Stranded Whole Transcriptome RNA‐Seq for All RNA Types

Miller, David F.; Yan, Pearlly; Fang, Fang; Buechlein, Aaron; Ford, James; Tang, Haixu; Huang, Tim H.M.; Burow, Matthew E.; Liu, Yunlong; Rusch, Douglas B.; Nephew, Kenneth P.

doi:10.1002/0471142905.hg1114s84

Cited by 6 publications

(4 citation statements)

References 10 publications

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“…The estimate variation within each group were similar therefore student’s t -test was used to statistically analyze the significant difference among different groups by using Prism 4.0 (GraphPad Software). The genome-wide analysis experiments were conducted as described previously[ 56 , 57 ] using the Partek Genomics Suite (version 6.5).…”

Section: Methodsmentioning

confidence: 99%

NF-κB-HOTAIR axis links DNA damage response, chemoresistance and cellular senescence in ovarian cancer

et al. 2016

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The transcription factor nuclear factor kappa B (NF-κB) and the long non-coding RNA (lncRNA) HOTAIR (HOX transcript antisense RNA) play diverse functional roles in cancer. In this study, we show that upregulation of HOTAIR induced platinum resistance in ovarian cancer, and increased HOTAIR levels were observed in recurrent platinum-resistant ovarian tumors vs. primary ovarian tumors. To investigate the role of HOTAIR during DNA damage induced by platinum, we monitored double-strand breaks and show that HOTAIR expression results in sustained activation of DNA damage response after platinum treatment. We demonstrate that ectopic expression of HOTAIR induces NF-κB activation during DNA damage response and MMP-9 and IL-6 expression, both key NF-κB target genes. We show that HOTAIR regulates activation of NF-κB by decreasing Iκ-Bα (NF-κB inhibitor) and establish that by inducing prolonged NF-κB activation and expression of NF-κB target genes during DNA damage, HOTAIR plays a critical role in cellular senescence and platinum sensitivity. Our findings suggest that a NF-κB-HOTAIR axis drives a positive-feedback loop cascade during DNA damage response and contributes to cellular senescence and chemotherapy resistance in ovarian and other cancers.

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Section: Methodsmentioning

confidence: 99%

NF-κB-HOTAIR axis links DNA damage response, chemoresistance and cellular senescence in ovarian cancer

et al. 2016

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“…Tissues were extracted, flash frozen and stored at 2808C. Subsequent generation of RNA libraries was carried out at the Center for Genomics and Bioinformatics at Indiana University following established protocols [14]. For additional information on RNA extraction and RNA libraries, see the electronic supplementary material.…”

Section: Methodsmentioning

confidence: 99%

Differential gene expression in seasonal sympatry: mechanisms involved in diverging life histories

et al. 2016

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In an era of climate change, understanding the genetic and physiological mechanisms underlying flexibility in phenology and life history has gained greater importance. These mechanisms can be elucidated by comparing closely related populations that differ in key behavioural and physiological traits such as migration and timing of reproduction. We compared gene expression in two recently diverged dark-eyed Junco (Junco hyemalis) subspecies that live in seasonal sympatry during winter and early spring, but that differ in behaviour and physiology, despite exposure to identical environmental cues. We identified 547 genes differentially expressed in blood and pectoral muscle. Genes involved in lipid transport and metabolism were highly expressed in migrant juncos, while genes involved in reproductive processes were highly expressed in resident breeders. Seasonal differences in gene expression in closely related populations residing in the same environment provide significant insights into mechanisms underlying variation in phenology and life history, and have potential implications for the role of seasonal timing differences in gene flow and reproductive isolation.

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“…Advances in high‐throughput deep sequencing of the transcriptome and the ENCODE project over the last two decades have demonstrated that only approximately 2% of the genome codes for proteins, while the largest genome fraction encodes for thousands of non‐coding RNAs . These results indicate that non‐coding RNAs, which were considered as “transcriptional noises,” play a critical role in the gene control across all kingdoms of life.…”

Section: Introductionmentioning

confidence: 99%

Long non‐coding RNAs in cutaneous biology and proliferative skin diseases: Advances and perspectives

et al. 2019

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Advances in transcriptome sequencing have revealed that the genome fraction largely encodes for thousands of non‐coding RNAs. Long non‐coding RNAs (lncRNAs), which are a class of non–protein‐coding RNAs longer than approximately 200 nucleotides in length, are emerging as key epigenetic regulators of gene expression recently. Intensive studies have characterized their crucial roles in cutaneous biology and diseases. In this review, we address the promotive or suppressive effects of lncRNAs on cutaneous physiological processes. Then, we focus on the pathogenic role of dysfunctional lncRNAs in a variety of proliferative skin diseases. These evidences suggest that lncRNAs have indispensable roles in the processes of skin biology. Additionally, lncRNAs might be promising biomarkers and therapeutic targets for cutaneous disorders.

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Stranded Whole Transcriptome RNA‐Seq for All RNA Types

Cited by 6 publications

References 10 publications

NF-κB-HOTAIR axis links DNA damage response, chemoresistance and cellular senescence in ovarian cancer

NF-κB-HOTAIR axis links DNA damage response, chemoresistance and cellular senescence in ovarian cancer

Differential gene expression in seasonal sympatry: mechanisms involved in diverging life histories

Long non‐coding RNAs in cutaneous biology and proliferative skin diseases: Advances and perspectives

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