scholarly journals Bioinformatic Identification of a Breast‐Specific Transcript Profile

2020 ◽  
Vol 14 (6) ◽  
pp. 2000007
Author(s):  
Chen Chen ◽  
Liwen Yang ◽  
Mahdi Rivandi ◽  
André Franken ◽  
Tanja Fehm ◽  
...  
Keyword(s):  
Transcript Profile ◽  
Specific Transcript

scholarly journals Dendritic Cell-Specific Transcript: Dendritic Cell Marker and Regulator of TLR-Induced Cytokine Production

2012 ◽  
Vol 189 (1) ◽  
pp. 138-145 ◽  
Author(s):  
Saartje Hontelez ◽  
Marleen Ansems ◽  
Nina Karthaus ◽  
Malou Zuidscherwoude ◽  
Maaike W. Looman ◽  
...  
Keyword(s):  
Dendritic Cell ◽  
Cytokine Production ◽  
Cell Marker ◽  
Specific Transcript

scholarly journals CRISPRi enables isoform-specific loss-of-function screens and identification of gastric cancer-specific isoform dependencies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rebecca Davies ◽  
Ling Liu ◽  
Sheng Taotao ◽  
Natasha Tuano ◽  
Richa Chaturvedi ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Functional Dependencies ◽  
Loss Of Function ◽  
Genetic Screens ◽  
Transcript Isoforms ◽  
Specific Loss ◽  
Current Loss ◽  
Specific Transcript ◽  
Multiple Promoters ◽  
Poor Patient

Abstract Introduction Genes contain multiple promoters that can drive the expression of various transcript isoforms. Although transcript isoforms from the same gene could have diverse and non-overlapping functions, current loss-of-function methodologies are not able to differentiate between isoform-specific phenotypes. Results Here, we show that CRISPR interference (CRISPRi) can be adopted for targeting specific promoters within a gene, enabling isoform-specific loss-of-function genetic screens. We use this strategy to test functional dependencies of 820 transcript isoforms that are gained in gastric cancer (GC). We identify a subset of GC-gained transcript isoform dependencies, and of these, we validate CIT kinase as a novel GC dependency. We further show that some genes express isoforms with opposite functions. Specifically, we find that the tumour suppressor ZFHX3 expresses an isoform that has a paradoxical oncogenic role that correlates with poor patient outcome. Conclusions Our work finds isoform-specific phenotypes that would not be identified using current loss-of-function approaches that are not designed to target specific transcript isoforms.

scholarly journals Knockdown of lncRNA X inactive specific transcript (XIST) radiosensitizes non-small cell lung cancer (NSCLC) cells through regulation of miR-16-5p/WEE1 G2 checkpoint kinase (WEE1) axis

2021 ◽  
Vol 35 ◽  
pp. 205873842096608
Author(s):  
Ran Du ◽  
Feng Jiang ◽  
Yanhua Yin ◽  
Jinfen Xu ◽  
Xia Li ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Western Blot ◽  
Small Cell ◽  
Luciferase Reporter ◽  
Small Cell Lung ◽  
Luciferase Reporter Gene ◽  
G2 Checkpoint ◽  
Qrt Pcr ◽  
Specific Transcript

Long non-coding RNA (lncRNA) X inactive specific transcript (XIST) is reported to play an oncogenic role in non-small cell lung cancer (NSCLC). However, the role of XIST in regulating the radiosensitivity of NSCLC cells remains unclear. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expressions of XIST and miR-16-5p in NSCLC in tissues and cells, and Western blot was used to assess the expression of WEE1 G2 checkpoint kinase (WEE1). Cell counting kit-8 (CCK-8), colony formation and flow cytometry assays were used to determine cell viability and apoptosis after NSCLC cells were exposed to different doses of X-rays. The interaction between XIST and miR-16-5p was confirmed by StarBase database, qRT-PCR and dual-luciferase reporter gene assays. TargetScan database was used to predict WEE1 as a target of miR-16-5p, and their targeting relationship was further validated by Western blot, qRT-PCR and dual-luciferase reporter gene assays. XIST was highly expressed in both NSCLC tissue and cell lines, and knockdown of XIST repressed NSCLC cell viability and cell survival, and facilitated apoptosis under the irradiation. MiR-16-5p was a target of XIST, and rescue experiments demonstrated that miR-16-5p inhibitors could reverse the role of XIST knockdown on radiosensitivity in NSCLC cells. WEE1 was validated as a target gene of miR-16-5p, and WEE1 could be negatively regulated by XIST. XIST promotes the radioresistance of NSCLC cells by regulating the expressions of miR-16-5p and WEE1, which can be a novel target for NSCLC therapy.

scholarly journals Review Application of RNA-seq to reveal the transcript profile in bacteria

2011 ◽  
Vol 10 (3) ◽  
pp. 1707-1718 ◽  
Author(s):  
A.C. Pinto ◽  
H.P. Melo-Barbosa ◽  
A. Miyoshi ◽  
A. Silva ◽  
V. Azevedo
Keyword(s):  
Transcript Profile ◽  
Rna Seq

scholarly journals Root-Specific Transcript Profiling of Contrasting Rice Genotypes in Response to Salinity Stress

2011 ◽  
Vol 4 (1) ◽  
pp. 25-41 ◽  
Author(s):  
Olivier Cotsaftis ◽  
Darren Plett ◽  
Alexander A.T. Johnson ◽  
Harkamal Walia ◽  
Clyde Wilson ◽  
...  
Keyword(s):  
Salinity Stress ◽  
Transcript Profiling ◽  
Specific Transcript ◽  
Rice Genotypes

The testis-specific transcript (ferT) of the tyrosine kinase FER is expressed during spermatogenesis in a stage-specific manner

1990 ◽  
Vol 10 (9) ◽  
pp. 5021-5025
Author(s):  
E Keshet ◽  
A Itin ◽  
K Fischman ◽  
U Nir
Keyword(s):  
In Situ Hybridization ◽  
Tyrosine Kinase ◽  
Tyrosine Kinases ◽  
Meiotic Prophase ◽  
Hybridization Analysis ◽  
Pachytene Stage ◽  
Specific Transcript ◽  
Specific Manner

ferT is a testis-specific transcript of FER encoding a truncated version of the potential tyrosine kinase. Using in situ hybridization analysis, we found that ferT was transiently expressed during spermatogenesis and that expression was restricted to spermatocytes at the pachytene stage of meiotic prophase. This pattern of expression is unprecedented by other tyrosine kinases and suggests a role for ferT in a particular stage of spermatogenesis.

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