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https://www.readbyqxmd.com/read/28068310/visualizing-the-secondary-and-tertiary-architectural-domains-of-lncrna-repa
#1
Fei Liu, Srinivas Somarowthu, Anna Marie Pyle
Long noncoding RNAs (lncRNAs) are important for gene expression, but little is known about their structures. RepA is a 1.6-kb mouse lncRNA comprising the same sequence as the 5' region of Xist, including A and F repeats. It has been proposed to facilitate the initiation and spread of X-chromosome inactivation, although its exact role is poorly understood. To gain insight into the molecular mechanism of RepA and Xist, we determined a complete phylogenetically validated secondary-structural map of RepA through SHAPE and DMS chemical probing of a homogeneously folded RNA in vitro...
January 9, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28059474/csa-promotes-xist-expression-to-regulate-human-trophoblast-cells-proliferation-and-invasion-through-mir-144-titin-axis
#2
Nanhui Yu, Ying Liang, Hong Zhu, Hongying Mo, Haiping Pei
In our previous study, we revealed that Cyclosporin A (CsA) could inhibit miR-144 expression to regulate proliferation and invasion of human trophoblast (HT) cells through miR-144 targeting titin. This partially demonstrated the mechanism by which CsA promotes titin expression to increase the vitality of HT cells. However, the mechanism by which CsA inhibits miR-144 expression remains to be investigated. Recently, the interaction between lncRNA and miRNA has been frequently reported to play major role in several biological processes...
January 6, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28034840/establishment-of-porcine-xist-knockout-model-using-crispr-cas9-system
#3
Li Guoling, Zhong Cuili, Ni Sheng, Liu Dewu, Cai Gengyuan, Li Zicong, Yang Huaqiang, Wu Zhenfang
Somatic cell nuclear transfer technique has great applications in livestock breeding, production of genetically modified animals, rescue of endangered species and treatment of human diseases. However, the currently low efficiency in animals cloning, an average of less than 5%, greatly hindered the rapid development of this technique. Among many factors which affect the efficiency of cloning pigs, X chromosome inactivation is an important one. Moreover, Xist gene is closely related to X chromosome inactivation, suggesting that it may directly or indirectly affects cloning efficiency...
December 20, 2016: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/27989770/human-naive-pluripotent-stem-cells-model-x-chromosome-dampening-and-x-inactivation
#4
Anna Sahakyan, Rachel Kim, Constantinos Chronis, Shan Sabri, Giancarlo Bonora, Thorold W Theunissen, Edward Kuoy, Justin Langerman, Amander T Clark, Rudolf Jaenisch, Kathrin Plath
Naive human embryonic stem cells (hESCs) can be derived from primed hESCs or directly from blastocysts, but their X chromosome state has remained unresolved. Here, we show that the inactive X chromosome (Xi) of primed hESCs was reactivated in naive culture conditions. Like cells of the blastocyst, the resulting naive cells contained two active X chromosomes with XIST expression and chromosome-wide transcriptional dampening and initiated XIST-mediated X inactivation upon differentiation. Both establishment of and exit from the naive state (differentiation) happened via an XIST-negative XaXa intermediate...
January 5, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/27989768/xact-noncoding-rna-competes-with-xist-in-the-control-of-x-chromosome-activity-during-human-early-development
#5
Céline Vallot, Catherine Patrat, Amanda J Collier, Christophe Huret, Miguel Casanova, Tharvesh M Liyakat Ali, Matteo Tosolini, Nelly Frydman, Edith Heard, Peter J Rugg-Gunn, Claire Rougeulle
Sex chromosome dosage compensation is essential in most metazoans, but the developmental timing and underlying mechanisms vary significantly, even among placental mammals. Here we identify human-specific mechanisms regulating X chromosome activity in early embryonic development. Single-cell RNA sequencing and imaging revealed co-activation and accumulation of the long noncoding RNAs (lncRNAs) XACT and XIST on active X chromosomes in both early human pre-implantation embryos and naive human embryonic stem cells...
January 5, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/27989715/human-embryonic-stem-cells-do-not-change-their-x-inactivation-status-during-differentiation
#6
Sanjeet Patel, Giancarlo Bonora, Anna Sahakyan, Rachel Kim, Constantinos Chronis, Justin Langerman, Sorel Fitz-Gibbon, Liudmilla Rubbi, Rhys J P Skelton, Reza Ardehali, Matteo Pellegrini, William E Lowry, Amander T Clark, Kathrin Plath
Applications of embryonic stem cells (ESCs) require faithful chromatin changes during differentiation, but the fate of the X chromosome state in differentiating ESCs is unclear. Female human ESC lines either carry two active X chromosomes (XaXa), an Xa and inactive X chromosome with or without XIST RNA coating (Xi(XIST+)Xa;XiXa), or an Xa and an eroded Xi (XeXa) where the Xi no longer expresses XIST RNA and has partially reactivated. Here, we established XiXa, XeXa, and XaXa ESC lines and followed their X chromosome state during differentiation...
January 3, 2017: Cell Reports
https://www.readbyqxmd.com/read/27934601/establishment-of-human-embryonic-stem-cell-line-with-a-complex-abnormal-karyotype-and-the-stable-xist-expression
#7
Leiyu Deng, Dehua Cheng, Guangxiu Lu, Ge Lin
The embryonic stem cell line chHES-3XISTa was derived from heterogeneous chHES-3 cells. chHES-3XISTa showed a new abnormal karyotype of 46,XX with 8 derivation chromosomes and expressed X inactive specific transcript (XIST) in continual culture. Tri-methylation of H3 Lys-27 (H3K27me3) punctate enrichment located in RNA Polymerase II hole was also found in all chHES-3XISTa cells. Pluripotent markers and differentiate capability in vitro were confirmed by immunochemistry staining.
November 5, 2016: Stem Cell Research
https://www.readbyqxmd.com/read/27911852/long-non-coding-rna-xist-promotes-cell-growth-and-invasion-through-regulating-mir-497-macc1-axis-in-gastric-cancer
#8
Lei Ma, Yongjian Zhou, Xiaojun Luo, Hai Gao, Xubin Deng, Yingjie Jiang
Abnormal expression of long non-coding RNA (lncRNAs) often contributes to unrestricted growth and invasion of cancer cells. LncRNA XIST expression is up-regulated in several cancers, however, its modulatory mechanism in gastric cancer (GC) has not been elucidated. In the present study, we found that XIST expression was significantly increased in GC tissues and cell lines. LncRNA XIST promoted cell cycle progression from the G1 phase to the S phase and protected cells from apoptosis, which contributed to GC cell growth...
November 28, 2016: Oncotarget
https://www.readbyqxmd.com/read/27899965/increased-expression-of-long-non-coding-rna-xist-predicts-favorable-prognosis-of-cervical-squamous-cell-carcinoma-subsequent-to-definitive-chemoradiation-therapy
#9
Reiko Kobayashi, Ryu Miyagawa, Hideomi Yamashita, Teppei Morikawa, Kae Okuma, Masashi Fukayama, Kuni Ohtomo, Keiichi Nakagawa
The present retrospective study aimed to examine the association between the expression of long non-protein-coding RNAs (lncRNAs) and clinical prognosis in the pretreatment formalin-fixed, paraffin-embedded (FFPE) tissue samples of cervical squamous cell carcinoma patients that underwent platinum-based chemoradiation therapy. Between 2001 and 2013, 49 consecutive patients with squamous cell cervical carcinoma were selected for the present study (median follow-up period, 44.1 months). The patients possessed an International Federation of Gynecology and Obstetrics stage of IB1/IIA1 (with pelvic lymph node metastasis), IB2 or IIA2-IVA, and had been treated with definitive chemoradiation therapy...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899588/a-high-throughput-approach-to-profile-rna-structure
#10
Riccardo Delli Ponti, Stefanie Marti, Alexandros Armaos, Gian Gaetano Tartaglia
Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. We trained CROSS using data from high-throughput experiments such as Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE; Mouse and HIV transcriptomes) and Parallel Analysis of RNA Structure (PARS; Human and Yeast transcriptomes) as well as high-quality NMR/X-ray structures (PDB database)...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27880931/an-xist-related-small-rna-regulates-kras-g-quadruplex-formation-beyond-x-inactivation
#11
Yuli C Chang, Chien-Chih Chiu, Chung-Yee Yuo, Wen-Ling Chan, Ya-Sian Chang, Wen-Hsin Chang, Shou-Mei Wu, Han-Lin Chou, Ta-Chih Liu, Chi-Yu Lu, Wen-Kuang Yang, Jan-Gowth Chang
X-inactive-specific transcript (XIST), a long non-coding RNA, is essential for the initiation of X-chromosome inactivation. However, little is known about other roles of XIST in the physiological process in eukaryotic cells. In this study, the bioinformatics approaches revealed XIST could be processed into a small non-coding RNA XPi2. The XPi2 RNA was confirmed by a northern blot assay; its expression was gender-independent, suggesting the role of XPi2 was beyond X-chromosome inactivation. The pull-down assay combined with LC-MS-MS identified two XPi2-associated proteins, nucleolin and hnRNP A1, connected to the formation of G-quadruplex...
November 17, 2016: Oncotarget
https://www.readbyqxmd.com/read/27870435/a-general-theory-of-sexual-differentiation
#12
REVIEW
Arthur P Arnold
A general theory of mammalian sexual differentiation is proposed. All biological sex differences are the result of the inequality in effects of the sex chromosomes, which are the only factors that differ in XX vs. XY zygotes. This inequality leads to male-specific effects of the Y chromosome, including expression of the testis-determining gene Sry that causes differentiation of testes. Thus, Sry sets up lifelong sex differences in effects of gonadal hormones. Y genes also act outside of the gonads to cause male-specific effects...
January 2, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27819659/a-statistical-test-for-conserved-rna-structure-shows-lack-of-evidence-for-structure-in-lncrnas
#13
Elena Rivas, Jody Clements, Sean R Eddy
Many functional RNAs have an evolutionarily conserved secondary structure. Conservation of RNA base pairing induces pairwise covariations in sequence alignments. We developed a computational method, R-scape (RNA Structural Covariation Above Phylogenetic Expectation), that quantitatively tests whether covariation analysis supports the presence of a conserved RNA secondary structure. R-scape analysis finds no statistically significant support for proposed secondary structures of the long noncoding RNAs HOTAIR, SRA, and Xist...
January 2017: Nature Methods
https://www.readbyqxmd.com/read/27788132/maintenance-of-xist-imprinting-depends-on-chromatin-condensation-state-and-rnf12-dosage-in-mice
#14
Atsushi Fukuda, Atsushi Mitani, Toshiyuki Miyashita, Takashi Sado, Akihiro Umezawa, Hidenori Akutsu
In female mammals, activation of Xist (X-inactive specific transcript) is essential for establishment of X chromosome inactivation. During early embryonic development in mice, paternal Xist is preferentially expressed whereas maternal Xist (Xm-Xist) is silenced. Unlike autosomal imprinted genes, Xist imprinting for Xm-Xist silencing was erased in cloned or parthenogenetic but not fertilized embryos. However, the molecular mechanism underlying the variable nature of Xm-Xist imprinting is poorly understood. Here, we revealed that Xm-Xist silencing depends on chromatin condensation states at the Xist/Tsix genomic region and on Rnf12 expression levels...
October 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27780979/long-non-coding-rnas-spatial-amplifiers-that-control-nuclear-structure-and-gene-expression
#15
Jesse M Engreitz, Noah Ollikainen, Mitchell Guttman
Over the past decade, it has become clear that mammalian genomes encode thousands of long non-coding RNAs (lncRNAs), many of which are now implicated in diverse biological processes. Recent work studying the molecular mechanisms of several key examples - including Xist, which orchestrates X chromosome inactivation - has provided new insights into how lncRNAs can control cellular functions by acting in the nucleus. Here we discuss emerging mechanistic insights into how lncRNAs can regulate gene expression by coordinating regulatory proteins, localizing to target loci and shaping three-dimensional (3D) nuclear organization...
December 2016: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/27776968/downregulation-of-long-non-coding-rnas-jpx-and-xist-is-associated-with-the-prognosis-of-hepatocellular-carcinoma
#16
Weijie Ma, Haitao Wang, Wei Jing, Fuling Zhou, Lei Chang, Zhenfei Hong, Hailing Liu, Zhisu Liu, Yufeng Yuan
BACKGROUND: The expression profiles and biological relevance of long non-coding RNA XIST and its activator JPX in hepatocellular carcinoma (HCC) are not well elucidated. We measured JPX and XIST expression levels in HCC, evaluated their clinical significance in HCC progression, and verified their potential as biomarkers for diagnosing HCC. METHODS: JPX and XIST expression in 68 HCC tissues and adjacent normal tissues were evaluated by quantitative reverse transcription-PCR (qRT-PCR); their association with pathologic features and overall survival was analyzed...
October 21, 2016: Clinics and Research in Hepatology and Gastroenterology
https://www.readbyqxmd.com/read/27716834/round-spermatid-injection-rescues-female-lethality-of-a-paternally-inherited-xist-deletion-in-mouse
#17
Federica Federici, Aristea Magaraki, Evelyne Wassenaar, Catherina J H van Veen-Buurman, Christine van de Werken, Esther B Baart, Joop S E Laven, J Anton Grootegoed, Joost Gribnau, Willy M Baarends
In mouse female preimplantation embryos, the paternal X chromosome (Xp) is silenced by imprinted X chromosome inactivation (iXCI). This requires production of the noncoding Xist RNA in cis, from the Xp. The Xist locus on the maternally inherited X chromosome (Xm) is refractory to activation due to the presence of an imprint. Paternal inheritance of an Xist deletion (XpΔXist) is embryonic lethal to female embryos, due to iXCI abolishment. Here, we circumvented the histone-to-protamine and protamine-to-histone transitions of the paternal genome, by fertilization of oocytes via injection of round spermatids (ROSI)...
October 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27696910/effect-of-sex-of-embryo-on-developmental-competence-epigenetic-status-and-gene-expression-in-buffalo-bubalus-bubalis-embryos-produced-by-hand-made-cloning
#18
Anjit Sandhu, Sushil K Mohapatra, Himanshu Agrawal, Manoj K Singh, Prabhat Palta, Suresh K Singla, Manmohan S Chauhan, Radhey S Manik
Buffalo embryos were produced by hand-made cloning using skin fibroblasts from male and female buffaloes (n = 4 each) as donor cells for examining the effect of sex. Although the rate of blastocyst formation (43.8% ± 1.31% vs. 42.2% ± 1.22%) was similar, the total cell number (333 ± 10.4 vs. 270 ± 10.9) was higher (p < 0.05) whereas the apoptotic index (6.39 ± 0.25 vs. 8.52 ± 0.38) was lower (p < 0.05) for male than for female blastocysts. In the blastocysts, the global level of H3K18ac was found to be in the following order: male>female>IVF (in vitro fertilization) blastocysts (p < 0...
October 2016: Cellular Reprogramming
https://www.readbyqxmd.com/read/27659978/identification-of-rna-protein-interactions-through-in-vitro-rna-pull-down-assays
#19
Claire Barnes, Aditi Kanhere
Recent advances in next-generation sequencing have revealed that majority of the human genome is transcribed into long and short RNA (ncRNA) transcripts. Many ncRNAs function by interacting with proteins and forming regulatory complexes. RNA-protein interactions are vital in controlling core cellular processes like transcription and translation. Therefore identifying proteins that interact with ncRNAs is central to deciphering ncRNA functions. Here we describe an RNA-protein pull-down assay, which enables the identification of proteins that interact with an RNA under study...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27642011/regulation-of-x-linked-gene-expression-during-early-mouse-development-by-rlim
#20
Feng Wang, JongDae Shin, Jeremy M Shea, Jun Yu, Ana Bošković, Meg Byron, Xiaochun Zhu, Alex K Shalek, Aviv Regev, Jeanne B Lawrence, Eduardo M Torres, Lihua J Zhu, Oliver J Rando, Ingolf Bach
Mammalian X-linked gene expression is highly regulated as female cells contain two and male one X chromosome (X). To adjust the X gene dosage between genders, female mouse preimplantation embryos undergo an imprinted form of X chromosome inactivation (iXCI) that requires both Rlim (also known as Rnf12) and the long non-coding RNA Xist. Moreover, it is thought that gene expression from the single active X is upregulated to correct for bi-allelic autosomal (A) gene expression. We have combined mouse genetics with RNA-seq on single mouse embryos to investigate functions of Rlim on the temporal regulation of iXCI and Xist...
September 19, 2016: ELife
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