Research Topic

Transcriptional Regulation at the Single-Molecule & Single-Cell Level in Plants

About this Research Topic

The central dogma of molecular biology states that the genetic information encoded in DNA is transcribed into RNA and then translated into proteins. RNA splicing is a process at the transcriptional level which leads to the generation of multiple isoforms and subsequent altered gene expression. The process of splicing fundamentally changes the information content of the RNA transcript, which directly impacts the translation of that genetic information into proteins. Regulation of splicing therefore represents a critical step of gene expression.

Previous methods using short-read approaches were not able to capture the full-length transcript due to the read length limitation, but with the development of long-read technology, led by PacBio and Oxford Nanopore, it is now possible to study the transcriptome for each organism at full-length level, which unveils the complexity and stories in the RNA world missing from previous studies. Recent advances in approaches to single-cell RNA-seq (scRNA-seq) has equipped us with a unique opportunity to study transcriptional changes at cellular resolution in any given organism. scRNA-seq has revolutionised and stimulated cellular studies in animal-based research: it not only facilitates the discovery of new cell types, but also enables the study of cellular gene network regulation and transcriptomic changes underlying cell fate choices and organ functionality.

In this Research Topic, we aim to focus on transcriptional regulation in plants using next-generation sequencing (NGS), single-molecule sequencing and single-cell technologies which allow the analysis of RNA splicing and gene expression, whether short or long at high resolution. Together with other technologies such as ATAC-seq, ChIP-seq, etc., these approaches have opened new ways in understanding gene functions in the organism, we also interested in detailed functional characterization of different isoforms.

Manuscripts we would like to be submitted include:
● Alternative splicing study in plants;
● Comparison of different sequencing platforms or different methods;
● New methods or protocols for sequencing native RNA;
● Application of single-molecule, long-read sequencing in de novo characterization of transcriptomes of different organisms, tissues or cell types;
● New methods or protocols for intact 5’UTR, 3’UTR and intact RNA isoform identification;
● Epitranscriptome analysis, including RNA methylation;
● Application of full-length transcripts for genome annotation;
● Study of allele-specific transcript using long-read sequencing;
● Functional characterization of individual isoforms from alternative splicing;
● RNA-seq study at single-cell level, either short-reads or long-reads.


Keywords: Transcription, Single-molecule, Single-cell, RNA-seq, splicing


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

The central dogma of molecular biology states that the genetic information encoded in DNA is transcribed into RNA and then translated into proteins. RNA splicing is a process at the transcriptional level which leads to the generation of multiple isoforms and subsequent altered gene expression. The process of splicing fundamentally changes the information content of the RNA transcript, which directly impacts the translation of that genetic information into proteins. Regulation of splicing therefore represents a critical step of gene expression.

Previous methods using short-read approaches were not able to capture the full-length transcript due to the read length limitation, but with the development of long-read technology, led by PacBio and Oxford Nanopore, it is now possible to study the transcriptome for each organism at full-length level, which unveils the complexity and stories in the RNA world missing from previous studies. Recent advances in approaches to single-cell RNA-seq (scRNA-seq) has equipped us with a unique opportunity to study transcriptional changes at cellular resolution in any given organism. scRNA-seq has revolutionised and stimulated cellular studies in animal-based research: it not only facilitates the discovery of new cell types, but also enables the study of cellular gene network regulation and transcriptomic changes underlying cell fate choices and organ functionality.

In this Research Topic, we aim to focus on transcriptional regulation in plants using next-generation sequencing (NGS), single-molecule sequencing and single-cell technologies which allow the analysis of RNA splicing and gene expression, whether short or long at high resolution. Together with other technologies such as ATAC-seq, ChIP-seq, etc., these approaches have opened new ways in understanding gene functions in the organism, we also interested in detailed functional characterization of different isoforms.

Manuscripts we would like to be submitted include:
● Alternative splicing study in plants;
● Comparison of different sequencing platforms or different methods;
● New methods or protocols for sequencing native RNA;
● Application of single-molecule, long-read sequencing in de novo characterization of transcriptomes of different organisms, tissues or cell types;
● New methods or protocols for intact 5’UTR, 3’UTR and intact RNA isoform identification;
● Epitranscriptome analysis, including RNA methylation;
● Application of full-length transcripts for genome annotation;
● Study of allele-specific transcript using long-read sequencing;
● Functional characterization of individual isoforms from alternative splicing;
● RNA-seq study at single-cell level, either short-reads or long-reads.


Keywords: Transcription, Single-molecule, Single-cell, RNA-seq, splicing


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

29 March 2021 Manuscript
28 June 2021 Manuscript Extension

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

29 March 2021 Manuscript
28 June 2021 Manuscript Extension

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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