Defining Candidate Imprinted loci in <i>Bos taurus</i>
Using a whole-genome assembly of <i>Bos taurus</i>, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, i...
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MDPI AG
2023-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/5/1036 |
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| author | Minou Bina |
| author_facet | Minou Bina |
| author_sort | Minou Bina |
| collection | DOAJ |
| description | Using a whole-genome assembly of <i>Bos taurus</i>, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: <i>CNNM1</i> and <i>CNR1</i>. I also give examples of candidate ICRs in loci that influence muscle development: <i>SIX1</i> and <i>BCL6</i>. By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the <i>SIX1</i> promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of <i>BCL6</i> locus to regulatory proteins in mouse ESCs and examined tissues. |
| first_indexed | 2024-03-11T03:43:13Z |
| format | Article |
| id | doaj.art-f61bbcb3affb452083f74283e1d58fef |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T03:43:13Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-f61bbcb3affb452083f74283e1d58fef2023-11-18T01:29:35ZengMDPI AGGenes2073-44252023-05-01145103610.3390/genes14051036Defining Candidate Imprinted loci in <i>Bos taurus</i>Minou Bina0Department of Chemistry, Purdue University, West Lafayette, IN 47907, USAUsing a whole-genome assembly of <i>Bos taurus</i>, I applied my bioinformatics strategy to locate candidate imprinting control regions (ICRs) genome-wide. In mammals, genomic imprinting plays essential roles in embryogenesis. In my strategy, peaks in plots mark the locations of known, inferred, and candidate ICRs. Genes in the vicinity of candidate ICRs correspond to potential imprinted genes. By displaying my datasets on the UCSC genome browser, one could view peak positions with respect to genomic landmarks. I give two examples of candidate ICRs in loci that influence spermatogenesis in bulls: <i>CNNM1</i> and <i>CNR1</i>. I also give examples of candidate ICRs in loci that influence muscle development: <i>SIX1</i> and <i>BCL6</i>. By examining the ENCODE data reported for mice, I deduced regulatory clues about cattle. I focused on DNase I hypersensitive sites (DHSs). Such sites reveal accessibility of chromatin to regulators of gene expression. For inspection, I chose DHSs in chromatin from mouse embryonic stem cells (ESCs) ES-E14, mesoderm, brain, heart, and skeletal muscle. The ENCODE data revealed that the <i>SIX1</i> promoter was accessible to the transcription initiation apparatus in mouse ESCs, mesoderm, and skeletal muscles. The data also revealed accessibility of <i>BCL6</i> locus to regulatory proteins in mouse ESCs and examined tissues.https://www.mdpi.com/2073-4425/14/5/1036BCL6bull spermatogenesiscattle genomicscattle musclecattle spermatogenesisCNNM1 |
| spellingShingle | Minou Bina Defining Candidate Imprinted loci in <i>Bos taurus</i> Genes BCL6 bull spermatogenesis cattle genomics cattle muscle cattle spermatogenesis CNNM1 |
| title | Defining Candidate Imprinted loci in <i>Bos taurus</i> |
| title_full | Defining Candidate Imprinted loci in <i>Bos taurus</i> |
| title_fullStr | Defining Candidate Imprinted loci in <i>Bos taurus</i> |
| title_full_unstemmed | Defining Candidate Imprinted loci in <i>Bos taurus</i> |
| title_short | Defining Candidate Imprinted loci in <i>Bos taurus</i> |
| title_sort | defining candidate imprinted loci in i bos taurus i |
| topic | BCL6 bull spermatogenesis cattle genomics cattle muscle cattle spermatogenesis CNNM1 |
| url | https://www.mdpi.com/2073-4425/14/5/1036 |
| work_keys_str_mv | AT minoubina definingcandidateimprintedlociinibostaurusi |