scholarly journals Identifying Splicing Regulatory Elements with de Bruijn Graphs

2014 ◽  
Vol 21 (12) ◽  
pp. 880-897 ◽  
Author(s):  
Eman Badr ◽  
Lenwood S. Heath
Keyword(s):  
Regulatory Elements ◽  
De Bruijn Graphs ◽  
Splicing Regulatory Elements ◽  
De Bruijn

scholarly journals Buffering Updates Enables Efficient Dynamic de Bruijn Graphs

2021 ◽  
Author(s):  
Jarno Alanko ◽  
Bahar Alipanahi ◽  
Jonathen Settle ◽  
Christina Boucher ◽  
Travis Gagie
Keyword(s):  
De Bruijn Graphs ◽  
De Bruijn

scholarly journals Functional characterization of splicing regulatory elements

2021 ◽  
Author(s):  
Scott I Adamson ◽  
Lijun Zhan ◽  
Brenton R Graveley
Keyword(s):  
High Throughput ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Small Subset ◽  
General Sequence ◽  
Splicing Regulators ◽  
Splicing Regulatory Elements

Background: RNA binding protein-RNA interactions mediate a variety of processes including pre-mRNA splicing, translation, decay, polyadenylation and many others. Previous high-throughput studies have characterized general sequence features associated with increased and decreased splicing of certain exons, but these studies are limited by not knowing the mechanisms, and in particular, the mediating RNA binding proteins, underlying these associations. Results: Here we utilize ENCODE data from diverse data modalities to identify functional splicing regulatory elements and their associated RNA binding proteins. We identify features which make splicing events more sensitive to depletion of RNA binding proteins, as well as which RNA binding proteins act as splicing regulators sensitive to depletion. To analyze the sequence determinants underlying RBP-RNA interactions impacting splicing, we assay tens of thousands of sequence variants in a high-throughput splicing reporter called Vex-seq and confirm a small subset in their endogenous loci using CRISPR base editors. Finally, we leverage other large transcriptomic datasets to confirm the importance of RNA binding proteins which we designed experiments around and identify additional RBPs which may act as additional splicing regulators of the exons studied. Conclusions: This study identifies sequence and other features underlying splicing regulation mediated specific RNA binding proteins, as well as validates and identifies other potentially important regulators of splicing in other large transcriptomic datasets.

scholarly journals Cartesian products of graphs as subgraphs of de Bruijn graphs of dimension at least three

1997 ◽  
Vol 79 (1-3) ◽  
pp. 3-34 ◽  
Author(s):  
Thomas Andreae ◽  
Martin Hintz ◽  
Michael Nölle ◽  
Gerald Schreiber ◽  
Gerald W. Schuster ◽  
...  
Keyword(s):  
Cartesian Products ◽  
De Bruijn Graphs ◽  
De Bruijn ◽  
Cartesian Products Of Graphs

scholarly journals Integrating long-range connectivity information into de Bruijn graphs

2018 ◽  
Vol 34 (15) ◽  
pp. 2556-2565 ◽  
Author(s):  
Isaac Turner ◽  
Kiran V Garimella ◽  
Zamin Iqbal ◽  
Gil McVean
Keyword(s):  
Long Range ◽  
De Bruijn Graphs ◽  
Connectivity Information ◽  
De Bruijn
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