Functional consequences of bidirectional promoters

W Wei, V Pelechano, AI Järvelin, LM Steinmetz - Trends in Genetics, 2011 - cell.com
Several studies have shown that promoters of protein-coding genes are origins of pervasive
non-coding RNA transcription and can initiate transcription in both directions. However, only …

[HTML][HTML] The new (dis) order in RNA regulation

AI Järvelin, M Noerenberg, I Davis… - Cell Communication and …, 2016 - Springer
RNA-binding proteins play a key role in the regulation of all aspects of RNA metabolism, from
the synthesis of RNA to its decay. Protein-RNA interactions have been thought to be mostly …

Unconventional RNA‐binding proteins step into the virus–host battlefront

M Garcia‐Moreno, AI Järvelin… - Wiley Interdisciplinary …, 2018 - Wiley Online Library
The crucial participation of cellular RNA‐binding proteins (RBPs) in virtually all steps of virus
infection has been known for decades. However, most of the studies characterizing this …

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

E Ntini, AI Järvelin, J Bornholdt, Y Chen… - Nature structural & …, 2013 - nature.com
Active human promoters produce promoter-upstream transcripts (PROMPTs). Why these
RNAs are coupled to decay, whereas their neighboring promoter-downstream mRNAs are not, …

[HTML][HTML] Assessment of metagenomic assembly using simulated next generation sequencing data

DR Mende, AS Waller, S Sunagawa, AI Järvelin… - PloS one, 2012 - journals.plos.org
Due to the complexity of the protocols and a limited knowledge of the nature of microbial
communities, simulating metagenomic sequences plays an important role in testing the …

[PDF][PDF] Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection

…, M Noerenberg, B Cerikan, H Chen, AI Järvelin… - Molecular Cell, 2021 - cell.com
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus
disease 2019 (COVID-19). SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to …

[PDF][PDF] System-wide profiling of RNA-binding proteins uncovers key regulators of virus infection

M Garcia-Moreno, M Noerenberg, S Ni, AI Järvelin… - Molecular cell, 2019 - cell.com
The compendium of RNA-binding proteins (RBPs) has been greatly expanded by the
development of RNA-interactome capture (RIC). However, it remained unknown if the complement …

Alternative polyadenylation diversifies post‐transcriptional regulation by selective RNA–protein interactions

…, S Clauder‐Münster, B Klaus, AI Järvelin… - Molecular systems …, 2014 - embopress.org
Recent research has uncovered extensive variability in the boundaries of transcript isoforms,
yet the functional consequences of this variation remain largely unexplored. Here, we …

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

S Wilkening, V Pelechano, AI Järvelin… - Nucleic acids …, 2013 - academic.oup.com
The use of alternative poly(A) sites is common and affects the post-transcriptional fate of mRNA,
including its stability, subcellular localization and translation. Here, we present a method …

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters

…, AA Pai, J Herudek, M Lubas, N Meola, AI Järvelin… - Nature …, 2016 - nature.com
Mammalian transcriptomes are complex and formed by extensive promoter activity. In
addition, gene promoters are largely divergent and initiate transcription of reverse-oriented …