ReviewInternational journal of molecular sciences2019
RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism.
Review in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
25 citing papers in PubMed.
- Functional and regulatory complexity: challenges and prospects for understanding rice WRKY transcription factors.Journal of experimental botany · 2026Review
- Protocol for chromatin immunoprecipitation using isolated antheridia of Marchantia polymorpha.STAR protocols · 2026Article
- From binding to networks: methods for identifying transcription factor targets in plant systems.Frontiers in plant science · 2026Review
- Enhancer profiling uncovers Jmjd1c as an essential suppressor in neuropathic pain by targeting Socs3.Genes & diseases · 2025Article
- Accelerating crop improvement via integration of transcriptome-based network biology and genome editing.Planta · 2025Review
- Classification of and detection techniques for RNAi-induced effects in GM plants.Frontiers in plant science · 2025Review
- The Polygenic Nature of Multiple Sclerosis: Genetic Variants, Immunological Modulation, and Environmental Connections.Endocrine, metabolic & immune disorders drug targets · 2025Review
- Generic and queryable data integration schema for transcriptomics and epigenomics studies.Computational and structural biotechnology journal · 2024Article
- MARK4 aggravates cardiac dysfunction in mice with STZ-induced diabetic cardiomyopathy by regulating ACSL4-mediated myocardial lipid metabolism.Scientific reports · 2024Article
- Identification of Key Genes and Pathways for Anaerobic Germination Tolerance in Rice Using Weighted Gene Co-Expression Network Analysis (WGCNA) in Association with Quantitative Trait Locus (QTL) Mapping.Rice (New York, N.Y.) · 2024Article
- Comparative Transcriptomic Analysis ofPlants (Basel, Switzerland) · 2024Article
- Airborne fine particulate matter exposure induces transcriptomic alterations resembling asthmatic signatures: insights from integrated omics analysis.Environmental epigenetics · 2024Article
- A hybrid approach for predicting transcription factors.Frontiers in bioinformatics · 2024Article
- Article
- Application of Multi-Perspectives in Tea Breeding and the Main Directions.International journal of molecular sciences · 2023Review
- Article
- Complementing Hi-C information for 3D chromatin reconstruction by ChromStruct.Frontiers in bioinformatics · 2023Article
- Genome-Wide Super-Enhancer-Based Analysis: Identification of Prognostic Genes in Oral Squamous Cell Carcinoma.International journal of molecular sciences · 2022Article
- Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data.Journal of integrative bioinformatics · 2021Article
- Naringenin ameliorates homocysteine induced endothelial damage via the AMPKα/Sirt1 pathway.Journal of advanced research · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.