiothoracic and Respiratory Science, Second University of Naples, Naples, Italy
| | - G Balercia
- Division of Endocrinology, Department of Clinical and Molecular Sciences, Umberto I Hospital, Polytechnic University of Marche, Via Conca 71, 60126, Ancona, Italy
| | - E A Jannini
- Department of Systems Medicine, Tor Vergata University of Rome, Rome, Italy
| | - A Ferlin
- Unit of Andrology and Reproductive Medicine, Department of Medicine, University of Padova, Padova, Italy
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119
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Sridhar B, Rivas-Astroza M, Nguyen TC, Chen W, Yan Z, Cao X, Hebert L, Zhong S. Systematic Mapping of RNA-Chromatin Interactions In Vivo. Curr Biol 2017; 27:602-609. [PMID: 28132817 DOI: 10.1016/j.cub.2017.01.011] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 12/22/2016] [Accepted: 01/06/2017] [Indexed: 12/15/2022]
Abstract
RNA molecules can attach to chromatin. It remains difficult to know what RNAs are associated with chromatin and where the genomic target loci of these RNAs are. Here, we present MARGI (mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells. The gist of this technology is to ligate chromatin-associated RNAs (caRNAs) with their target genomic sequences by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to a sequencing library for paired-end sequencing. Using MARGI, we produced RNA-genome interaction maps for human embryonic stem cells (ESCs) and human embryonic kidney (HEK) cells. MARGI revealed hundreds of caRNAs, including previously known XIST, SNHG1, NEAT1, and MALAT1, as well as each caRNA's genomic interaction loci. Using a cross-species experiment, we estimated that approximately 2.2% of MARGI-identified interactions were false positives. In ESCs and HEK cells, the RNA ends of more than 5% of MARGI read pairs were mapped to distal or inter-chromosomal locations as compared to the locations of their corresponding DNA ends. The majority of transcription start sites are associated with distal or inter-chromosomal caRNAs. Chromatin-immunoprecipitation-sequencing (ChIP-seq)-reported H3K27ac and H3K4me3 levels are positively correlated, while H3K9me3 is negatively correlated, with MARGI-reported RNA attachment levels. The MARGI technology should facilitate revealing novel RNA functions and their genomic target regions.
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Affiliation(s)
- Bharat Sridhar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcelo Rivas-Astroza
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tri C Nguyen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Weizhong Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhangming Yan
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiaoyi Cao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lucie Hebert
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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120
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Abstract
Vast parts of mammalian genomes encode for transcripts that are not further translated into proteins. The purpose of the majority of such noncoding ribonucleic acids (RNAs) remained paradoxical for a long time. However, a growing body of evidence demonstrates that long noncoding RNAs are dynamically expressed in different cell types, diseases, or developmental stages to execute a wide variety of regulatory roles at virtually every step of gene expression and translation. Indeed, long noncoding RNAs influence gene expression via epigenetic modulations, through regulating alternative splicing, or by acting as molecular sponges. The abundance of long noncoding RNAs in the cardiovascular system indicates that they may be part of a complex regulatory network governing physiology and pathology of the heart. In this review, we discuss the multifaceted functions of long noncoding RNAs and highlight the current literature with an emphasis on cardiac development and disease. Furthermore, as the enormous spectrum of long noncoding RNAs potentially opens up new avenues for diagnosis and prevention of heart failure, we ultimately evaluate the futuristic prospects of long noncoding RNAs as biomarkers, and therapeutic targets for the treatment of cardiovascular disorders, as well.
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Affiliation(s)
- Christian Bär
- From Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Shambhabi Chatterjee
- From Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Thomas Thum
- From Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
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121
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Abstract
X-chromosome inactivation, which was discovered by Mary Lyon in 1961 results in random silencing of one X chromosome in female mammals. This review is dedicated to Mary Lyon, who passed away last year. She predicted many of the features of X inactivation, for e.g., the existence of an X inactivation center, the role of L1 elements in spreading of silencing and the existence of genes that escape X inactivation. Starting from her published work here we summarize advances in the field.
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122
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van den Berge M, Sijen T. A male and female RNA marker to infer sex in forensic analysis. Forensic Sci Int Genet 2016; 26:70-76. [PMID: 27816848 DOI: 10.1016/j.fsigen.2016.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/17/2016] [Accepted: 10/24/2016] [Indexed: 01/18/2023]
Abstract
In forensics, DNA profiling is used for the identification of the donor of a trace, while messenger RNA (mRNA) profiling can be applied to identify the cellular origin such as body fluids or organ tissues. The presence of male cell material can be readily assessed by the incorporation of Y-chromosomal markers in quantitation or STR profiling systems. However, no forensic marker exists to positively identify female cell material; merely the presence of female DNA is deduced from the absence of a Y peak, or unbalanced X-Y signals at the Amelogenin locus or unbalanced response of the total and Y-specific quantifier. The presence of two X-chromosomes in female cells invokes dosage compensation, which is achieved through inactivation of one of the X-chromosomes in females. Since this process involves specific RNA molecules, identification of female cellular material may be possible through RNA profiling. Additionally, male material may be identified through RNAs expressed from the Y-chromosome. RNAs preferentially expressed in either sex were assessed for their potential to act as sex markers in forensic RNA assays. To confirm sex-specificity, body fluids and organ tissues of multiple donors of either sex were tested. Additionally, sensitivity of the markers and the suitability of positively identifying male-female mixtures were assessed and degraded samples were used to assess performance of the markers in forensic settings. The addition of sex-specific markers is of added informative value in any RNA profiling system and both markers were incorporated into existing RNA assays that either target body fluids or organs. These are the first forensic assays that enable positive identification of female cellular material.
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Affiliation(s)
- M van den Berge
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands, The Netherlands.
| | - T Sijen
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands, The Netherlands.
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123
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Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol 2016; 17:756-770. [DOI: 10.1038/nrm.2016.126] [Citation(s) in RCA: 420] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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124
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Sanchis-Segura C, Becker JB. Why we should consider sex (and study sex differences) in addiction research. Addict Biol 2016; 21:995-1006. [PMID: 27029841 DOI: 10.1111/adb.12382] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/31/2022]
Abstract
Among mammals, every cell has a biological sex, and the sex of an individual pervades its body and brain. In this review, we describe the processes through which mammals become phenotypically male or female by organizational and activational influences of genes and hormones throughout development. We emphasized that the molecular and cellular changes triggered by sex chromosomes and steroid hormones may generate sex differences in overt physiological functions and behavior, but they may alternatively promote end-point convergences between males and females. Clinical and pre-clinical evidences suggest that sex and gender differences modulate drug consumption as well as of the transition towards drug-promoted pathological states such as dependence and addiction. Additionally, sex differences in drug pharmacokinetics and pharmacodynamics will also influence dependence and addiction as well as side effects of drugs. These effects will further interact with socially gendered factors to result in sex differences in the access to, engagement in and efficacy of any therapeutic attempt. Finally, we maintain that 'sex sameness' is as important as 'sex differences' when building a complete understanding of biology for both males and females and provide a framework with which to classify and guide investigation into the mechanisms mediating sex differences and sex sameness.
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Affiliation(s)
- Carla Sanchis-Segura
- Departament de Psicologia básica, clínica i psicobiologia. Área de Psicobiología; Universitat Jaume I; Castellón de la Plana Spain
| | - Jill B. Becker
- Department of Psychology and Molecular and Behavioral Neuroscience Institute; University of Michigan; Ann Arbor MI USA
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125
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Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES. Nanoscale imaging of RNA with expansion microscopy. Nat Methods 2016; 13:679-84. [PMID: 27376770 PMCID: PMC4965288 DOI: 10.1038/nmeth.3899] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/18/2016] [Indexed: 12/24/2022]
Abstract
The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-molecule linker that enables RNA to be covalently attached to a swellable polyelectrolyte gel synthesized throughout a biological specimen. Then, postexpansion, fluorescent in situ hybridization (FISH) imaging of RNA can be performed with high yield and specificity as well as single-molecule precision in both cultured cells and intact brain tissue. Expansion FISH (ExFISH) separates RNAs and supports amplification of single-molecule signals (i.e., via hybridization chain reaction) as well as multiplexed RNA FISH readout. ExFISH thus enables super-resolution imaging of RNA structure and location with diffraction-limited microscopes in thick specimens, such as intact brain tissue and other tissues of importance to biology and medicine.
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Affiliation(s)
- Fei Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Asmamaw T Wassie
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Allison J Cote
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anubhav Sinha
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shahar Alon
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shoh Asano
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Evan R Daugharthy
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jae-Byum Chang
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Adam Marblestone
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward S Boyden
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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126
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Wai DCC, Shihab M, Low JKK, Mackay JP. The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity. Nucleic Acids Res 2016; 44:9153-9165. [PMID: 27369384 PMCID: PMC5100589 DOI: 10.1093/nar/gkw590] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 06/16/2016] [Indexed: 12/22/2022] Open
Abstract
Classical zinc fingers (ZFs) are traditionally considered to act as sequence-specific DNA-binding domains. More recently, classical ZFs have been recognised as potential RNA-binding modules, raising the intriguing possibility that classical-ZF transcription factors are involved in post-transcriptional gene regulation via direct RNA binding. To date, however, only one classical ZF-RNA complex, that involving TFIIIA, has been structurally characterised. Yin Yang-1 (YY1) is a multi-functional transcription factor involved in many regulatory processes, and binds DNA via four classical ZFs. Recent evidence suggests that YY1 also interacts with RNA, but the molecular nature of the interaction remains unknown. In the present work, we directly assess the ability of YY1 to bind RNA using in vitro assays. Systematic Evolution of Ligands by EXponential enrichment (SELEX) was used to identify preferred RNA sequences bound by the YY1 ZFs from a randomised library over multiple rounds of selection. However, a strong motif was not consistently recovered, suggesting that the RNA sequence selectivity of these domains is modest. YY1 ZF residues involved in binding to single-stranded RNA were identified by NMR spectroscopy and found to be largely distinct from the set of residues involved in DNA binding, suggesting that interactions between YY1 and ssRNA constitute a separate mode of nucleic acid binding. Our data are consistent with recent reports that YY1 can bind to RNA in a low-specificity, yet physiologically relevant manner.
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Affiliation(s)
- Dorothy C C Wai
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Manar Shihab
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
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127
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Nistal M, Paniagua R, González-Peramato P, Reyes-Múgica M. Perspectives in Pediatric Pathology, Chapter 16. Klinefelter Syndrome and Other Anomalies in X and Y Chromosomes. Clinical and Pathological Entities. Pediatr Dev Pathol 2016; 19:259-77. [PMID: 25105890 DOI: 10.2350/14-06-1512-pb.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Manuel Nistal
- 1 Department of Pathology, Hospital La Paz, Universidad Autónoma de Madrid, Calle Arzobispo Morcillo No. 2, Madrid 28029, Spain
| | - Ricardo Paniagua
- 2 Department of Cell Biology, Universidad de Alcala, Madrid, Spain
| | - Pilar González-Peramato
- 1 Department of Pathology, Hospital La Paz, Universidad Autónoma de Madrid, Calle Arzobispo Morcillo No. 2, Madrid 28029, Spain
| | - Miguel Reyes-Múgica
- 3 Department of Pathology, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, One Children's Hospital Drive, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
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128
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Park JL, Kim JH, Seo E, Bae DH, Kim SY, Lee HC, Woo KM, Kim YS. Identification and evaluation of age-correlated DNA methylation markers for forensic use. Forensic Sci Int Genet 2016; 23:64-70. [DOI: 10.1016/j.fsigen.2016.03.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/11/2016] [Accepted: 03/16/2016] [Indexed: 12/11/2022]
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129
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Abstract
Motivation Recent studies have revealed that large numbers of non-coding RNAs are transcribed in humans, but only a few of them have been identified with their functions. Identification of the interaction target RNAs of the non-coding RNAs is an important step in predicting their functions. The current experimental methods to identify RNA–RNA interactions, however, are not fast enough to apply to a whole human transcriptome. Therefore, computational predictions of RNA–RNA interactions are desirable, but this is a challenging task due to the huge computational costs involved. Results Here, we report comprehensive predictions of the interaction targets of lncRNAs in a whole human transcriptome for the first time. To achieve this, we developed an integrated pipeline for predicting RNA–RNA interactions on the K computer, which is one of the fastest super-computers in the world. Comparisons with experimentally-validated lncRNA–RNA interactions support the quality of the predictions. Additionally, we have developed a database that catalogs the predicted lncRNA–RNA interactions to provide fundamental information about the targets of lncRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2307-5) contains supplementary material, which is available to authorized users.
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130
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Ruan X. Long Non-Coding RNA Central of Glucose Homeostasis. J Cell Biochem 2015; 117:1061-5. [DOI: 10.1002/jcb.25427] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Xiangbo Ruan
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH; Bethesda 20892 Maryland
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131
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LAKHOTIA SUBHASHC. Divergent actions of long noncoding RNAs on X-chromosome remodelling in mammals and Drosophila achieve the same end result: dosage compensation. J Genet 2015; 94:575-84. [DOI: 10.1007/s12041-015-0566-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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132
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Expression Signatures of Long Noncoding RNAs in Adolescent Idiopathic Scoliosis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:276049. [PMID: 26421281 PMCID: PMC4569756 DOI: 10.1155/2015/276049] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/31/2014] [Indexed: 12/31/2022]
Abstract
Purpose. Adolescent idiopathic scoliosis (AIS), the most common pediatric spinal deformity, is considered a complex genetic disease. Causing genes and pathogenesis of AIS are still unclear. This study was designed to identify differentially expressed long noncoding RNAs (lncRNAs) involving the pathogenesis of AIS. Methods. We first performed comprehensive screening of lncRNA and mRNA in AIS patients and healthy children using Agilent human lncRNA + mRNA Array V3.0 microarray. LncRNAs expression in different AIS patients was further evaluated using quantitative PCR. Results. A total of 139 lncRNAs and 546 mRNAs were differentially expressed between AIS patients and healthy control. GO and Pathway analysis showed that these mRNAs might be involved in bone mineralization, neuromuscular junction, skeletal system morphogenesis, nucleotide and nucleic acid metabolism, and regulation of signal pathway. Four lncRNAs (ENST00000440778.1, ENST00000602322.1, ENST00000414894.1, and TCONS_00028768) were differentially expressed between different patients when grouped according to age, height, classification, severity of scoliosis, and Risser grade. Conclusions. This study demonstrates the abnormal expression of lncRNAs and mRNAs in AIS, and the expression of some lncRNAs was related to clinical features. This study is helpful for further understanding of lncRNAs in pathogenesis, treatment, and prognosis of AIS.
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133
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Quantitatively imaging chromosomes by correlated cryo-fluorescence and soft x-ray tomographies. Biophys J 2015; 107:1988-1996. [PMID: 25418180 DOI: 10.1016/j.bpj.2014.09.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/28/2014] [Accepted: 09/09/2014] [Indexed: 11/24/2022] Open
Abstract
Soft x-ray tomography (SXT) is increasingly being recognized as a valuable method for visualizing and quantifying the ultrastructure of cryopreserved cells. Here, we describe the combination of SXT with cryogenic confocal fluorescence tomography (CFT). This correlative approach allows the incorporation of molecular localization data, with isotropic precision, into high-resolution three-dimensional (3-D) SXT reconstructions of the cell. CFT data are acquired first using a cryogenically adapted confocal light microscope in which the specimen is coupled to a high numerical aperture objective lens by an immersion fluid. The specimen is then cryo-transferred to a soft x-ray microscope (SXM) for SXT data acquisition. Fiducial markers visible in both types of data act as common landmarks, enabling accurate coalignment of the two complementary tomographic reconstructions. We used this method to identify the inactive X chromosome (Xi) in female v-abl transformed thymic lymphoma cells by localizing enhanced green fluorescent protein-labeled macroH2A with CFT. The molecular localization data were used to guide segmentation of Xi in the SXT reconstructions, allowing characterization of the Xi topological arrangement in near-native state cells. Xi was seen to adopt a number of different topologies with no particular arrangement being dominant.
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134
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Over-expression of XIST, the Master Gene for X Chromosome Inactivation, in Females With Major Affective Disorders. EBioMedicine 2015; 2:909-18. [PMID: 26425698 PMCID: PMC4563114 DOI: 10.1016/j.ebiom.2015.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/05/2015] [Accepted: 06/11/2015] [Indexed: 11/23/2022] Open
Abstract
Background Psychiatric disorders are common mental disorders without a pathological biomarker. Classic genetic studies found that an extra X chromosome frequently causes psychiatric symptoms in patients with either Klinefelter syndrome (XXY) or Triple X syndrome (XXX). Over-dosage of some X-linked escapee genes was suggested to cause psychiatric disorders. However, relevance of these rare genetic diseases to the pathogenesis of psychiatric disorders in the general population of psychiatric patients is unknown. Methods XIST and several X-linked genes were studied in 36 lymphoblastoid cell lines from healthy females and 60 lymphoblastoid cell lines from female patients with either bipolar disorder or recurrent major depression. XIST and KDM5C expression was also quantified in 48 RNA samples from postmortem human brains of healthy female controls and female psychiatric patients. Findings We found that the XIST gene, a master in control of X chromosome inactivation (XCI), is significantly over-expressed (p = 1 × 10− 7, corrected after multiple comparisons) in the lymphoblastoid cells of female patients with either bipolar disorder or major depression. The X-linked escapee gene KDM5C also displays significant up-regulation (p = 5.3 × 10− 7, corrected after multiple comparisons) in the patients' cells. Expression of XIST and KDM5C is highly correlated (Pearson's coefficient, r = 0.78, p = 1.3 × 10− 13). Studies on human postmortem brains supported over-expression of the XIST gene in female psychiatric patients. Interpretations We propose that over-expression of XIST may cause or result from subtle alteration of XCI, which up-regulates the expression of some X-linked escapee genes including KDM5C. Over-expression of X-linked genes could be a common mechanism for the development of psychiatric disorders between patients with those rare genetic diseases and the general population of female psychiatric patients with XIST over-expression. Our studies suggest that XIST and KDM5C expression could be used as a biological marker for diagnosis of psychiatric disorders in a significantly large subset of female patients. Research in context Due to lack of biological markers, diagnosis and treatment of psychiatric disorders are subjective. There is utmost urgency to identify biomarkers for clinics, research, and drug development. We found that XIST and KDM5C gene expression may be used as a biological marker for diagnosis of major affective disorders in a significantly large subset of female patients from the general population. Our studies show that over-expression of XIST and some X-linked escapee genes may be a common mechanism for development of psychiatric disorders between the patients with rare genetic diseases (XXY or XXX) and the general population of female psychiatric patients. XIST and KDM5C genes are over-expressed in a large subset of female patients with major affective disorders. Over-expression of XIST and KDM5C genes could be used as a biomarker for diagnosis of individual patients. Over-expression of XIST and X-linked escapee genes including KDM5C may cause major affective disorders.
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135
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Chen Q, Gao S, He W, Kou X, Zhao Y, Wang H, Gao S. Xist repression shows time-dependent effects on the reprogramming of female somatic cells to induced pluripotent stem cells. Stem Cells 2015; 32:2642-56. [PMID: 24965076 DOI: 10.1002/stem.1775] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 05/17/2014] [Accepted: 05/23/2014] [Indexed: 11/10/2022]
Abstract
Although the reactivation of silenced X chromosomes has been observed as part of the process of reprogramming female somatic cells into induced pluripotent stem cells (iPSCs), it remains unknown whether repression of the X-inactive specific transcript (Xist) can greatly enhance female iPSC induction similar to that observed in somatic cell nuclear transfer studies. In this study, we discovered that the repression of Xist plays opposite roles in the early and late phases of female iPSCs induction. Our results demonstrate that the downregulation of Xist by an isopropyl β-d-1-thiogalactopyranoside (IPTG)-inducible short hairpin RNA (shRNA) system can greatly impair the mesenchymal-to-epithelial transition (MET) in the early phase of iPSC induction but can significantly promote the transition of pre-iPSCs to iPSCs in the late phase. Furthermore, we demonstrate that although the knockdown of Xist did not affect the H3K27me3 modification on the X chromosome, macroH2A was released from the inactivated X chromosome (Xi). This enables the X chromosome silencing to be a reversible event. Moreover, we demonstrate that the supplementation of vitamin C (Vc) can augment and stabilize the reversible X chromosome by preventing the relocalization of macroH2A to the Xi. Therefore, our study reveals an opposite role of Xist repression in the early and late stages of reprogramming female somatic cells to pluripotency and demonstrates that the release of macroH2A by Xist repression enables the transition from pre-iPSCs to iPSCs.
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Affiliation(s)
- Qi Chen
- School of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences (NIBS), Beijing, China
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136
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Guyochin A, Maenner S, Chu ETJ, Hentati A, Attia M, Avner P, Clerc P. Live cell imaging of the nascent inactive X chromosome during the early differentiation process of naive ES cells towards epiblast stem cells. PLoS One 2014; 9:e116109. [PMID: 25546018 PMCID: PMC4278889 DOI: 10.1371/journal.pone.0116109] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 12/04/2014] [Indexed: 12/15/2022] Open
Abstract
Random X-chromosome inactivation ensures dosage compensation in mammals through the transcriptional silencing of one of the two X chromosomes present in each female cell. Silencing is initiated in the differentiating epiblast of the mouse female embryos through coating of the nascent inactive X chromosome by the non-coding RNA Xist, which subsequently recruits the Polycomb Complex PRC2 leading to histone H3-K27 methylation. Here we examined in mouse ES cells the early steps of the transition from naive ES cells towards epiblast stem cells as a model for inducing X chromosome inactivation in vitro. We show that these conditions efficiently induce random XCI. Importantly, in a transient phase of this differentiation pathway, both X chromosomes are coated with Xist RNA in up to 15% of the XX cells. In an attempt to determine the dynamics of this process, we designed a strategy aimed at visualizing the nascent inactive X-chromosome in live cells. We generated transgenic female XX ES cells expressing the PRC2 component Ezh2 fused to the fluorescent protein Venus. The fluorescent fusion protein was expressed at sub-physiological levels and located in nuclei of ES cells. Upon differentiation of ES cell towards epiblast stem cell fate, Venus-fluorescent territories appearing in interphase nuclei were identified as nascent inactive X chromosomes by their association with Xist RNA. Imaging of Ezh2-Venus for up to 24 hours during the differentiation process showed survival of some cells with two fluorescent domains and a surprising dynamics of the fluorescent territories across cell division and in the course of the differentiation process. Our data reveal a strategy for visualizing the nascent inactive X chromosome and suggests the possibility for a large plasticity of the nascent inactive X chromosome.
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Affiliation(s)
- Aurélia Guyochin
- Génétique Moléculaire Murine, CNRS URA2578, Institut Pasteur, Paris, France
- Université de Technologie de Compiègne, Compiègne, France
| | - Sylvain Maenner
- Génétique Moléculaire Murine, CNRS URA2578, Institut Pasteur, Paris, France
| | - Erin Tsi-Jia Chu
- Génétique Moléculaire Murine, CNRS URA2578, Institut Pasteur, Paris, France
| | - Asma Hentati
- Génétique Moléculaire Murine, CNRS URA2578, Institut Pasteur, Paris, France
- Université Blaise Pascal, Clermont-Ferrand, France
| | - Mikael Attia
- Génétique Moléculaire Murine, CNRS URA2578, Institut Pasteur, Paris, France
| | - Philip Avner
- Génétique Moléculaire Murine, CNRS URA2578, Institut Pasteur, Paris, France
- EMBL Monterotondo, Adriano Buzzati-Traverso Campus, Monterotondo, Italy
| | - Philippe Clerc
- Génétique Moléculaire Murine, CNRS URA2578, Institut Pasteur, Paris, France
- Epigénétique des Cellules Souches, Department of Developmental Biology, CNRS URA2578, Institut Pasteur, Paris, France
- * E-mail:
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137
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Inoue H, Yoshimura J, Iwabuchi K. Gene expression of protein-coding and non-coding RNAs related to polyembryogenesis in the parasitic wasp, Copidosoma floridanum. PLoS One 2014; 9:e114372. [PMID: 25469914 PMCID: PMC4255003 DOI: 10.1371/journal.pone.0114372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 11/06/2014] [Indexed: 11/18/2022] Open
Abstract
Polyembryony is a unique form of development in which many embryos are clonally produced from a single egg. Polyembryony is known to occur in many animals, but the underlying genetic mechanism responsible is unknown. In a parasitic wasp, Copidosoma floridanum, polyembryogenesis is initiated during the formation and division of the morula. In the present study, cDNA libraries were constructed from embryos at the cleavage and subsequent primary morula stages, times when polyembryogenesis is likely to be controlled genetically. Of 182 and 263 cDNA clones isolated from these embryos, 38% and 70%, respectively, were very similar to protein-coding genes obtained from BLAST analysis and 55 and 65 clones, respectively, were stage-specific. In our libraries we also detected a high frequency of long non-coding RNA. Some of these showed stage-specific expression patterns in reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis. The stage-specificity of expression implies that these protein-coding and non-coding genes are related to polyembryogenesis in C. floridanum. The non-coding genes are not similar to any known non-coding RNAs and so are good candidates as regulators of polyembryogenesis.
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Affiliation(s)
- Hiroki Inoue
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Jin Yoshimura
- Graduate School of Science and Technology, and Department of Mathematical and Systems Engineering, Shizuoka University, Hamamatsu, Shizuoka, Japan
- Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States of America
- Marine Biosystems Research Center, Chiba University, Kamogawa, Chiba, Japan
| | - Kikuo Iwabuchi
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- * E-mail:
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138
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Paschoal AR, Maracaja-Coutinho V, Setubal JC, Simões ZLP, Verjovski-Almeida S, Durham AM. Non-coding transcription characterization and annotation. RNA Biol 2014; 9:274-82. [DOI: 10.4161/rna.19352] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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139
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Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol 2014; 24:651-63. [PMID: 25441720 DOI: 10.1016/j.tcb.2014.08.009] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/18/2014] [Accepted: 08/28/2014] [Indexed: 02/07/2023]
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs) that play important roles in diverse biological processes. As a class, lncRNAs are generally enriched in the nucleus and, specifically, within the chromatin-associated fraction. Consistent with their localization, many lncRNAs have been implicated in the regulation of gene expression and in shaping 3D nuclear organization. In this review, we discuss the evidence that many nuclear-retained lncRNAs can interact with various chromatin regulatory proteins and recruit them to specific sites on DNA to regulate gene expression. Furthermore, we discuss the role of specific lncRNAs in shaping nuclear organization and their emerging mechanisms. Based on these examples, we propose a model that explains how lncRNAs may shape aspects of nuclear organization to regulate gene expression.
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140
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Abstract
Long non-coding RNAs (lncRNAs) are series of transcripts with important biological functions. Various diseases have been associated with aberrant expression of lncRNAs and the related dysregulation of mRNAs. In this review, we highlight the mechanisms of dynamic lncRNA expression. The chromatin state contributes to the low and specific expression of lncRNAs. The transcription of non-coding RNA genes is regulated by many core transcription factors applied to protein-coding genes. However, specific DNA sequences may allow their unsynchronized transcription with their location-associated mRNAs. Additionally, there are multiple mechanisms involved in the post-transcriptional regulation of lncRNAs. Among these, microRNAs might have indispensible regulatory effects on lncRNAs, based on recent discoveries.
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141
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Affiliation(s)
- John Rinn
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Beth Israel Deaconess Medical Center, Boston, MA 02215, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA.
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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142
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Genetic and pharmacological reactivation of the mammalian inactive X chromosome. Proc Natl Acad Sci U S A 2014; 111:12591-8. [PMID: 25136103 DOI: 10.1073/pnas.1413620111] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
X-chromosome inactivation (XCI), the random transcriptional silencing of one X chromosome in somatic cells of female mammals, is a mechanism that ensures equal expression of X-linked genes in both sexes. XCI is initiated in cis by the noncoding Xist RNA, which coats the inactive X chromosome (Xi) from which it is produced. However, trans-acting factors that mediate XCI remain largely unknown. Here, we perform a large-scale RNA interference screen to identify trans-acting XCI factors (XCIFs) that comprise regulators of cell signaling and transcription, including the DNA methyltransferase, DNMT1. The expression pattern of the XCIFs explains the selective onset of XCI following differentiation. The XCIFs function, at least in part, by promoting expression and/or localization of Xist to the Xi. Surprisingly, we find that DNMT1, which is generally a transcriptional repressor, is an activator of Xist transcription. Small-molecule inhibitors of two of the XCIFs can reversibly reactivate the Xi, which has implications for treatment of Rett syndrome and other dominant X-linked diseases. A homozygous mouse knockout of one of the XCIFs, stanniocalcin 1 (STC1), has an expected XCI defect but surprisingly is phenotypically normal. Remarkably, X-linked genes are not overexpressed in female Stc1(-/-) mice, revealing the existence of a mechanism(s) that can compensate for a persistent XCI deficiency to regulate X-linked gene expression.
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143
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Quénet D, Dalal Y. A long non-coding RNA is required for targeting centromeric protein A to the human centromere. eLife 2014; 3:e03254. [PMID: 25117489 PMCID: PMC4145801 DOI: 10.7554/elife.03254] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The centromere is a specialized chromatin region marked by the histone H3 variant CENP-A. Although active centromeric transcription has been documented for over a decade, the role of centromeric transcription or transcripts has been elusive. Here, we report that centromeric α-satellite transcription is dependent on RNA Polymerase II and occurs at late mitosis into early G1, concurrent with the timing of new CENP-A assembly. Inhibition of RNA Polymerase II-dependent transcription abrogates the recruitment of CENP-A and its chaperone HJURP to native human centromeres. Biochemical characterization of CENP-A associated RNAs reveals a 1.3 kb molecule that originates from centromeres, which physically interacts with the soluble pre-assembly HJURP/CENP-A complex in vivo, and whose down-regulation leads to the loss of CENP-A and HJURP at centromeres. This study describes a novel function for human centromeric long non-coding RNAs in the recruitment of HJURP and CENP-A, implicating RNA-based chaperone targeting in histone variant assembly. Before a cell divides, it copies its chromosomes. Initially, the two copies of each chromosome remain linked via their centromeres. These regions also serve as the attachment sites for the proteins that pull these two copies apart, and eventually segregate the chromosomes equally between the two newly formed cells. Chromosome segregation is the main function of centromeres; and in most organisms, the DNA in these regions is highly repetitive and is not thought to encode any proteins. However, it has been observed that cells need enzymes called RNA polymeraseswhich transcribe stretches of DNA into RNA moleculesto be able to separate the copies of their chromosomes correctly. This suggests that RNAs transcribed from centromeres might be required for cell division, but the identity and function of these RNAs remained elusive. Quénet and Dalal have now discovered that an RNA polymerase localizes to the DNA in human centromeres and produces RNA molecules during the early stages of the cell cycle. Two proteins–one called CENP-A and another that functions as its chaperone–that normally bind to the centromere and determine its structure were found less often in this region of the chromosome if the activity of the RNA polymerase was inhibited. Qunet and Dalal identified a specific RNA molecule that is transcribed from the centromeric DNA, which directly binds to the CENP-A protein and its chaperone before CENP-A is assembled onto the centromeric DNA. Reducing the levels of this RNA within the cells made them unable to separate their chromosomes correctly during cell divisions. Qunet and Dalal also demonstrated that this centromeric RNA is needed to specifically target both the CENP-A protein, via its chaperone, to the centromere. The findings of Qunet and Dalal demonstrate that RNAs produced from a specific part of the chromosome can help target DNA-binding proteins back to that region's DNA sequence. Following on from this work, the next challenge will be to determine if other RNA molecules are used for the same purpose in humans and other species.
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Affiliation(s)
- Delphine Quénet
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research,National Cancer Institute, Bethesda, United States
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research,National Cancer Institute, Bethesda, United States
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144
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Park CH, Lee SK. [Role of long non-coding ribonucleic acid in gastrointestinal cancer]. THE KOREAN JOURNAL OF GASTROENTEROLOGY 2014; 62:317-26. [PMID: 24365730 DOI: 10.4166/kjg.2013.62.6.317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
With the improvement of high-throughput genomic technology such as microarray and next-generation sequencing over the last ten to twenty year, we have come to know that the portion of the genome responsible for protein coding constitutes just approximately 1.5%. The remaining 98.5% of the genome not responsible for protein coding have been regarded as 'junk DNA'. More recently, however, 'Encyclopedia of DNA elements project' revealed that most of the junk DNA were transcribed to RNA regardless of being translated into proteins. In addition, many reports support that a lot of these non-coding RNAs play a role in gene regulation. In fact, there are various functioning short non-coding RNAs including rRNA, tRNA, small interfering RNA, and micro RNA. Mechanisms of these RNAs are relatively well-known. Until recently, however, little is known about long non-coding RNAs which consist of 200 nucleotides or more. In this article, we will review the representative long non-coding RNAs which have been reported to be related to gastrointestinal cancers and to play a certain role in its pathogenesis.
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Affiliation(s)
- Chan Hyuk Park
- Department of Internal Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-752, Korea
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145
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Differentiation-dependent requirement of Tsix long non-coding RNA in imprinted X-chromosome inactivation. Nat Commun 2014; 5:4209. [PMID: 24979243 PMCID: PMC4086345 DOI: 10.1038/ncomms5209] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 05/26/2014] [Indexed: 01/01/2023] Open
Abstract
Imprinted X-inactivation is a paradigm of mammalian transgenerational epigenetic regulation resulting in silencing of genes on the paternally inherited X-chromosome. The preprogrammed fate of the X-chromosomes is thought to be controlled in cis by the parent-of-origin-specific expression of two opposing long non-coding RNAs, Tsix and Xist, in mice. Exclusive expression of Tsix from the maternal-X has implicated it as the instrument through which the maternal germline prevents inactivation of the maternal-X in the offspring. Here, we show that Tsix is dispensable for inhibiting Xist and X-inactivation in the early embryo and in cultured stem cells of extra-embryonic lineages. Tsix is instead required to prevent Xist expression as trophectodermal progenitor cells differentiate. Despite induction of wild-type Xist RNA and accumulation of histone H3-K27me3, many Tsix-mutant X-chromosomes fail to undergo ectopic X-inactivation. We propose a novel model of lncRNA function in imprinted X-inactivation that may also apply to other genomically imprinted loci.
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146
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Fuchs C, Trazzi S, Torricella R, Viggiano R, De Franceschi M, Amendola E, Gross C, Calzà L, Bartesaghi R, Ciani E. Loss of CDKL5 impairs survival and dendritic growth of newborn neurons by altering AKT/GSK-3β signaling. Neurobiol Dis 2014; 70:53-68. [PMID: 24952363 PMCID: PMC4146476 DOI: 10.1016/j.nbd.2014.06.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/22/2014] [Accepted: 06/09/2014] [Indexed: 12/24/2022] Open
Abstract
Mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5) gene have been identified in a neurodevelopmental disorder characterized by early-onset intractable seizures, severe developmental delay, intellectual disability, and Rett's syndrome-like features. Since the physiological functions of CDKL5 still need to be elucidated, in the current study we took advantage of a new Cdkl5 knockout (KO) mouse model in order to shed light on the role of this gene in brain development. We mainly focused on the hippocampal dentate gyrus, a region that largely develops postnatally and plays a key role in learning and memory. Looking at the process of neurogenesis, we found a higher proliferation rate of neural precursors in Cdkl5 KO mice in comparison with wild type mice. However, there was an increase in apoptotic cell death of postmitotic granule neuron precursors, with a reduction in total number of granule cells. Looking at dendritic development, we found that in Cdkl5 KO mice the newly-generated granule cells exhibited a severe dendritic hypotrophy. In parallel, these neurodevelopmental defects were associated with impairment of hippocampus-dependent memory. Looking at the mechanisms whereby CDKL5 exerts its functions, we identified a central role of the AKT/GSK-3β signaling pathway. Overall our findings highlight a critical role of CDKL5 in the fundamental processes of brain development, namely neuronal precursor proliferation, survival and maturation. This evidence lays the basis for a better understanding of the neurological phenotype in patients carrying mutations in the CDKL5 gene. Loss of Cdkl5 decreases survival of postmitotic granule cells. Loss of Cdkl5 results in dendritic hypotrophy of newborn granule cells. Loss of Cdkl5 impairs hippocampus-dependent behavior. Loss of Cdkl5 alters the AKT/GSK-3β pathway.
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Affiliation(s)
- Claudia Fuchs
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Stefania Trazzi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Roberta Torricella
- Health Sciences and Technologies-Interdepartmental Center for Industrial Research (HST-ICIR), University of Bologna, Italy
| | - Rocchina Viggiano
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | | | - Elena Amendola
- Mouse Biology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, Italy
| | - Cornelius Gross
- Mouse Biology Unit, European Molecular Biology Laboratory (EMBL), Monterotondo, Italy
| | - Laura Calzà
- Health Sciences and Technologies-Interdepartmental Center for Industrial Research (HST-ICIR), University of Bologna, Italy
| | - Renata Bartesaghi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Elisabetta Ciani
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy.
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147
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Bhan A, Mandal SS. Long noncoding RNAs: emerging stars in gene regulation, epigenetics and human disease. ChemMedChem 2014; 9:1932-56. [PMID: 24677606 DOI: 10.1002/cmdc.201300534] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Indexed: 12/19/2022]
Abstract
Noncoding RNAs (ncRNAs) are classes of transcripts that are encoded by the genome and transcribed but never get translated into proteins. Though not translated into proteins, ncRNAs play pivotal roles in a variety of cellular functions. Here, we review the functions of long noncoding RNAs (lncRNAs) and their implications in various human diseases. Increasing numbers of studies demonstrate that lncRNAs play critical roles in regulation of protein-coding genes, maintenance of genomic integrity, dosage compensation, genomic imprinting, mRNA processing, cell differentiation, and development. Misregulation of lncRNAs is associated with a variety of human diseases, including cancer, immune and neurological disorders. Different classes of lncRNAs, their functions, mechanisms of action, and associations with different human diseases are summarized in detail, highlighting their as yet untapped potential in therapy.
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Affiliation(s)
- Arunoday Bhan
- Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019 (USA)
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148
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Malcom JW, Kudra RS, Malone JH. The sex chromosomes of frogs: variability and tolerance offer clues to genome evolution and function. J Genomics 2014; 2:68-76. [PMID: 25031658 PMCID: PMC4091447 DOI: 10.7150/jgen.8044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Frog sex chromosomes offer an ideal system for advancing our understanding of genome evolution and function because of the variety of sex determination systems in the group, the diversity of sex chromosome maturation states, the ease of experimental manipulation during early development. After briefly reviewing sex chromosome biology generally, we focus on what is known about frog sex determination, sex chromosome evolution, and recent, genomics-facilitated advances in the field. In closing we highlight gaps in our current knowledge of frog sex chromosomes, and suggest priorities for future research that can advance broad knowledge of gene dose and sex chromosome evolution.
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Affiliation(s)
- Jacob W Malcom
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269 USA
| | - Randal S Kudra
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269 USA
| | - John H Malone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269 USA
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149
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Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 2014; 21:198-206. [PMID: 24463464 PMCID: PMC3950333 DOI: 10.1038/nsmb.2764] [Citation(s) in RCA: 494] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 12/30/2013] [Indexed: 02/07/2023]
Abstract
RNA, including long noncoding RNA (lncRNA), is known to be an abundant and important structural component of the nuclear matrix. However, the molecular identities, functional roles and localization dynamics of lncRNAs that influence nuclear architecture remain poorly understood. Here, we describe one lncRNA, Firre, that interacts with the nuclear-matrix factor hnRNPU through a 156-bp repeating sequence and localizes across an ~5-Mb domain on the X chromosome. We further observed Firre localization across five distinct trans-chromosomal loci, which reside in spatial proximity to the Firre genomic locus on the X chromosome. Both genetic deletion of the Firre locus and knockdown of hnRNPU resulted in loss of colocalization of these trans-chromosomal interacting loci. Thus, our data suggest a model in which lncRNAs such as Firre can interface with and modulate nuclear architecture across chromosomes.
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Affiliation(s)
- Ezgi Hacisuleyman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Loyal A. Goff
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Cole Trapnell
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Adam Williams
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jorge Henao-Mejia
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lei Sun
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Patrick McClanahan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David G. Hendrickson
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Martin Sauvageau
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - David R. Kelley
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Michael Morse
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Jesse Engreitz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Eric S. Lander
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Mitch Guttman
- Department of Biology, California Institute of Technology, Pasadena, California, USA
| | - Harvey F. Lodish
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Richard Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Arjun Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John L. Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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150
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Zhu S, Hu X, Han S, Yu Z, Peng Y, Zhu J, Liu X, Qian L, Zhu C, Li M, Song G, Guo X. Differential expression profile of long non-coding RNAs during differentiation of cardiomyocytes. Int J Med Sci 2014; 11:500-7. [PMID: 24688315 PMCID: PMC3970104 DOI: 10.7150/ijms.7849] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 03/07/2014] [Indexed: 11/05/2022] Open
Abstract
Many long non-coding RNAs (lncRNAs) are species specific and seem to be less conserved than protein-coding genes. Some of them are involved in the development of the lateral mesoderm in the heart and in the differentiation of cardiomyocytes. The purpose of the study was to investigate the expression profiles of lncRNAs during the differentiation of P19 cells into cardiomyocytes, with a view to studying the biological function of lncRNAs and their involvement in the mechanism of heart development. First, we observed the morphology of P19 cells during differentiation using an inverted microscope. Then, cardiac troponin T (cTnT) expression was detected to validate that the cells had successfully differentiated into cardiac myocytes by real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR) and western blotting. Lastly, the expression profile of lncRNA genes was obtained using an lncRNA microarray and real-time RT-PCR analyses. The microarray results showed that 40 lncRNAs were differentially expressed, of which 28 were upregulated and 12 were downregulated in differentiated cardiomyocytes. The differentially expressed lncRNAs were further validated. Our results illustrated a critical role of lncRNAs during the differentiation of P19 cells into cardiac myocytes, which will provide the foundation for further study of the biological functions of lncRNAs and the mechanism of heart development.
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Affiliation(s)
- Shasha Zhu
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Xiaoshan Hu
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Shuping Han
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Zhangbin Yu
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Yuzhu Peng
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Jingai Zhu
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Xuehua Liu
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Lingmei Qian
- 2. Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Chun Zhu
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Mengmeng Li
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Guixian Song
- 2. Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xirong Guo
- 1. State key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
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