keyword
MENU ▼
Read by QxMD icon Read
search

Xist

keyword
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
#1
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
#2
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
#3
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
#4
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
#5
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...
November 7, 2016: Nature Methods
https://www.readbyqxmd.com/read/27788132/maintenance-of-xist-imprinting-depends-on-chromatin-condensation-state-and-rnf12-dosage-in-mice
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27620004/long-non-coding-rna-xist-regulates-gastric-cancer-progression-by-acting-as-a-molecular-sponge-of-mir-101-to-modulate-ezh2-expression
#13
Dong-Liang Chen, Huai-Qiang Ju, Yun-Xin Lu, Le-Zong Chen, Zhao-Lei Zeng, Dong-Sheng Zhang, Hui-Yan Luo, Feng Wang, Miao-Zhen Qiu, De-Shen Wang, Da-Zhi Xu, Zhi-Wei Zhou, Helene Pelicano, Peng Huang, Dan Xie, Feng-Hua Wang, Yu-Hong Li, Rui-Hua Xu
BACKGROUND: Long non-coding RNAs (lncRNAs) have emerged as critical regulators of tumor progression. However, the role and molecular mechanism of lncRNA XIST in gastric cancer is still unknown. METHODS: Real-time PCR analysis was performed to measure the expression levels of lncRNA XIST in gastric cancer tissues and cell lines, the correlation between lncRNA XIST expression and clinicopathological characteristics and prognosis was analyzed in gastric cancer patients...
September 13, 2016: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/27603915/dysregulated-expression-of-long-noncoding-rnas-in-ovarian-cancer
#14
Yancheng Zhong, Dan Gao, Shiwei He, Cijun Shuai, Shuping Peng
Ovarian cancer is the leading cause of death among women with gynecologic malignancies. The development and progression of ovarian cancer are complex and a multiple-step process. New biomarker molecules for diagnostic and prognostic are essential for novel therapeutic targets and to extend the survival time of patients with ovarian cancer. Long noncoding RNAs (lncRNAs) are non-protein-coding transcripts longer than 200 nucleotides that have recently been found as key regulators of various biological processes and to be involved in the development and progression of many diseases including cancers...
September 6, 2016: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/27602518/m-6-a-rna-methylation-promotes-xist-mediated-transcriptional-repression
#15
Deepak P Patil, Chun-Kan Chen, Brian F Pickering, Amy Chow, Constanza Jackson, Mitchell Guttman, Samie R Jaffrey
The long non-coding RNA X-inactive specific transcript (XIST) mediates the transcriptional silencing of genes on the X chromosome. Here we show that, in human cells, XIST is highly methylated with at least 78 N(6)-methyladenosine (m(6)A) residues-a reversible base modification of unknown function in long non-coding RNAs. We show that m(6)A formation in XIST, as well as in cellular mRNAs, is mediated by RNA-binding motif protein 15 (RBM15) and its paralogue RBM15B, which bind the m(6)A-methylation complex and recruit it to specific sites in RNA...
September 7, 2016: Nature
https://www.readbyqxmd.com/read/27578869/shape-reveals-transcript-wide-interactions-complex-structural-domains-and-protein-interactions-across-the-xist-lncrna-in-living-cells
#16
Matthew J Smola, Thomas W Christy, Kaoru Inoue, Cindo O Nicholson, Matthew Friedersdorf, Jack D Keene, David M Lee, J Mauro Calabrese, Kevin M Weeks
The 18-kb Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation during female eutherian mammalian development. Global structural architecture, cell-induced conformational changes, and protein-RNA interactions within Xist are poorly understood. We used selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to examine these features of Xist at single-nucleotide resolution both in living cells and ex vivo. The Xist RNA forms complex well-defined secondary structure domains and the cellular environment strongly modulates the RNA structure, via motifs spanning one-half of all Xist nucleotides...
September 13, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27573373/chromatin-xist-as-a-recruitment-tool
#17
Denise Waldron
No abstract text is available yet for this article.
October 2016: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/27569767/effects-of-rnai-mediated-knockdown-of-xist-on-the-developmental-efficiency-of-cloned-male-porcine-embryos
#18
Fang Zeng, Zhihua Huang, Yujuan Yuan, Junsong Shi, Gengyuan Cai, Dewu Liu, Zhenfang Wu, Zicong Li
Xist is an X-linked gene responsible for cis induction of X chromosome inactivation. Studies have indicated that Xist is abnormally activated in the active X chromosome in cloned mouse embryos due to loss of the maternal Xist-repressing imprint following enucleation during somatic cell nuclear transfer (SCNT). Inhibition of Xist expression by injecting small interfering RNA (siRNA) has been shown to enhance the in vivo developmental efficiency of cloned male mouse embryos by more than 10-fold. The purpose of this study was to investigate whether a similar procedure can be applied to improve the cloning efficiency in pigs...
August 29, 2016: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/27553879/effect-of-storage-time-on-gene-expression-data-acquired-from-unfrozen-archived-newborn-blood-spots
#19
Nhan T Ho, Julia V Busik, James H Resau, Nigel Paneth, Sok Kean Khoo
Unfrozen archived newborn blood spots (NBS) have been shown to retain sufficient messenger RNA (mRNA) for gene expression profiling. However, the effect of storage time at ambient temperature for NBS samples in relation to the quality of gene expression data is relatively unknown. Here, we evaluated mRNA expression from quantitative real-time PCR (qRT-PCR) and microarray data obtained from NBS samples stored at ambient temperature to determine the effect of storage time on the quality of gene expression. These data were generated in a previous case-control study examining NBS in 53 children with cerebral palsy (CP) and 53 matched controls...
November 2016: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/27542829/female-mice-lacking-xist-rna-show-partial-dosage-compensation-and-survive-to-term
#20
Lin Yang, James E Kirby, Hongjae Sunwoo, Jeannie T Lee
X-chromosome inactivation (XCI) compensates for differences in X-chromosome number between male and female mammals. XCI is orchestrated by Xist RNA, whose expression in early development leads to transcriptional silencing of one X chromosome in the female. Knockout studies have established a requirement for Xist with inviability of female embryos that inherit an Xist deletion from the father. Here, we report that female mice lacking Xist RNA can, surprisingly, develop and survive to term. Xist-null females are born at lower frequency and are smaller at birth, but organogenesis is mostly normal...
August 1, 2016: Genes & Development
keyword
keyword
12155
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"