12 papers · ranked by Valyu relevance
Mar Gonzàlez-Porta, Adam Frankish, Johan Rung, Jennifer Harrow + 1 more
'Alvis Brazma'] Background RNA sequencing has opened new avenues for the study of transcriptome composition. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts. However, it is still not clear to what extent this diversity prevails…
Jianfei Hu, Eli Boritz, William Wylie, Daniel C. Douek + 1 more
The dominance of the major transcript isoform relative to other isoforms from the same gene generated by alternative splicing (AS) is essential to the maintenance of normal cellular physiology. However, the underlying principles that determine such dominance remain unknown. Here, we analyzed the physical AS process and…
Kuo-Feng Tung, Chao-Yu Pan, Wen-chang Lin
The discovery and quantification of mRNA transcripts using short-read next-generation sequencing (NGS) data is a complicated task. There are far more alternative mRNA transcripts expressed by human genes than can be identified from NGS transcriptome data and various bioinformatic pipelines, while the numbers of…
Benpeng Miao, Xinlong Luo, Amina Ademovic, Yushan Yang + 2 more
Transposable elements (TEs) are vital components of eukaryotic genomes and have played a critical role in genome evolution. Although most TEs are silenced in the mammalian genome, increasing evidence suggests that certain TEs are actively involved in gene regulation during early developmental stages. However, the…
Yusuke Suenaga, Hiroyuki Kogashi, Kazuma Nakatani, Jason Lin + 10 more
Cancer cells express unique RNA transcripts; however, the factors determining their translation have remained unclear. We recently developed open reading frame (ORF) dominance as a measure that correlates with coding potential of RNAs. Upon calculating the ORF dominance of cancer-specific transcripts across 24 human…
N. Burghgraeve, S. Simon, S. Barral, I. Fobis-Loisy + 5 more
Small RNAs (sRNA) are central regulators of gene expression, yet identifying the molecular alphabet of sRNA-target interactions remains challenging. Here, we take advantage of the dominance hierarchy among self-incompatibility alleles in Arabidopsis halleri to evaluate the base-pairing requirements for effective…
Carlos Alfonso-Gonzalez, Ivano Legnini, Sarah Holec, Laura Arrigoni + 7 more
'Hasan Can Ozbulut' 'Fernando Mateos' 'David Koppstein' 'Agnieszka Rybak-Wolf' 'Ulrike Bönisch' 'Nikolaus Rajewsky' 'Valérie Hilgers'] Title: Summary The generation of distinct messenger RNA isoforms through alternative RNA processing modulates the expression and function of genes, often in a cell-type-specific manner.…
Adam Porter, Norman Johnson, Alexander Y. Tulchinsky
We report a new mechanism for allelic dominance in regulatory genetic interactions that we call binding dominance. We investigated a biophysical model of gene regulation, where the fractional occupancy of a transcription factor (TF) on the cis-regulated promoter site it binds to is determined by binding energy (–ΔG)…
Alex McCann, Jieqiong Lou, Mehdi Moustaqil, Ailisa Blum + 10 more
Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism…
Nevena Cvetesic, Malgorzata Borkowska, Yuki Hatanaka, Changwei Yu + 6 more
Core promoters integrate regulatory inputs of genes^1–3^. Global dynamics of promoter usage can reveal systemic changes in how genomic sequence is interpreted by the cell^4^ Here we report the first analysis of promoter dynamics and code switching in the mammalian germ line, characterising the full cycle of transitions…
Murat Bastepe
The currently estimated number of genes in the human genome is much smaller than previously predicted. As an explanation for this disparity, most individual genes have multiple transcriptional units that represent a variety of biologically important gene products. GNAS exemplifies a gene of such complexity. One of its…
Karl Grieshop, Eddie K. H. Ho, Katja R. Kasimatis
The last decade has seen increasing theoretical and empirical support for beneficial reversals of dominance enabling selection to maintain genetic variation for fitness through various forms of genetic tradeoffs. Dominance reversals are characterized by the beneficial allele for a given context (e.g., niche, time…