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You searched for: Subject "alternative splicing" Remove constraint Subject: "alternative splicing"
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1. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing

Author:
Nicole M. Martinez; Amanda Su; Margaret C. Burns; Julia K. Nussbacher; Cassandra Schaening; Shashank Sathe; Gene W. Yeo; Wendy V. Gilbert
Source:
Molecular cell 2022 v.82 no.3 pp. 645-659.e9
ISSN:
1097-2765
Subject:
alternative splicing,   etc   ; gene expression; humans;     Show all 3 Subjects
Abstract:
... Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine profiling on chromatin-associated RNA from human cells, we identified pseudouridines i ...
DOI:
10.1016/j.molcel.2021.12.023

2. Gene architecture directs splicing outcome in separate nuclear spatial regions

Author:
Luna Tammer; Ofir Hameiri; Ifat Keydar; Vanessa Rachel Roy; Asaf Ashkenazy-Titelman; Noélia Custódio; Itay Sason; Ronna Shayevitch; Victoria Rodríguez-Vaello; José Rino; Galit Lev Maor; Yodfat Leader; Doha Khair; Erez Lieberman Aiden; Ran Elkon; Manuel Irimia; Roded Sharan; Yaron Shav-Tal; Maria Carmo-Fonseca; Gil Ast
Source:
Molecular cell 2022 v.82 no.5 pp. 1021-1034.e8
ISSN:
1097-2765
Subject:
alternative splicing,   etc   ; architecture; cells; environment; exons; games; introns; organizations;     Show all 8 Subjects
Abstract:
... How the splicing machinery defines exons or introns as the spliced unit has remained a puzzle for 30 years. Here, we demonstrate that peripheral and central regions of the nucleus harbor genes with two distinct exon-intron GC content architectures that differ in the splicing outcome. Genes with low GC content exons, flanked by long introns with lower GC content, are localized in the periphery, and ...
DOI:
10.1016/j.molcel.2022.02.001

3. Structural characterization and expression analysis of novel MAPK1 transcript variants with the development of a multiplexed targeted nanopore sequencing approach

Author:
Konstantina Athanasopoulou; Panagiotis G. Adamopoulos; Andreas Scorilas
Source:
international journal of biochemistry & cell biology 2022 v.150 pp. 106272
ISSN:
1357-2725
Subject:
alternative splicing,   etc   ; humans; mitogen-activated protein kinase; nanopores; transcription (genetics);     Show all 5 Subjects
Abstract:
... Mitogen-activated protein kinases (MAPKs) represent a protein family firmly involved in many signaling cascades, regulating a vast spectrum of stimulated cellular processes. Studies have shown that alternatively spliced isoforms of MAPKs play a crucial role in determining the desired cell fate in response to specific stimulations. Although the implication of most MAPKs transcript variants in the M ...
DOI:
10.1016/j.biocel.2022.106272

4. Notch is an alternative splicing gene in brown planthopper, Nilaparvata lugens

Author:
Ding‐Bang Hu; Shuai Xiao; Yefu Wang; Hong‐Xia Hua
Source:
Archives of insect biochemistry and physiology 2022 v.110 no.3 pp. e21894
ISSN:
0739-4462
Subject:
alternative splicing,   etc   ; Nilaparvata lugens; exons; insect biochemistry; phenotype; sensation; transcription (genetics);     Show all 7 Subjects
Abstract:
... Much research has assumed that Notch codes one protein. Then the protein will be cleaved into two parts and regenerates a heterodimers receptor to construct Notch signal pathways to regulate development in the past three decades. Here, we show that Notch in brown planthopper is a complex alternatively spliced gene has at least three transcriptional start sites, four exon skips, and 21 transcriptio ...
DOI:
10.1002/arch.21894

5. Non-canonical splice junction processing increases the diversity of RBFOX2 splicing isoforms

Author:
Sunkyung Choi; Namjoon Cho; Kee K. Kim
Source:
international journal of biochemistry & cell biology 2022 v.144 pp. 106172
ISSN:
1357-2725
Subject:
alternative splicing,   etc   ; biochemistry; cytoplasmic granules; exons; journals; regulatory sequences; sodium arsenite;     Show all 7 Subjects
Abstract:
... The underlying mechanisms of splicing regulation through non-canonical splice junction processing remain largely unknown. Here, we identified two RBFOX2 splicing isoforms by alternative 3' splice site selection of exon 9; the non-canonical splice junction processed RBFOX2 transcript (RBFOX2-N.C.) was expressed by the selection of the 3' splice GG acceptor sequence. The cytoplasmic localization of ...
DOI:
10.1016/j.biocel.2022.106172

6. Ets family proteins regulate the EMT transcription factors Snail and ZEB in cancer cells

Author:
Mai Koizumi Ichikawa; Kaori Endo; Yuka Itoh; Asami Hotta Osada; Yujiro Kimura; Koichiro Ueki; Kunio Yoshizawa; Keiji Miyazawa; Masao Saitoh
Source:
FEBS Open Bio 2022 v.12 no.7 pp. 1353-1364
ISSN:
2211-5463
Subject:
alternative splicing,   etc   ; epithelium; exons; gene expression; mutation; neoplasm progression; post-translational modification; transcription factors;     Show all 8 Subjects
Abstract:
... The epithelial–mesenchymal transition (EMT) is a crucial morphological event that occurs during epithelial tumor progression. Snail and ZEB1/2 (ZEB1 and ZEB2), known as EMT transcription factors, are key regulators of this transition. ZEB1/2 are positively correlated with EMT phenotypes and the aggressiveness of cancers. On the contrary, Snail is also correlated with the aggressiveness of cancers, ...
DOI:
10.1002/2211-5463.13415

7. Engineered U1 snRNAs to modulate alternatively spliced exons

Author:
Samuel T. Hatch; Aaron A. Smargon; Gene W. Yeo
Source:
Methods 2022 v.205 pp. 140-148
ISSN:
1046-2023
Subject:
alternative splicing,   etc   ; dysautonomia; exons; gene transfer; muscular atrophy; muscular dystrophy; small nuclear RNA; therapeutics; transcriptomics;     Show all 9 Subjects
Abstract:
... Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, Duchenne muscular dystrophy, and spinal muscular atrophy. Small nuclear RNA (snRNA) compon ...
DOI:
10.1016/j.ymeth.2022.06.008

8. Identification of Protein Isoforms Using Reference Databases Built from Long and Short Read RNA-Sequencing

Author:
Aidan P. Tay; Joshua J. Hamey; Gabriella E. Martyn; Laurence O. W. Wilson; Marc R. Wilkins
Source:
Journal of proteome research 2022 v.21 no.7 pp. 1628-1639
ISSN:
1535-3907
Subject:
alternative splicing,   etc   ; humans; peptides; protein isoforms; proteome; proteomics; research; sequence analysis; tandem mass spectrometry; transcriptomics;     Show all 10 Subjects
Abstract:
... Alternative splicing can lead to distinct protein isoforms. These can have different functions in specific cells and tissues or in different developmental stages. In this study, we explored whether transcripts assembled from long read, nanopore-based, direct RNA-sequencing (RNA-seq) could improve the identification of protein isoforms in human K562 cells. By comparing with Illumina-based short rea ...
DOI:
10.1021/acs.jproteome.1c00968

9. Molecular identification and function characterization of four alternative splice variants of trim25 in Japanese flounder (Paralichthys olivaceus)

Author:
Yanan Guo; Zhaodi Sun; Yitong Zhang; Guixing Wang; Zhongwei He; Yufeng Liu; Yuqin Ren; Yufen Wang; Yuanshuai Fu; Jilun Hou
Source:
Fish & shellfish immunology 2022 v.120 pp. 142-154
ISSN:
1050-4648
Subject:
alternative splicing,   etc   ; Paralichthys olivaceus; antiviral properties; blood; flounder; innate immunity; interleukin-8; kidneys; liver; organelles; polyinosinic-polycytidylic acid; shellfish;     Show all 12 Subjects
Abstract:
... Trim25 is a member of Tripartite Motif (TRIM) family. Previous studies report that trim25 modulates antiviral activity by activating RIG-I. In this study we explored the four alternative splicing (AS) variants X1-X4 of Japanese flounder trim25. The sequences of the AS variants were highly conserved. Expression levels of trim25 X1-X4 were increased after 12 h of poly I:C treatment in vitro. In vivo ...
DOI:
10.1016/j.fsi.2021.11.022

10. Identification and validation of a major gene for kernel length at the P1 locus in Triticum polonicum

Author:
Songyue Chai; Qin Yao; Rui Liu; Wenhui Xiang; Xue Xiao; Xing Fan; Jian Zeng; Lina Sha; Houyang Kang; Haiqin Zhang; Dan Long; Dandan Wu; Yonghong Zhou; Yi Wang
Source:
crop journal 2022 v.10 no.2 pp. 387-396
ISSN:
2214-5141
Subject:
alternative splicing,   etc   ; Triticum; brassinosteroids; cultivars; introns; loci; major genes; quantitative polymerase chain reaction; quantitative traits; seeds; sequence deletion; wheat;     Show all 12 Subjects
Abstract:
... Kernel size, one of the traits that determine wheat yield, is controlled by multiple quantitative trait loci. Polish wheat (Triticum polonicum) has elongated and plump kernel and is a valuable material for breeding high-yielding wheat cultivars. However, genes or loci determining kernel length (KL) in Polish wheat are unknown. We identified and validated a major KL gene, KL-PW, at the P1 locus in ...
DOI:
10.1016/j.cj.2021.07.006

11. A MITE variation‐associated heat‐inducible isoform of a heat‐shock factor confers heat tolerance through regulation of JASMONATE ZIM‐DOMAIN genes in rice

Author:
Nai Wu; Yilong Yao; Denghao Xiang; Hao Du; Zedong Geng; Wanneng Yang; Xianghua Li; Tingting Xie; Faming Dong; Lizhong Xiong
Source:
The new phytologist 2022 v.234 no.4 pp. 1315-1331
ISSN:
0028-646X
Subject:
alternative splicing,   etc   ; alleles; genome-wide association study; heat; heat shock proteins; heat stress; heat tolerance; jasmonic acid; leaf area; loci; rice; transposons;     Show all 12 Subjects
Abstract:
... High temperatures cause huge yield losses in rice. Heat‐shock factors (Hsfs) are key transcription factors which regulate the expression of heat stress‐responsive genes, but natural variation in and functional characterization of Hsfs have seldom been reported. A significant heat response locus was detected via a genome‐wide association study (GWAS) using green leaf area as an indicative trait. A ...
DOI:
10.1111/nph.18068

12. hnRNP A/B Proteins: An Encyclopedic Assessment of Their Roles in Homeostasis and Disease

Author:
Patricia A. Thibault; Aravindhan Ganesan; Subha Kalyaanamoorthy; Joseph-Patrick W. E. Clarke; Hannah E. Salapa; Michael C. Levin
Source:
Biology 2021 v.10 no.8 pp. -
ISSN:
2079-7737
Subject:
alternative splicing,   etc   ; RNA; homeostasis; metabolism;     Show all 4 Subjects
Abstract:
... The hnRNP A/B family of proteins is canonically central to cellular RNA metabolism, but due to their highly conserved nature, the functional differences between hnRNP A1, A2/B1, A0, and A3 are often overlooked. In this review, we explore and identify the shared and disparate homeostatic and disease-related functions of the hnRNP A/B family proteins, highlighting areas where the proteins have not b ...
DOI:
10.3390/biology10080712

13. RNA-Seq data of ALKBH5 and FTO double knockout HEK293T human cells

Author:
Egor A. Smolin; Andrey I. Buyan; Dmitry N. Lyabin; Ivan V. Kulakovskiy; Irina A. Eliseeva
Source:
Data in Brief 2022 v.42 pp. 108187
ISSN:
2352-3409
Subject:
alternative splicing,   etc   ; demethylation; epigenetics; gene expression; humans;     Show all 5 Subjects
Abstract:
... N6-methyladenosine (m6A) is the most abundant, highly dynamic mRNA modification that regulates mRNA splicing, stability, and translation. The m6A epigenetic mark is erased by RNA demethylases ALKBH5 (AlkB Homolog 5) and FTO (Fat mass and obesity-associated protein). The ALKBH5 and FTO RNA demethylases recognize m6A in similar nucleotide contexts. Therefore, these proteins can partially substitute ...
DOI:
10.1016/j.dib.2022.108187

14. Alternative Splicing and Hypoxia Puzzle in Alzheimer’s and Parkinson’s Diseases

Author:
Eglė Jakubauskienė; Arvydas Kanopka
Source:
Genes 2021 v.12 no.8 pp. -
ISSN:
2073-4425
Subject:
alternative splicing,   etc   ; angiogenesis; erythropoiesis; genes; humans; hypoxia; neurogenesis;     Show all 7 Subjects
Abstract:
... Alternative pre-mRNA splicing plays a very important role in expanding protein diversity as it generates numerous transcripts from a single protein-coding gene. Therefore, alterations lead this process to neurological human disorders, including Alzheimer’s and Parkinson’s diseases. Moreover, accumulating evidence indicates that the splicing machinery highly contributes to the cells’ ability to ada ...
DOI:
10.3390/genes12081272

15. Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2

Author:
Xiliang Wang; Yao He; Qiming Zhang; Xianwen Ren; Zemin Zhang
Source:
Genomics, proteomics & bioinformatics 2021 v.19 no.2 pp. 253-266
ISSN:
1672-0229
Subject:
alternative splicing,   etc   ; bioinformatics; chromium; genomics; mitochondria; proteomics; sequence analysis; transcriptome;     Show all 8 Subjects
Abstract:
... Single-cell RNA sequencing (scRNA-seq) is generally used for profiling transcriptome of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data ...
DOI:
10.1016/j.gpb.2020.02.005

16. BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments

Author:
Yuanhua Huang; Guido Sanguinetti
Source:
Genome biology 2021 v.22 no.1 pp. 251
ISSN:
1474-760X
Subject:
alternative splicing,   etc   ; RNA; computational methodology; genes; phenotype; technology; transcription (genetics); transcriptomics;     Show all 8 Subjects
Abstract:
... RNA splicing is an important driver of heterogeneity in single cells through the expression of alternative transcripts and as a determinant of transcriptional kinetics. However, the intrinsic coverage limitations of scRNA-seq technologies make it challenging to associate specific splicing events to cell-level phenotypes. BRIE2 is a scalable computational method that resolves these issues by regres ...
DOI:
10.1186/s13059-021-02461-5

17. Identification of novel Taz isoforms and functional comparison in pluripotency maintenance of mouse embryonic stem cells

Author:
Yixiao Xu; Lianlian Liu; Xueyue Wang; Yuyan Huang; Yuda Cheng; Junlei Zhang; Jiali Wang; Yanping Tian; Jiaxiang Xiong; Yi Yang; Bangqi Ren; Wei Wu; Ping He; Yue Zhang; Binyu Zhao; Jiaqi Wang; Meng Yu; Jiangjun Wang; Rui Jian; Yong Liu; Yan Ruan
Source:
Gene 2021 v.773 pp. 145383
ISSN:
0378-1119
Subject:
alternative splicing,   etc   ; apoptosis; binding capacity; embryonic stem cells; genes; mice; phenotype;     Show all 7 Subjects
Abstract:
... Alternative splicing (AS) is a key process to expand the diversity of mRNA and protein from the genome and it is crucial for fate determination of embryonic stem cells (ESCs) by encoding isoforms with different functions to regulate the balance between pluripotency maintenance and differentiation. Since the role of the Hippo pathway in ESCs is controversial, there may be novel isoforms of Taz, a k ...
DOI:
10.1016/j.gene.2020.145383

18. Regulation of alternative splicing of PaFT and PaFDL1, the FT and FD homologs in Platanus acerifolia

Author:
Changsheng Shao; Fangfang Cai; Yanping Zhang; Zhiru Bao; Gehui Shi; Manzhu Bao; Jiaqi Zhang
Source:
Gene 2022 v.830 pp. 146506
ISSN:
0378-1119
Subject:
alternative splicing,   etc   ; Platanus acerifolia; exons; introns; loci; protein isoforms; site-directed mutagenesis;     Show all 7 Subjects
Abstract:
... Alternative splicing (AS) selects different alternative splice sites and produces a variety of transcripts with different exon/intron combinations, which may result in multiple protein isoforms. The splicing signals include cis-elements and RNA structures; however, the mechanisms of AS regulation in plants have yet to be elucidated. Previous studies have shown that in Platanus acerifolia, the FLOW ...
DOI:
10.1016/j.gene.2022.146506

19. Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana

Author:
Ibtissam Jabre; Saurabh Chaudhary; Wenbin Guo; Maria Kalyna; Anireddy S. N. Reddy; Weizhong Chen; Runxuan Zhang; Cornelia Wilson; Naeem H. Syed
Source:
new phytologist 2021 v.229 no.4 pp. 1937-1945
ISSN:
0028-646X
Subject:
alternative splicing,   etc   ; Arabidopsis thaliana; exons; introns; major genes; nucleosomes; sequence analysis; temperature; transcriptome;     Show all 9 Subjects
Abstract:
... Alternative splicing (AS) is a major gene regulatory mechanism in plants. Recent evidence supports co‐transcriptional splicing in plants, hence the chromatin state can impact AS. However, how dynamic changes in the chromatin state such as nucleosome occupancy influence the cold‐induced AS remains poorly understood. Here, we generated transcriptome (RNA‐Seq) and nucleosome positioning (MNase‐Seq) d ...
DOI:
10.1111/nph.17062

20. Full-length codling moth transcriptome atlas revealed by single-molecule real-time sequencing

Author:
Longsheng Xing; Qiang Wu; Yu Xi; Cong Huang; Wanxue Liu; Fanghao Wan; Wanqiang Qian
Source:
Genomics 2022 v.114 no.2 pp. 110299
ISSN:
0888-7543
Subject:
alternative splicing,   etc   ; Cydia pomonella; data collection; genomics; insects; reverse transcriptase polymerase chain reaction; transcriptome;     Show all 7 Subjects
Abstract:
... Over the past decade, second-generation sequencing (SGS) has been widely used to elucidate the transcriptome across many organisms. However, the full-length (FL) transcripts and alternative splice (AS) isoforms could not be confidently and accurately defined with SGS. Pacific biosciences (PacBio) single-molecule real-time sequencing was conducted to obtain FL transcriptome data in the codling moth ...
DOI:
10.1016/j.ygeno.2022.110299