scholarly journals Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

2018 ◽  
Author(s):  
EE Burke ◽  
JG Chenoweth ◽  
JH Shin ◽  
L Collado-Torres ◽  
SK Kim ◽  
...  
Keyword(s):  
Neuronal Differentiation ◽  
Gene Networks ◽  
Splice Variants ◽  
Neuronal Cultures ◽  
Human Brain Tissue ◽  
Specific Expression ◽  
Individual Transcript ◽  
Human Neurons ◽  
Cell Type Specific Expression ◽  
Induced Pluripotent

SummaryHuman induced pluripotent stem cells (hiPSCs) are a powerful model of neural differentiation and maturation. We present a hiPSC transcriptomics resource on corticogenesis from 5 iPSC donor and 13 subclonal lines across nine time points over 5 broad conditions: self-renewal, early neuronal differentiation, neural precursor cells (NPCs), assembled rosettes, and differentiated neuronal cells that were validated using electrophysiology. We identified widespread changes in the expression of individual transcript features and their splice variants, gene networks, and global patterns of transcription. We next demonstrated that co-culturing human NPCs with rodent astrocytes resulted in mutually synergistic maturation, and that cell type-specific expression data can be extracted using only sequencing read alignments without potentially disruptive cell sorting. We lastly developed and validated a computational tool to estimate the relative neuronal maturity of iPSC-derived neuronal cultures and human brain tissue, which were maturationally heterogeneous but contained subsets of cells most akin to adult human neurons.

scholarly journals HIV-1: To Splice or Not to Splice, That Is the Question

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 181
Author(s):  
Ann Emery ◽  
Ronald Swanstrom
Keyword(s):  
Full Length ◽  
Regulatory Sequences ◽  
Supporting Evidence ◽  
Control Mechanisms ◽  
Genomic Rna ◽  
Cis Acting ◽  
Splicing Regulators ◽  
Individual Transcript ◽  
Mrna Transcripts ◽  
Hiv 1

The transcription of the HIV-1 provirus results in only one type of transcript—full length genomic RNA. To make the mRNA transcripts for the accessory proteins Tat and Rev, the genomic RNA must completely splice. The mRNA transcripts for Vif, Vpr, and Env must undergo splicing but not completely. Genomic RNA (which also functions as mRNA for the Gag and Gag/Pro/Pol precursor polyproteins) must not splice at all. HIV-1 can tolerate a surprising range in the relative abundance of individual transcript types, and a surprising amount of aberrant and even odd splicing; however, it must not over-splice, which results in the loss of full-length genomic RNA and has a dramatic fitness cost. Cells typically do not tolerate unspliced/incompletely spliced transcripts, so HIV-1 must circumvent this cell policing mechanism to allow some splicing while suppressing most. Splicing is controlled by RNA secondary structure, cis-acting regulatory sequences which bind splicing factors, and the viral protein Rev. There is still much work to be done to clarify the combinatorial effects of these splicing regulators. These control mechanisms represent attractive targets to induce over-splicing as an antiviral strategy. Finally, splicing has been implicated in latency, but to date there is little supporting evidence for such a mechanism. In this review we apply what is known of cellular splicing to understand splicing in HIV-1, and present data from our newer and more sensitive deep sequencing assays quantifying the different HIV-1 transcript types.

scholarly journals TREND-DB – A Transcriptome-wide Atlas of the Dynamic Landscape of Alternative Polyadenylation

2020 ◽  
Author(s):  
Federico Marini ◽  
Denise Scherzinger ◽  
Sven Danckwardt
Keyword(s):  
Gene Regulation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Therapeutic Potential ◽  
Alternative Polyadenylation ◽  
Functional Enrichment ◽  
Rna Modifications ◽  
Posttranscriptional Gene Regulation ◽  
Individual Transcript ◽  
Dynamic Landscape

AbstractAlternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3’end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3’end maturation is closely linked to transcription, RNA processing, and even epigenetic (histone/DNA/RNA) modifications. Here we present TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), a resource cataloging the dynamic landscape of APA after depletion of >170 proteins involved in various facets of transcriptional, co- and posttranscriptional gene regulation, epigenetic modifications, and further processes. TREND-DB visualizes the dynamics of transcriptome 3’end diversification (TREND) in a highly interactive manner; it provides a global APA network map and allows interrogating genes affected by specific APA-regulators, and vice versa. It also permits condition-specific functional enrichment analyses of APA-affected genes, which suggest wide biological and clinical relevance across all RNAi conditions. The implementation of the UCSC Genome Browser provides additional customizable layers of gene regulation accounting for individual transcript isoforms (e.g. epigenetics, miRNA binding sites, RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps to identify their diagnostic and therapeutic potential.

scholarly journals Assembly, Annotation, and Integration of UNIGENE Clusters into the Human Genome Draft

2001 ◽  
Vol 11 (5) ◽  
pp. 904-918
Author(s):  
Degen Zhuo ◽  
Wei D. Zhao ◽  
Fred A. Wright ◽  
Hee-Yung Yang ◽  
Jian-Ping Wang ◽  
...  
Keyword(s):  
Human Genome ◽  
Positional Cloning ◽  
Physical Map ◽  
Sequence Contigs ◽  
New Genes ◽  
Human Genes ◽  
Individual Transcript ◽  
Genome Draft ◽  
Human Transcript ◽  
The Individual

The recent release of the first draft of the human genome provides an unprecedented opportunity to integrate human genes and their functions in a complete positional context. However, at least three significant technical hurdles remain: first, to assemble a complete and nonredundant human transcript index; second, to accurately place the individual transcript indices on the human genome; and third, to functionally annotate all human genes. Here, we report the extension of the UNIGENE database through the assembly of its sequence clusters into nonredundant sequence contigs. Each resulting consensus was aligned to the human genome draft. A unique location for each transcript within the human genome was determined by the integration of the restriction fingerprint, assembled genomic contig, and radiation hybrid (RH) maps. A total of 59,500 UNIGENE clusters were mapped on the basis of at least three independent criteria as compared with the 30,000 human genes/ESTs currently mapped in Genemap'99. Finally, the extension of the human transcript consensus in this study enabled a greater number of putative functional assignments than the 11,000 annotated entries in UNIGENE. This study reports a draft physical map with annotations for a majority of the human transcripts, called the Human Index of Nonredundant Transcripts (HINT). Such information can be immediately applied to the discovery of new genes and the identification of candidate genes for positional cloning.

scholarly journals TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation

2020 ◽  
Vol 49 (D1) ◽  
pp. D243-D253
Author(s):  
Federico Marini ◽  
Denise Scherzinger ◽  
Sven Danckwardt
Keyword(s):  
Gene Regulation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Therapeutic Potential ◽  
Alternative Polyadenylation ◽  
Functional Enrichment ◽  
Rna Modifications ◽  
Individual Transcript ◽  
Dynamic Landscape ◽  
Transcriptional Gene Regulation

Abstract Alternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3′ end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3′ end maturation is closely linked to transcription, RNA processing and even epigenetic (histone/DNA/RNA) modifications. Here, we present TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), a resource cataloging the dynamic landscape of APA after depletion of >170 proteins involved in various facets of transcriptional, co- and post-transcriptional gene regulation, epigenetic modifications and further processes. TREND-DB visualizes the dynamics of transcriptome 3′ end diversification (TREND) in a highly interactive manner; it provides a global APA network map and allows interrogating genes affected by specific APA-regulators and vice versa. It also permits condition-specific functional enrichment analyses of APA-affected genes, which suggest wide biological and clinical relevance across all RNAi conditions. The implementation of the UCSC Genome Browser provides additional customizable layers of gene regulation accounting for individual transcript isoforms (e.g. epigenetics, miRNA-binding sites and RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps identify their diagnostic and therapeutic potential.

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