Alternative splicing

Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability.

11p vimichaelfaraday 25-03-2022 20 1   Download

Heterogeneous nuclear ribonucleoprotein (HNRNP) A1 and A2 are the most abundant HNRNPs with nearly identical functions, and play important roles in regulating gene expression at multiple levels (i.e. transcription, posttranscription, and translation). However, the expression and regulation mechanism of HNRNPA1 and A2 themselves remain unclear. In this study, the amino acid sequences of HNRNPA1 and HNRNPA2 were compared and found to have 78% and 86% homology in key functional domains.

10p thiencuuchu 27-11-2021 10 1   Download

1976, Walter Fiers và cộng sự → trình tự hoàn chỉnh một RNA virus 1977, Richard Roberts và Phillip Sharp → alternative splicing 1986, Thomas R. Cech → self-splicing Kary Mullis → kỹ thuật PCR 1989, Thomas R. Cech và Sydney Altman → ribozyme 1990s, các cơ chế RNA antisense và RNA interference

27p htc_12 13-05-2013 112 32   Download

The heterogeneous nuclear ribonucleoprotein (hnRNP) type I, a modulator of alternative splicing, localizes in the nucleoplasm of mammalian cells and in a discrete perinucleolar structure. HnRNP I contains a novel type of bipartite nuclear localization signal (NLS) at the N-terminus of the protein that we have previously named nuclear determinant localization type I (NLD-I). Recently, a neural counterpart of hnRNP I has been identified that contains a putative NLS with two strings of basic amino acids separated by a spacer of 30 residues....

8p system191 01-06-2013 25 3   Download

Hepatopoietin (HPO) is a novel human hepatotrophic growth factor. Recently, we demonstrated that the extra-cellular ligand form of HPO can stimulate proliferation of hepatic cells via its specific receptor, which is on the surface of these cells.Also, the intracellular formofHPOpotentiates the transcriptional factor AP-1. Intriguingly, a variety of HPO complexes with different molecular masses were detected in hepatocytes.

6p research12 23-04-2013 25 5   Download

E2F transcription factors play an important role in the regulation of cell cycle progression. E2F6, the most recently identified member of the E2F family, is a retinoblastoma-protein-independent transcriptional repressor that is required for developmental patterning of the axial skeleton. It has recently been shown that theE2f6locus produces two different mRNAs, E2F6 and E2F6b. The E2F6b mRNA contains an additional exon that is inserted by alternative splicing.

7p tumor12 22-04-2013 32 1   Download

The intracellular role of placental protein 17b (PP17b)/ TIP47has been controversial, because it is considered tobe a protein required for mannose 6-phosphate receptor trans-port from endosome totrans-Golgi as well as a neutral lipid droplet-associatedprotein.The similaritybetween theamino acid sequences of PP17 variants, adipophilin and perilipins, andbetween their gene structures indicate that PP17baswell as other alternatively spliced PP17 variants belong to the lipid storage droplet protein family, containing also some differentiation factors....

13p tumor12 20-04-2013 38 3   Download

PSA (prostate-specific antigen), the most useful serum marker for prostate cancer, is encoded by thehKLK3gene and is present in the serumas amixture of several molecular species. This work was performed to identify the hKLK3 transcripts in order to determine how many proteins resembling PSA are synthesized from thehKLK3gene and secreted in blood. Combined Northern blotting, molecular cloninganddatabase searching showed that thehKLK3gene produces at least 15 transcripts ranging in size from 0.7 to 6.1 kb. Polysomal distribution analysis revealed that the transcripts shorter than 3.

9p tumor12 20-04-2013 54 2   Download

TheRel/NF-jBfamilyof transcription factorsplaykey roles in morphogenesis and immune responses. We reported previously that As-rel1 and As-rel2 of the ascidianHalo-cynthia roretziare involved in notochord formation. The As-rel1 protein is a typical Rel/NF-jB family member, whereas the As-rel2 protein is a novel truncated product of As-rel1 that lacks a nuclear localization signal and the unique C-terminal region. Here, we present conclusive evi-dence that As-rel1 and As-rel2 are generated from a single gene by alternative splicing....

10p fptmusic 12-04-2013 39 2   Download

Regulator of G protein signaling (RGS) proteins act as GTPase-activating proteins (GAPs) for Gasubunits and negatively regulate G protein-coupled receptor signaling. Using RGS5 gene-specific RT-PCR, we have identified a novel alternative splicing variant of RGS5 mRNA in human ocular tissues. The alternative splicing of RGS5 mRNA occurred at position +44 (GenBank NM_003617), spliced out 174 bp (+44 to +218 bp) of the cod-ing region, and encoded an RGS5s protein with a 108 amino acid N-ter-minal deletion. ...

0p awards 05-04-2013 36 2   Download

Interaction of cytokines with their cognate receptors leads to the activation of latent transcription factors, the signal transducer and activator of transcription (STAT) proteins. Numerous studies have identified the critical roles played by STAT proteins in regulating cell proliferation, differ-entiation and survival. Consequently, the activity of STAT proteins is negatively regulated by a variety of different mechanisms, which include alternative splicing, covalent modifications, protein–protein interactions with negative regulatory proteins and proteolytic processing by pro-teases....

8p awards 05-04-2013 38 4   Download

Eukaryotic initiation factor (eIF) 4B is part of the protein complex involved in the recognition and binding of mRNA to the ribosome. Drosophila eIF4Bis a single-copy gene that encodes two isoforms, termed eIF4B-L (52.2 kDa) and eIF4B-S (44.2 kDa), generated as a result of the alternative recognition of two polyadeynlation signals during tran-scription termination and subsequent alternative splicing of the two pre-mRNAs. Both eIF4B mRNAs and proteins are expressed during the entire embryogenesis and life cycle....

14p dell39 03-04-2013 36 4   Download

A homologue of interleukin 18 has been identified from rainbow trout,Oncorhynchus mykiss. The trout IL-18gene spans 3.7 kb and consists of six exons and five introns, sharing the same gene organization with its human coun-terpart. The putative translated protein is 199 amino acids in length with no predicted signal peptide. Analysis of the multiple sequence alignment reveals a conserved ICE cut site, resulting in a mature peptide of 162 amino acids. The trout IL-18 shares 41–45% similarity with known IL-18 molecules and contains an IL-1 family signature motif....

11p dell39 03-04-2013 53 3   Download

Acetylcholinesterase subunits of type T (AChET) possess an alternatively spliced C-terminal peptide (t peptide) which endows them with amphiphilic properties, the capacity to form various homo-oligomers and to associate, as a tetra-mer, with anchoring proteins containing a proline rich attachment domain (PRAD). The t peptide contains seven conserved aromatic residues.

15p dell39 03-04-2013 39 3   Download

We used differential scanning calorimetry (DSC) and circular dichroism (CD) to investigate thermal unfolding of recombinant fibroblast isoforms ofa-tropomyosin (Tm) in comparison with that of smooth muscle Tm. These two nonmuscle Tm isoforms 5a and 5b differ internally only by exons 6b⁄6a, and they both differ from smooth muscle Tm by the N-terminal exon 1b which replaces the muscle-specific exons 1a and 2a.

13p dell39 27-03-2013 39 3   Download

G-protein-coupled receptor kinases (GRK) are known to phosphorylate agonist-occupied G-protein-coupled receptors. We expressed and function-ally characterized mouse GRK6 proteins encoded by four distinct mRNAs generated by alternative RNA splicing from a single gene, mGRK6-A to mGRK6-D.

13p dell39 27-03-2013 41 4   Download

VRK is a new kinase family of unknown function. Endogenous human vacinia-related kinase 2 (VRK2) protein is present in both the nucleus and the cytosol, which is a consequence of alternative splicing of two VRK2 messages coding for proteins of 508 and 397 amino acids, respectively.

18p inspiron33 26-03-2013 47 5   Download

The human kallikrein (KLK) family consists of 15 genes located on human chromosome 19q13.4. KLK11⁄hippostasin is a member of the kallikrein family and is expressed in various tissues. Two types of KLK11 isoforms, isoform 1 and isoform 2, have been predicted from cDNA sequences. Iso-form 1 has been isolated from human hippocampus, whereas isoform 2 has been isolated from prostate.

9p inspiron33 25-03-2013 41 4   Download

Activation of the superoxide-producing NADPH oxidase Nox1 requires both the organizer protein Noxo1 and the activator protein Noxa1. Here we describe an alternative splicing form of Noxo1, Noxo1c, which is expressed in the testis and fetal brain.

15p inspiron33 25-03-2013 33 2   Download

We recently cloned a novel osmotic stress transcription factor 1 (OSTF1) from gills of euryhaline tilapia (Oreochromis mossambicus) and demonstra-ted that acute hyperosmotic stress transiently increases OSTF1 mRNA and protein abundance [Fiol DF, Ku¨ltz D (2005) Proc Natl Acad Sci USA 102, 927–932].

16p inspiron33 23-03-2013 33 2   Download