Genome-Wide Profiling of Transcription Initiation with STRIPE-seq

Policastro, Robert A.; Zentner, Gabriel E.

doi:10.1007/978-1-0716-2257-5_2

Cited by 2 publications

(1 citation statement)

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“…Isoforms of the same gene may possess different biological functions, e.g., TP73 isoforms whose coding sequence (CDS) includes a transactivation domain are considered apoptotic, while TP73 isoforms whose CDS lacks this transactivation domain, are considered anti-apoptotic [ 204 ]. Quantification of the expression of individual isoforms may be achieved by using methods for profiling the sequence of initiation of transcription [ 205 ] through STRIPE-seq [ 206 ] or Tn5Prime [ 207 ] or by using certain scRNA-Seq methods with increased read mapping across all transcripts and the ability to detect splice variants, such as Smart-seq2 [ 208 ]. Integrating the results of the aforementioned methods into coexpression analysis would facilitate the study of the specific functions of protein isoforms and their coexpressed partners.…”

Section: Limitations and Perspectives In Coexpression Analysismentioning

confidence: 99%

Approaches in Gene Coexpression Analysis in Eukaryotes

Zogopoulos

Saxami

Malatras

et al. 2022

Biology

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Gene coexpression analysis constitutes a widely used practice for gene partner identification and gene function prediction, consisting of many intricate procedures. The analysis begins with the collection of primary transcriptomic data and their preprocessing, continues with the calculation of the similarity between genes based on their expression values in the selected sample dataset and results in the construction and visualisation of a gene coexpression network (GCN) and its evaluation using biological term enrichment analysis. As gene coexpression analysis has been studied extensively, we present most parts of the methodology in a clear manner and the reasoning behind the selection of some of the techniques. In this review, we offer a comprehensive and comprehensible account of the steps required for performing a complete gene coexpression analysis in eukaryotic organisms. We comment on the use of RNA-Seq vs. microarrays, as well as the best practices for GCN construction. Furthermore, we recount the most popular webtools and standalone applications performing gene coexpression analysis, with details on their methods, features and outputs.

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Section: Limitations and Perspectives In Coexpression Analysismentioning

confidence: 99%

Approaches in Gene Coexpression Analysis in Eukaryotes

Zogopoulos

Saxami

Malatras

et al. 2022

Biology

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Building integrative functional maps of gene regulation

Pratt

Moore

et al. 2022

Human Molecular Genetics

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Every cell in the human body inherits a copy of the same genetic information. The three billion base pairs of DNA in the human genome, and the roughly 50 000 coding and non-coding genes they contain, must thus encode all the complexity of human development and cell and tissue type diversity. Differences in gene regulation, or the modulation of gene expression, enable individual cells to interpret the genome differently to carry out their specific functions. Here we discuss recent and ongoing efforts to build gene regulatory maps, which aim to characterize all sequences in a genome for their roles in regulating gene expression. Many researchers and consortia have identified such regulatory elements using functional assays and evolutionary analyses; we discuss the results, strengths, and shortcomings of their approaches. We also discuss new techniques the field can leverage and emerging challenges it will face while striving to build gene regulatory maps of ever-increasing resolution and comprehensiveness.

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Genome-Wide Profiling of Transcription Initiation with STRIPE-seq

Cited by 2 publications

References 46 publications

Approaches in Gene Coexpression Analysis in Eukaryotes

Approaches in Gene Coexpression Analysis in Eukaryotes

Building integrative functional maps of gene regulation

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