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Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Updated: May 27, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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CiliateBase: a resource for ciliate functional genomics integrating dynamic transcriptomics, epigenomics and

Dan Liu^1,2,3,4,5, Leisheng Shi⁶, Zhaorui Zhou⁵

¹State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191 China.

Marine Life Science & Technology

|May 26, 2026

Summary

CiliateBase is a new functional genomics database integrating omics data from 96 experiments and 69 species. This resource aids research into ciliate gene functions and regulatory networks.

Keywords:

Ciliate Database Functional genomics Omics data

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

Genomics
Bioinformatics
Eukaryotic Biology

Background:

Ciliates are diverse unicellular eukaryotes crucial for ecology, evolution, and epigenetics.
Advancements in sequencing technology have led to a surge in omics data for ciliates.
Existing data are fragmented, hindering comprehensive functional genomics studies.

Purpose of the Study:

To establish a centralized functional genomics database for ciliates.
To integrate diverse omics data for analyzing gene function and regulatory networks.
To provide user-friendly tools for ciliate researchers.

Main Methods:

Compiled high-throughput sequencing data from 96 functional gene knockdown/knockout experiments in model ciliates (Tetrahymena thermophila, Paramecium tetraurelia, Oxytricha trifallax).
Integrated additional omics data from 69 ciliate species.
Developed CiliateBase (http://ciliatebase.maolab.org/) with tools for RNA-seq, ChIP-seq, MNase-seq, and RIP-seq analysis, including Gene Ontology and KEGG pathway enrichment.

Main Results:

Established CiliateBase, a comprehensive database for ciliate functional genomics.
Integrated multiple omics data types for in-depth analysis of gene function and regulation.
Provided tools for gene expression, GO, and KEGG pathway analysis with data visualization.

Conclusions:

CiliateBase offers a robust platform for exploring functional genomics in ciliates.
The database facilitates easy access, search, and analysis of ciliate omics data.
This resource significantly advances research in ciliate evolutionary biology, ecology, and epigenetics.