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Comparative Analysis of Alternative Splicing in Homo sapiens, Mus musculus and Rattus norvegicus Transcriptomes
Bahar Taneri
Jan 01, 0001
Analyzing transcriptomes in the context of all available genome and transcript sequence data has the potential to reveal biologically meaningful insight into functional properties of genes and complexity of genomes. Alternative...
Published by: Rockefeller University
Functional Alleles of Chicken BG Genes, Members of the Butyrophilin Gene Family, in Peripheral T Cells.
B-G B7 family Adaptive Immunity innate immunity Membrane Protein Alleles Alternative Splicing Amino Acid Sequence Animals Butyrophilins Chickens Cloning Molecular Exons Gene Expression Haplotypes Introns Models Molecular Multigene Family Phylogeny Protein Conformation Sequence Analysis DNA Structure-Activity Relationship T-Lymphocytes
A survey of best practices for RNA-seq data analysis.
Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J Gaffney, Laura L Elo, Xuegong Zhang, Ali Mortazavi
Jan 13, 2016
Functional characterization of obesity-associated variants involving the α and β isoforms of human SH2B1.
Laura R Pearce, Ray Joe, Michael E Doche, Hsiao-Wen Su, Julia M Keogh, Elana Henning, Lawrence S Argetsinger, Elena G Bochukova, Joel M Cline, Sumedha Garg, Sadia Saeed, Steven Shoelson, Stephen O'Rahilly, Inês Barroso, Liangyou Rui, I Sadaf Farooqi, Christin Carter-Su
Jul 17, 2014
A Regulatory Axis between Epithelial Splicing Regulatory Proteins and Estrogen Receptor α Modulates the Alternative Transcriptome of Luminal Breast Cancer.
Jamal Elhasnaoui, Giulio Ferrero, Valentina Miano, Lorenzo Franchitti, Isabella Tarulli, Lucia Coscujuela Tarrero, Santina Cutrupi, Michele De Bortoli
Jul 19, 2022
Epithelial splicing regulatory proteins 1 and 2 (ESRP1/2) control the splicing pattern during epithelial to mesenchymal transition (EMT) in a physiological context and in cancer, including breast cancer (BC). Here, we report...
A Regulatory Axis between Epithelial Splicing Regulatory Proteins and Estrogen Receptor α Modulates the Alternative Transcriptome of Luminal Breast Cancer.
Jamal Elhasnaoui, Giulio Ferrero, Valentina Miano, Lorenzo Franchitti, Isabella Tarulli, Lucia Coscujuela Tarrero, Santina Cutrupi, Michele De Bortoli
Sep 02, 2022
Epithelial splicing regulatory proteins 1 and 2 (ESRP1/2) control the splicing pattern during epithelial to mesenchymal transition (EMT) in a physiological context and in cancer, including breast cancer (BC). Here, we report...
EMT splicing signature ESRP1 ESRP2 Rac1 Rac1b Alternative Splicing Breast Cancer Alternative Splicing Breast Neoplasms Cell Line Tumor Epithelial-Mesenchymal Transition Estrogen Receptor alpha Female Gene Expression Regulation Neoplastic Humans RNA-Binding Proteins Transcription Factors Transcriptome
Molecular characterization of cbfβ gene and identification of new transcription variants
The CBFβ gene encodes a transcription factor that, in combination with CBFα (also called Runx, runt-related transcription factor) regulates expression of several target genes. CBFβ interacts with all Runx family members, such...
Molecular characterization of cbfβ gene and identification of new transcription variants
The CBFβ gene encodes a transcription factor that, in combination with CBFα (also called Runx, runt-related transcription factor) regulates expression of several target genes. CBFβ interacts with all Runx family members, such...
Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins.
MB Coelho, DB Ascher, C Gooding, E Lang, H Maude, D Turner, M Llorian, DEV Pires, J Attig, CWJ Smith
Jun 10, 2016
DDX17 Specifically, and Independently of DDX5, Controls Use of the HIV A4/5 Splice Acceptor Cluster and Is Essential for Efficient Replication of HIV.
Nyaradzai Sithole, Claire A Williams, Aisling M Vaughan, Julia C Kenyon, Andrew ML Lever
Sep 10, 2018
A4/A5 3′ splice site cluster DDX17/HIV-1 splicing factors Alternative Splicing Amino Acid Motifs Cell Line Tumor Cells Cultured DEAD-box RNA Helicases Gene Expression Regulation Viral Gene Knockdown Techniques HIV Infections HIV-1 Humans Protein Binding Protein Interaction Domains and Motifs RNA Splice Sites
DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3'-End Usage.
Jamal Elhasnaoui, Valentina Miano, Giulio Ferrero, Elena Doria, Antonette E Leon, Aline SC Fabricio, Laura Annaratone, Isabella Castellano, Anna Sapino, Michele De Bortoli
Aug 21, 2020
DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1...
Essential requirement for polypyrimidine tract binding proteins 1 and 3 in the maturation and maintenance of mature B cells in mice.
The maturation of immature B cells and the survival of mature B cells is stringently controlled to maintain a diverse repertoire of antibody specificities while avoiding self-reactivity. At the molecular level this is regulated...
PTBP1 PTBP3 RNA binding proteins mature B cells posttranscriptional gene expression regulation 3' Untranslated Regions Alternative Splicing Animals B-Lymphocytes Gene Expression Regulation Heterogeneous-Nuclear Ribonucleoproteins Mice Mice Inbred C57BL Mice Knockout Polypyrimidine Tract-Binding Protein Signal Transduction Transcriptome
Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases.
Polypyrimidine tract-binding proteins are essential for B cell development
Elisa Monzón-Casanova, Louise S Matheson, Kristina Tabbada, Kathi Zarnack, Christopher WJ Smith, Martin Turner
Mar 06, 2020
Polypyrimidine tract-binding protein 1 (PTBP1) is a RNA-binding protein (RBP) expressed throughout B cell development. Deletion of Ptbp1 in mouse pro-B cells results in upregulation of PTBP2 and normal B cell development. We...
Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers.
Erick E Nakagaki-Silva, Clare Gooding, Miriam Llorian, Aishwarya G Jacob, Frederick Richards, Adrian Buckroyd, Sanjay Sinha, Christopher WJ Smith
Jun 24, 2019
RNA binding protein Alternative Splicing Chromosomes Gene Expression rat smooth muscle super-enhancer Animals Cell Line Enhancer Elements Genetic Gene Expression Profiling Gene Expression Regulation HEK293 Cells Humans Muscle Smooth Vascular Myocytes Smooth Muscle Nuclear Proteins RNA Interference RNA Splicing RNA-Binding Proteins Rats Trans-Activators
Alternative splicing modifies the effect of mutations in COL11A1 and results in recessive type 2 Stickler syndrome with profound hearing loss.
Allan J Richards, Gregory S Fincham, Annie McNinch, David Hill, Arabella V Poulson, Bruce Castle, Melissa M Lees, Anthony T Moore, John D Scott, Martin P Snead
Sep 22, 2021
BACKGROUND: Stickler syndromes types 1, 2 and 3 are usually dominant disorders caused by mutations in the genes COL2A1, COL11A1 and COL11A2 that encode the fibrillar collagens types II and XI present in cartilage and vitreous....
Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms.
Miguel de la Hoya, Omar Soukarieh, Irene López-Perolio, Ana Vega, Logan C Walker, Yvette van Ierland, Diana Baralle, Marta Santamariña, Vanessa Lattimore, Juul Wijnen, Philip Whiley, Ana Blanco, Michela Raponi, Jan Hauke, Barbara Wappenschmidt, Alexandra Becker, Thomas vO Hansen, Raquel Behar, KConFaB Investigators, Diether Niederacher, Norbert Arnold, Bernd Dworniczak, Doris Steinemann, Ulrike Faust, Wendy Rubinstein, Peter J Hulick, Claude Houdayer, Sandrine M Caputo, Laurent Castera, Tina Pesaran, Elizabeth Chao, Carole Brewer, Melissa C Southey, Christi J van Asperen, Christian F Singer, Jan Sullivan, Nicola Poplawski, Phuong Mai, Julian Peto, Nichola Johnson, Barbara Burwinkel, Harald Surowy, Stig E Bojesen, Henrik Flyger, Annika Lindblom, Sara Margolin, Jenny Chang-Claude, Anja Rudolph, Paolo Radice, Laura Galastri, Janet E Olson, Emily Hallberg, Graham G Giles, Roger L Milne, Irene L Andrulis, Gord Glendon, Per Hall, Kamila Czene, Fiona Blows, Mitul Shah, Qin Wang, Joe Dennis, Kyriaki Michailidou, Lesley McGuffog, Manjeet K Bolla, Antonis C Antoniou, Douglas F Easton, Fergus J Couch, Sean Tavtigian, Maaike P Vreeswijk, Michael Parsons, Huong D Meeks, Alexandra Martins, David E Goldgar, Amanda B Spurdle
May 18, 2016
Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus.
Christopher A Odhams, Andrea Cortini, Lingyan Chen, Amy L Roberts, Ana Viñuela, Alfonso Buil, Kerrin S Small, Emmanouil T Dermitzakis, David L Morris, Timothy J Vyse, Deborah S Cunninghame Graham
Nov 26, 2019
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more...
Alternative Splicing Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor Chromosome Mapping Female Gene Expression Regulation Genetic Predisposition to Disease Genome-Wide Association Study Haplotypes Humans Lupus Erythematosus Systemic Male Polymorphism Single Nucleotide Quantitative Trait Loci RNA Untranslated T Cell Transcription Factor 1
An atlas of mouse CD4(+) T cell transcriptomes.
Michael JT Stubbington, Bidesh Mahata, Valentine Svensson, Andrew Deonarine, Jesper K Nissen, Alexander G Betz, Sarah A Teichmann
May 16, 2019
BACKGROUND: CD4(+) T cells are key regulators of the adaptive immune system and can be divided into T helper (Th) cells and regulatory T (Treg) cells. During an immune response Th cells mature from a naive state into one of...
Alternative Splicing Animals Cell Differentiation Cluster Analysis Flow Cytometry Gene Expression Profiling Gene Expression Regulation Immune System Mice Mice Inbred C57BL principal component analysis Protein Isoforms RNA Messenger Sequence Analysis RNA Signal Transduction T-Lymphocytes Helper-Inducer T-Lymphocytes Regulatory Th17 Cells Transcriptome Up-Regulation
Nanoscale Mobility of the Apo State and TARP Stoichiometry Dictate the Gating Behavior of Alternatively Spliced AMPA Receptors.
G Brent Dawe, Md Fahim Kadir, Raminta Venskutonytė, Amanda M Perozzo, Yuhao Yan, Ryan PD Alexander, Camilo Navarrete, Eduardo A Santander, Marika Arsenault, Christian Fuentes, Mark RP Aurousseau, Karla Frydenvang, Nelson P Barrera, Jette S Kastrup, J Michael Edwardson, Derek Bowie
Apr 16, 2019
Neurotransmitter-gated ion channels are allosteric proteins that switch on and off in response to agonist binding. Most studies have focused on the agonist-bound, activated channel while assigning a lesser role to the apo or...
X-ray crystallography Alternative Splicing Atomic force microscopy channel gating Electrophysiology Ion channel ionotropic glutamate receptor Patch clamp protein conformations synapse Allosteric Regulation Allosteric Site Alternative Splicing Animals cerebellum Cryoelectron Microscopy Crystallography X-Ray HEK293 Cells Humans Ion Channel Gating Membrane Proteins Mice Microscopy Atomic Force Patch-Clamp Techniques Protein Domains Protein Isoforms Protein Structure Quaternary Protein Structure Tertiary Purkinje Cells Receptors AMPA
Splicing predictions, minigene analyses, and ACMG-AMP clinical classification of 42 germline PALB2 splice-site variants.
Alberto Valenzuela-Palomo, Elena Bueno-Martínez, Lara Sanoguera-Miralles, Víctor Lorca, Eugenia Fraile-Bethencourt, Ada Esteban-Sánchez, Susana Gómez-Barrero, Sara Carvalho, Jamie Allen, Alicia García-Álvarez, Pedro Pérez-Segura, Leila Dorling, Douglas F Easton, Peter Devilee, Maaike PG Vreeswijk, Miguel de la Hoya, Eladio A Velasco
Jan 07, 2022
PALB2 loss-of-function variants confer high risk of developing breast cancer. Here we present a systematic functional analysis of PALB2 splice-site variants detected in approximately 113,000 women in the large-scale sequencing...
PALB2 VUS aberrant splicing Breast Cancer clinical interpretation functional assay minigene splicing susceptibility genes Alternative Splicing Biomarkers Tumor Breast Neoplasms Case-Control Studies Databases Genetic Exons Fanconi Anemia Complementation Group N Protein Female Humans MCF-7 Cells Protein Isoforms RNA Splice Sites
Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells.
Li Chen, Ruirui Yang, Tony Kwan, Chao Tang, Stephen Watt, Yiming Zhang, Guillaume Bourque, Bing Ge, Kate Downes, Mattia Frontini, Willem H Ouwehand, Jing-Wen Lin, Nicole Soranzo, Tomi Pastinen, Lu Chen
Nov 09, 2020
Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.
Stephanie M Linker, Lara Urban, Stephen J Clark, Mariya Chhatriwala, Shradha Amatya, Davis J McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle, Marc Jan Bonder
Apr 10, 2019
BACKGROUND: Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied across...
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