The goal of this assignment is to use the Internet-based Genes and Disease site (NCBI) to view the assignment of genes to chromosomes.

  1. WHAT CHROMOSOME DID YOU CHOOSE?

I chose Chromosome 4.

2 & 3.  STATE THE NUMBER OF GENES AND BASE PAIRS ON THE CHROMOSOME YOU CHOSE.

Chromosome 4 contains approximately 1600 genes and approximately 190 million base pairs, of which ~95% have been determined.

4.  LIST ONE DISEASE (DUE TO A MUTATED GENE) ASSOCIATED WITH THIS CHROMOSOME.         

Huntington Disease

5.  STATE THE NORMAL FUNCTION OF THE GENE (NOT THE DISEASE) YOU LISTED IN #4.  Chromosome 4 has various complex functions throughout the body. Chromosome 4 contains genes that carry instructions for producing proteins and performing several functions in the body. The gene’s normal functions are involved in development and growth throughout life. In addition, Chromosome 4 aids in metabolic processes which help break down nutrients, regulate energy, and contribute to maintaining proper metabolic balance within the body. Chromosome 4 is involved in neuronal growth, synaptic plasticity, neurotransmitter regulation, and other functions for brain structure and activity.

Introduction to BLAST

6.  WHAT IS THE TOP SEQUENCE DESCRIPTION MATCH FOR YOUR QUERY SEQUENCE? 

Homo sapiens CFTR promoter region (LOC111674463) on chromosome 7

7.  WHAT IS THE FUNCTION OF THIS SEQUENCE?

The function of the sequence provided includes regulatory elements which play a role in controlling the activity of the CFTR gene. There is an enhancer located at DHS-3.4kb which cooperates with other enhancers for CFTR gene activity. Next, the function of this sequence and the core promoter of CFTR gene is regulated by cAMP and protein kinase A, this is important in transcription and gene expression. Polymorphisms in the region of this sequence influence and affect transcription factors which affect the CFTR gene promoter.

8.  WHAT GENE (PROTEIN) IS THIS SEQUENCE ASSOCIATED WITH?

CFTR

9.  WHAT DOES THE ENCODED PROTEIN DO IN THE BODY? 

The CFTR protein is known to act as a chloride (Cl–) channel expressed in the exocrine glands of several body systems where it also regulates other ion channels, including the epithelial sodium (Na+) channel (ENaC) that plays a key role in salt absorption. This function is crucial to the osmotic balance of the mucus and its viscosity.

Article Citation (Nature format):

Hanssens, L. S., Duchateau, J. & Casimir, G. J. CFTR Protein: Not Just a Chloride Channel? Cells 10, 2844 (2021). https://doi.org/10.3390/cells10112844

10.  FOR WHAT DISEASE IS A MUTATED FORM OF THIS GENE RESPONSIBLE? 

Cystic Fibrosis

11.  ON WHAT CHROMOSOME IS THE GENE LOCATED? 

Chromosome 7

12.  WHAT SPECIES (STATE THE SCIENTIFIC NAME) OTHER THAN HOMO SAPIENS ALSO HAS A 100% IDENTITY (PER. Ident) FOR THIS SEQUENCE?

Pan troglodytes

13.  DOES IT SURPRISE YOU THAT THIS/THESE SPECIES ALSO HAS A 100% SIMILARITY IN IDENTITY?  WHY OR WHY NOT?

No, it does not surprise me that Homo sapiens and Pan troglodytes have a 100% similarity in identity for this search. Homo sapiens (humans) and Pan troglodytes (Chimpanzees) are both similar in genetic identification and DNA sequence.

FOR EACH, STATE WHAT THE GENE IS (#14-17).  (Again, give the description of the gene or gene product.)

14.  NM_145556: TAR DNA binding protein, (Tardbp)

15.  NM_013444: UBQLN2 ubiquilin 2

16.  NM_001010850: FUS RNA binding protein 

17.  KJ174530: superoxide dismutase 1

18.  WHAT DISEASE IS ASSOCIATED WITH MUTATIONS OF THE GENES REFERENCED IN #14-#17?  WHAT IS A “COMMON NAME” OF THE DISEASE? 

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Lou Gehrig Disease

19.  WHAT IS GENBANK? 

GenBank is a database with information about genetic sequences. GenBank is primarily used to store and provide access to genetic sequencing information for different organisms. It is a valuable tool for researchers, educators, or students looking at genetic information.

20.  WHAT IS THE HIERARCHY AMONG THE NATIONAL INSTITUTES OF HEALTH, THE NATIONAL LIBRARY OF MEDICINE, AND THE NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION?  WHERE DO GENBANK AND BLAST BELONG?

The hierarchy among the NIH, NLM, and NCBI are all within the Department of Health and Human Services. The National Institutes of Health is responsible for biomedical and health research primarily conducted by institutions across the United States. Next, the National Library of Medicine follows, and it is a branch of NIH that serves primarily as a biomedical library. The National Library of Medicine contains tools and resources for researchers, educators, healthcare professionals as well as the public. Last, the National Center for Biotechnology Information. This is a division that creates and maintains databases and resources related to biology, genetics, and genomics. The NCBI includes GenBank, PubMed, and BLAST.

GenBank is maintained by the NCBI, and BLAST is a tool that was developed by the NCBI.

In conclusion, The National Institutes of Health oversees the National Library of Medicine which includes the National Center for Biotechnology Information. The National Center for Biotechnology Information manages GenBank and BLAST.

21.  REFLECT ON ONE THING THAT YOU LEARNED FROM DOING THIS ASSIGNMENT.

I learned a lot from this assignment, but one of the most interesting facts I learned is how all the various databases used in the Genome Assignment are interconnected. GenBank, which is maintained by the NCBI as discussed in question #20, as well as BLAST serve as powerful tools for the analysis of genetic data. Using these resources helps in understanding genes, their genetic variations, and the diseases associated with mutations.