An epigenetic role of mitochondria in cancer

Y Liu, C Chen, X Wang, Y Sun, J Zhang, J Chen, Y Shi - Cells, 2022 - mdpi.com
Mitochondria are not only the main energy supplier but are also the cell metabolic center
regulating multiple key metaborates that play pivotal roles in epigenetics regulation. These …

[HTML][HTML] Choosing the right tool for the job: RNAi, TALEN, or CRISPR

M Boettcher, MT McManus - Molecular cell, 2015 - cell.com
The most widely used approach for defining gene function is to reduce or completely disrupt
its normal expression. For over a decade, RNAi has ruled the lab, offering a magic bullet to …

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Y Ji, Z Zhou, H Liu, RV Davuluri - Bioinformatics, 2021 - academic.oup.com
Motivation Deciphering the language of non-coding DNA is one of the fundamental
problems in genome research. Gene regulatory code is highly complex due to the existence …

Cancer transcriptome profiling at the juncture of clinical translation

M Cieślik, AM Chinnaiyan - Nature Reviews Genetics, 2018 - nature.com
Methodological breakthroughs over the past four decades have repeatedly revolutionized
transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to …

Promoter DNA hypermethylation and paradoxical gene activation

J Smith, S Sen, RJ Weeks, MR Eccles, A Chatterjee - Trends in cancer, 2020 - cell.com
DNA methylation is a stable epigenetic modification that contributes to the spatiotemporal
regulation of gene expression. The manner in which DNA methylation contributes to …

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

LW Barrett, S Fletcher, SD Wilton - Cellular and molecular life sciences, 2012 - Springer
There is now compelling evidence that the complexity of higher organisms correlates with
the relative amount of non-coding RNA rather than the number of protein-coding genes …

The landscape of isoform switches in human cancers

K Vitting-Seerup, A Sandelin - Molecular Cancer Research, 2017 - AACR
Alternative usage of transcript isoforms from the same gene has been hypothesized as an
important feature in cancers. However, differential usage of gene transcripts between …

RNA processing and its regulation: global insights into biological networks

DD Licatalosi, RB Darnell - Nature Reviews Genetics, 2010 - nature.com
In recent years views of eukaryotic gene expression have been transformed by the finding
that enormous diversity can be generated at the RNA level. Advances in technologies for …

Distal alternative last exons localize mRNAs to neural projections

JM Taliaferro, M Vidaki, R Oliveira, S Olson, L Zhan… - Molecular cell, 2016 - cell.com
Spatial restriction of mRNA to distinct subcellular locations enables local regulation and
synthesis of proteins. However, the organizing principles of mRNA localization remain …

Direct detection of alternative open reading frames translation products in human significantly expands the proteome

B Vanderperre, JF Lucier, C Bissonnette, J Motard… - PloS one, 2013 - journals.plos.org
A fully mature mRNA is usually associated to a reference open reading frame encoding a
single protein. Yet, mature mRNAs contain unconventional alternative open reading frames …