Homo sapiens (Human) Ribosomal RNA Sequences Identification

The ribosome, essential for protein synthesis in all living organisms, is an intricate molecular machine responsible for translating genetic information into functional proteins. In humans, the study of ribosomal RNA (rRNA) and the genes encoding ribosomal proteins (RPs) offers a window into the heart of cellular function and development. 

As biotechnological advancements in RNA interference (RNAi), CRISPR, and other gene-editing technologies continue, understanding the precise rRNA sequences within human cells becomes important for uncovering the complexities of gene expression. 

This identification is at the forefront of research, allowing scientists to explore cellular mechanisms with unprecedented clarity and opening doors to new therapeutic avenues and precision medicine strategies. 

Below, you are going to explore human ribosomal RNA sequences, their methods, challenges, and more. Let’s uncover these insights below!

Methods for Identifying Human Ribosomal RNA Sequences

Source: NIH

To identify human ribosomal RNA (rRNA) sequences, researchers can employ techniques like RNA sequencing (RNA-seq), Polymerase Chain Reaction (PCR), and phylogenetic analysis, focusing on specific rRNA regions like 18S, 5.8S, and 28S. 

1. RNA Sequencing (RNA-Seq)

This is a very powerful tool that can be used to analyze the entire transcriptome that also includes Homo sapiens (human) ribosomal RNA sequences. The RNA sequencing tool can be used to identify and quantify the different rRNA regions like 18S, 5.8S, and 28S. However, in many RNA-Seq experiments, rRNA is typically depleted to focus on mRNA and other non-coding RNAs. However, it can still be used for the direct identification of rRNA sequences, especially if the experiment is for rRNA analysis.

2. Polymerase Chain Reaction (PCR)

PCR remains a foundational method for amplifying specific rRNA sequences. Researchers can design primers that target particular regions of the rRNA genes, such as the 18S or 28S rRNA genes, to amplify these sequences from human samples. Long-range PCR can be used to amplify larger fragments, spanning from the 18S to the 28S rRNA genes, providing a broader range of information. This method can be followed by cloning the PCR product for further analysis or sequencing.

3. Phylogenetic Analysis

While this method is more commonly used to study evolutionary relationships, it can also be applied to rRNA sequences, particularly for comparing rRNA sequences across different species or in the context of identifying conserved regions. Phylogenetic analysis can help classify rRNA sequences and understand their evolutionary history, but it is not typically a standalone method for identifying rRNA in a given sample.

These are the various methods for identifying human ribosomal RNA (rRNA) sequences, each of which provides unique advantages. However, RNA-Seq stands out as the most powerful tool for analyzing Homo sapiens ribosomal RNA sequences. Let us delve deeper into its applications and the inherent challenges it presents.

RNA-seq Application & Challenges in Identifying rRNA Sequences

RNA-seq offers several advantages and applications in the identification of human ribosomal RNA sequencing, including the 18S, 5.8S, and 28S rRNA regions. Several applications quantify rRNA species, identify rRNA regions, analyze rRNA modifications, and, lastly, perform non-depleted ribonucleic acid analysis. The advantages of using this tool are that it offers high sensitivity, a comprehensive, unbiased snapshot of all RNA samples, and high-resolution data.  

Challenges in rRNA identification using RNA-seq

With advantages come considerations, such as challenges and some concerns that need to be taken care of, such as standard RNA-Seq protocols, in which rRNA is often depleted to focus on other RNA types. This means that for rRNA analysis, special protocols or no depletion methods are needed to ensure rRNA sequences are retained. Other than this, data interpretation can also take place due to the highly repetitive nature of rRNA sequences; distinguishing between homologous rRNA regions from different species or within the same species can be challenging. Computational tools and databases need to be optimized for accurate mapping of rRNA sequences.

In this section, you will learn about the different methods for ribosomal RNA processing and human ribosomal RNA sequencing identification. 

Resources for Accessing Human Ribosomal RNA Sequences

Do you know?  Ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome and plays a crucial role in protein synthesis across all living organisms. It makes up about 60% of the ribosome’s mass, with the remaining 40% consisting of proteins. Ribosomes are composed of two major rRNAs and more than 50 proteins, which come together to form the large subunit (LSU) and small subunit (SSU).  

The resources for accessing human ribosomal RNA sequences are below: 

1. NCBI Gene Database: The National Center for Biotechnology Information (NCBI) provides detailed information on human rRNA genes, including sequences for 18S, 5.8S, 28S, and 5S rRNAs.
2. Ensembl: a genome database that includes comprehensive data on human ribosomal RNA sequences, genomic coordinates, gene annotations, and related information for rRNA genes.
3. UCSC Genome Browser: The University of California, Santa Cruz (UCSC) Genome Browser offers access to human rRNA sequences within the context of the entire human genome. Users can search for specific rRNA gene loci and visualize them alongside other genomic features.
4. Ribosomal RNA Database (Silva): The SILVA database contains rRNA sequence data for many species, including humans, and provides a rich resource for studying ribosomal sequences across different organisms.
5. GENBANK: GenBank offers a wide collection of annotated sequences, including human rRNA sequences. Searching GenBank using specific rRNA gene names or identifiers can yield relevant sequence data.
6. European Nucleotide Archive (ENA): The ENA provides access to nucleotide sequence data for a wide range of organisms, including humans. It includes rRNA sequences and is a good resource for researchers looking to download large datasets.
7. The Ribosomal Database Project (RDP): RDP is another resource for ribosomal RNA sequences. It offers access to rRNA gene sequences from a wide range of organisms, including humans, and provides tools for sequence alignment and phylogenetic analysis.

Researchers widely use these resources to obtain, analyze, and work with human rRNA sequences for various applications in genomics, bioinformatics, and molecular biology.

Process of retrieving rRNA data

To retrieve rRNA data, follow the systematic approach below. This process allows the retrieval, examination, and comparison of rRNA sequences, which is essential for molecular biology research and genetic studies.

1. Choose a Database: To find rRNA sequences, use databases like NCBI Gene, Ensembl, UCSC Genome Browser, or SILVA.
2. Search for rRNA Sequences: To find human rRNA sequences, use gene names (e.g., 18S, 28S) or accession numbers.
3. Download Data: Download the sequences in formats like FASTA, GenBank, or FASTQ for analysis.
4. Analyze Sequences (Optional): Use tools like BLAST or alignment software to analyze and compare the sequences.

Formats of Accessible rRNA Sequence Information

• FASTA: Simple text format for storing nucleotide sequences.
• GenBank: Detailed format with annotations about the sequence.
• FASTQ: Format used for raw sequencing data with quality scores.

This streamlined process helps you retrieve and work with human rRNA sequences efficiently. 

Handling Ribosomal RNA in Sequencing Projects

The Ribosomal Database Project (RDP), is a curated resource that provides ribosome-related data, analysis services, and software tools. They have also provided relevant information about handling ribosomal RNA (rRNA) in sequencing projects.

Here’s how it relates to handling rRNA in sequencing:

1. RDP Data and Services: The RDP offers aligned and phylogenetically ordered rRNA sequences from various organisms, including those from GenBank and EMBL. These sequences are curated and annotated, which is important for sequencing projects that involve rRNA data.
2. rRNA Sequence Handling: The RDP also offers services like ribosomal probe checking, phylogenetic placement of user-submitted sequences, and screening for chimeric rRNA sequences, which are critical for ensuring the accuracy of rRNA data in sequencing projects.
3. Sequence Alignment and Analysis Tools: The RDP provides various programs and services, such as sequence alignment editors (e.g., Editor AE2, Editor GDE), phylogenetic tree inference (e.g., fastDNAml), and secondary structure analysis tools. These tools are essential for handling, analyzing, and interpreting rRNA sequences in sequencing projects.
4. Data Access: RDP also mentioned how rRNA sequences can be accessed via web-based portals, FTP, and API, which provides flexibility in how researchers can retrieve and work with rRNA data in their sequencing projects.

The above content outlines how rRNA sequences are handled in the context of the Ribosomal Database Project (RDP), offering tools for data analysis, alignment, and ensuring the quality of rRNA sequences in sequencing projects.

Comparison of Ribosomal Genes and Proteins

Sources: The structure of ribosomes NIH

Below is the distinction between ribosomal RNA (rRNA) and ribosomal protein (RPs), which is essential for accurately identifying and analyzing human ribosomal RNA sequences for several reasons. It provides an understanding of the functional role, evolutionary insights, disease understanding, and gene identification and analysis. Let’s explore below!

Distinguishing Between Ribosomal RNA (rRNA) and Ribosomal Proteins (RPs)

Ribosomal RNA (rRNA) and ribosomal proteins (RPs) play critical roles in the structure and function of ribosomes. rRNA serves as the fundamental force driving the catalytic activity of ribosomes, particularly in peptide bond formation and the reading of genetic code. The rRNA in ribosomes is evolutionarily conserved and functions as a ribozyme, controlling peptide synthesis. 

On the other hand, ribosomal proteins (RPs) are bound to rRNA, provide structural stability, assist in the assembly of ribosomal subunits, and facilitate the correct folding of rRNA. The interaction between rRNA and RPs is essential for the ribosome’s function, ensuring the proper translation of mRNA into proteins.

Transcript ID Retrieval for Ribosomal Proteins

The identification and retrieval of ribosomal proteins (RPs) from various databases are essential for understanding ribosome structure and function. RPs can be retrieved through transcript IDs, which link specific genes encoding ribosomal proteins to their corresponding protein sequences. These sequences can be found in curated databases like the Ribosomal Database Project (RDP) or other genomic repositories such as NCBI Gene or Ensembl. 

These platforms provide detailed annotations, including the function, structure, and evolutionary conservation of RPs. Transcript ID retrieval helps researchers identify the exact proteins involved in ribosome biogenesis, including their roles in various diseases like ribosomopathies. rRNA and ribosomal protein (RP) mutations can lead to diseases, and transcript ID retrieval is important for understanding and studying ribosomal protein genes.

Conclusion

Human ribosomal RNA (rRNA) sequences are fundamental to understanding cellular protein synthesis and evolutionary relationships. Identifying these sequences through methods like RNA-seq, Northern blotting, and phylogenetic analysis offers crucial insights into ribosomal function and evolution. While RNA-seq provides high sensitivity for rRNA identification, challenges such as rRNA depletion in standard protocols and the repetitive nature of rRNA sequences must be addressed for accurate results. 

Access to databases such as NCBI Gene, Ensembl, and the Ribosomal Database Project (RDP) is essential for retrieving and analyzing these sequences. As a researcher, if you are looking to expand your knowledge to gain a detailed understanding of gene expression, alternative splicing, and the overall transcriptome of a cell or tissue under different conditions. Then, choose Biostate.ai, which provides comprehensive RNA sequencing insights of any sample at an affordable rate. Handle the full procedure and offer high-quality and reliable results. Get Your Quote Today.