scholarly journals Multiple Alternative Promoters and Alternative Splicing Enable Universal Transcription-Based Logic Computation in Mammalian Cells

Cell Reports ◽  
2020 ◽  
Vol 33 (9) ◽  
pp. 108437
Author(s):  
Jiten Doshi ◽  
Katie Willis ◽  
Angela Madurga ◽  
Christoph Stelzer ◽  
Yaakov Benenson
Keyword(s):  
Alternative Splicing ◽  
Mammalian Cells ◽  
Alternative Promoters ◽  
Logic Computation ◽  
Multiple Alternative

scholarly journals Design and application of circular RNAs with protein-sponge function

2020 ◽  
Vol 48 (21) ◽  
pp. 12326-12335
Author(s):  
Silke Schreiner ◽  
Anna Didio ◽  
Lee-Hsueh Hung ◽  
Albrecht Bindereif
Keyword(s):  
Alternative Splicing ◽  
Mammalian Cells ◽  
Regulatory Networks ◽  
Rna Binding ◽  
Molecular Medicine ◽  
Circular Rnas ◽  
Ca Repeat ◽  
New Strategy ◽  
Nuclear Ribonucleoprotein ◽  
Splicing Patterns

Abstract Circular RNAs (circRNAs) are a class of noncoding RNAs, generated from pre-mRNAs by circular splicing of exons and functionally largely uncharacterized. Here we report on the design, expression, and characterization of artificial circRNAs that act as protein sponges, specifically binding and functionally inactivating hnRNP (heterogeneous nuclear ribonucleoprotein) L. HnRNP L regulates alternative splicing, depending on short CA-rich RNA elements. We demonstrate that designer hnRNP L-sponge circRNAs with CA-repeat or CA-rich sequence clusters can efficiently and specifically modulate splicing-regulatory networks in mammalian cells, including alternative splicing patterns and the cellular distribution of a splicing factor. This new strategy can in principle be applied to any RNA-binding protein, opening up new therapeutic strategies in molecular medicine.

scholarly journals Expression of Multiple UNC-13 Proteins in theCaenorhabditis elegans Nervous System

2000 ◽  
Vol 11 (10) ◽  
pp. 3441-3452 ◽  
Author(s):  
Rebecca Eustance Kohn ◽  
Janet S. Duerr ◽  
John R. McManus ◽  
Angie Duke ◽  
Terese L. Rakow ◽  
...  
Keyword(s):  
Nervous System ◽  
Alternative Splicing ◽  
Neurotransmitter Release ◽  
Null Allele ◽  
Alternative Promoters ◽  
Cellular Functions ◽  
Deletion Allele ◽  
Transgenic Expression ◽  
C Elegans ◽  
Entire Gene

The Caenorhabditis elegans UNC-13 protein and its mammalian homologues are important for normal neurotransmitter release. We have identified a set of transcripts from the unc-13locus in C. elegans resulting from alternative splicing and apparent alternative promoters. These transcripts encode proteins that are identical in their C-terminal regions but that vary in their N-terminal regions. The most abundant protein form is localized to most or all synapses. We have analyzed the sequence alterations, immunostaining patterns, and behavioral phenotypes of 31 independentunc-13 alleles. Many of these mutations are transcript-specific; their phenotypes suggest that the different UNC-13 forms have different cellular functions. We have also isolated a deletion allele that is predicted to disrupt all UNC-13 protein products; animals homozygous for this null allele are able to complete embryogenesis and hatch, but they die as paralyzed first-stage larvae. Transgenic expression of the entire gene rescues the behavior of mutants fully; transgenic overexpression of one of the transcripts can partially compensate for the genetic loss of another. This finding suggests some degree of functional overlap of the different protein products.

scholarly journals AUGmenting the proteome: Novel initiation codons and their role in protein isoform generation

2015 ◽  
Vol 37 (2) ◽  
pp. 19-23
Author(s):  
Mark J. Coldwell ◽  
Joanne L. Cowan
Keyword(s):  
Alternative Splicing ◽  
Translation Initiation ◽  
Messenger Rna ◽  
Genetic Material ◽  
Protein Sequencing ◽  
Protein Isoforms ◽  
Alternative Promoters ◽  
Alternative Translation ◽  
Initial Hypothesis ◽  
Protein Isoform

As the field of molecular biology developed, and the understanding of how inherited genetic material results in the expression of proteins was established, the initial hypothesis was that one gene gave rise to one protein1. As researchers delved deeper into the organization of the genetic code and advances in messenger RNA (mRNA) and protein sequencing were subsequently made, it has become abundantly clear that multiple mechanisms exist meaning that many mRNAs encode more than one version of a protein. Although alternative promoters and alternative splicing play a considerable role in the generation of protein isoforms, in this article we discuss how usage of alternative translation initiation codons in eukaryotes can also lead to an expanded proteome.

scholarly journals Given Dimensions of Neoplastic Events as Aberrantly Operative Alternative Splicing

2010 ◽  
Vol 2010 ◽  
pp. 1-5
Author(s):  
Lawrence M. Agius
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Molecular Characterization ◽  
Malignant Transformation ◽  
The Real ◽  
Tumor Lesion ◽  
Neoplastic Process ◽  
Multiple Alternative ◽  
The Given

The provision of dynamic splicing events constitutes the reflected nature of neoplasia that locally infiltrates and systemically spreads in terms of evolutionary attributes of the primary and various secondary pathways in malignant transformation. The significant diversity in molecular characterization of the given tumor lesion would adaptively conform to dynamics of splicing as enhanced or silenced exons of the premessenger RNA molecule. The proteins synthesized are in turn potential modifiers in further gene expression within such contexts as RNA:protein and RNA:DNA binding events. The recognition of pathways of incremental scope would underline the development of lesions, such as tumors, as multiple alternative splicing phenomena primarily affecting molecular physicochemical identity. It is within contexts of operative intervention and modification that the real identity of the malignant neoplastic process arises, within terms of reference of contextual splicing events. Disrupted gene expression is thus a referential pathway in the modification of splicing that may prove constitutive or alternative, in first instance, but also aberrant as the lesion progresses locally and systemically.

Multiple Alternative Splicing Markers for Ovarian Cancer

2008 ◽  
Vol 68 (3) ◽  
pp. 657-663 ◽  
Author(s):  
Roscoe Klinck ◽  
Anne Bramard ◽  
Lyna Inkel ◽  
Geneviève Dufresne-Martin ◽  
Julien Gervais-Bird ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Alternative Splicing ◽  
Multiple Alternative

The mRNA encoding TAFI is alternatively spliced in different cell types and produces intracellular forms of the protein lacking TAFIa activity

2013 ◽  
Vol 109 (06) ◽  
pp. 1033-1044 ◽  
Author(s):  
Joellen H. H. Lin ◽  
Dragana Novakovic ◽  
Christina M. Rizzo ◽  
Branislava Zagorac ◽  
Mathieu Garand ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Mammalian Cells ◽  
Mononuclear Cells ◽  
Recombinant Expression ◽  
Cell Types ◽  
Coagulation Cascade ◽  
Peptidase Activity ◽  
Peripheral Blood Mononuclear ◽  
Mrna Variant ◽  
Alternatively Spliced

SummaryTAFI (thrombin-activatable fibrinolysis inhibitor) is a pro-carboxypeptidase, encoded by the CPB2 gene in humans that links the coagulation cascade to fibrinolysis and inflammation. The liver is the main source for plasma TAFI, and TAFI expression has been documented in platelets and monocyte-derived macrophages. A recent study reported an alternatively spliced CPB2 mRNA variant lacking exon 7 (Δ7) in HepG2 cells and liver. Another study identified a CPB2 mRNA variant lacking exon 7 and a 52 bp deletion in exon 11 (Δ7+11) in human hippocampus. We have examined alternative splicing of CPB2 mRNA in various cell types by RT-PCR and have assessed the functional properties of TAFI variants encoded by these transcripts by recombinant expression in mammalian cells. We identified the Δ7 exon skipping event in liver, Dami megakaryoblasts, THP-1-derived macrophages, peripheral blood mononuclear cells, platelets, testis, cerebellum, and SH-SY5Y neuroblastoma cells. The Δ11 alternative splicing event was notably absent in liver cells. We also detected a novel exon Δ7+8 skipping event in liver and megakaryocytes. Of note, we detected non-alternatively spliced CPB2 transcripts in brain tissues, suggesting the expression of full-length TAFI in brain. Experiments using cultured mammalian cells transfected with wild-type CPB2-, Δ7-, Δ7+11 -, and_Δ11 -cDNA revealed that alternatively spliced TAFI is stored inside the cells, cannot be activated by thrombin-thrombomodulin, and does not have TAFIa activity. The alternative splicing events clearly do not give rise to a secreted protein with basic carboxy-peptidase activity, but the intracellular forms may possess novel functions related to intracellular proteolysis.

Multiple alternative splicing of mouse Dmrt1 during gonadal differentiation

2007 ◽  
Vol 352 (3) ◽  
pp. 630-634 ◽  
Author(s):  
Heng Lu ◽  
Xiao Huang ◽  
Liao Zhang ◽  
Yiqing Guo ◽  
Hanhua Cheng ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Gonadal Differentiation ◽  
Multiple Alternative

scholarly journals Author Correction: Synthetic RNA-based logic computation in mammalian cells

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Satoshi Matsuura ◽  
Hiroki Ono ◽  
Shunsuke Kawasaki ◽  
Yi Kuang ◽  
Yoshihiko Fujita ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Logic Computation

scholarly journals Tissue-dependent expression of heat shock factor 2 isoforms with distinct transcriptional activities.

1995 ◽  
Vol 15 (10) ◽  
pp. 5288-5293 ◽  
Author(s):  
M L Goodson ◽  
O K Park-Sarge ◽  
K D Sarge
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Mammalian Cells ◽  
Protein Gene ◽  
Heat Shock Factor ◽  
Dependent Manner ◽  
Heat Shock Protein Gene ◽  
Mouse Tissues

Heat shock factor 2 (HSF2) functions as a transcriptional regulator of heat shock protein gene expression in mammalian cells undergoing processes of differentiation and development. Our previous studies demonstrated high regulated expression and unusual constitutive DNA-binding activity of the HSF2 protein in mouse testes, suggesting that HSF2 functions to regulate heat shock protein gene expression in spermatogenic cells. The purpose of this study was to test whether HSF2 regulation in testes is associated with alterations in the HSF2 polypeptide expressed in testes relative to other mouse tissues. Our results show that mouse cells express not one but two distinct HSF2 proteins and that the levels of these HSF2 isoforms are regulated in a tissue-dependent manner. The testes express predominantly the 71-kDa HSF2-alpha isoform, while the heart and brain express primarily the 69-kDa HSF2-beta isoform. These isoforms are generated by alternative splicing of HSF2 pre-mRNA, which results in the inclusion of an 18-amino-acid coding sequence in the HSF2-alpha mRNA that is skipped in the HSF2-beta mRNA. HSF2 alternative splicing is also developmentally regulated, as our results reveal a switch in expression from the HSF2-beta mRNA isoform to the HSF2-alpha isoform during testis postnatal developmental. Transfection analysis shows that the HSF2-alpha protein, the predominant isoform expressed in testis cells, is a more potent transcriptional activator than the HSF2-beta isoform. These results reveal a new mechanism for the control of HSF2 function in mammalian cells, in which regulated alternative splicing is used to modulate HSF2 transcriptional activity in a tissue-dependent manner.

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