Molecular analysis of repetitive DNA elements from Entamoeba histolytica, which encode small RNAs and contain matrix/scaffold attachment recognition sequences

• Published in: Molecular and biochemical parasitology Vol. 126; no. 1; pp. 35 - 42
• Main Authors: Banerjee, Sulagna, Lohia, Anuradha
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 2003
• Subjects: Animals; Base Sequence; Chromosomes - genetics; Clustered repeats; Entamoeba; Entamoeba histolytica - cytology; Entamoeba histolytica - genetics; Entamoeba histolytica - metabolism; Matrix Attachment Region Binding Proteins - metabolism; Models, Genetic; Nuclear Matrix - metabolism; Nuclear matrix proteins; Nuclear Matrix-Associated Proteins - analysis; Nuclear Matrix-Associated Proteins - genetics; Repetitive DNA; Repetitive Sequences, Nucleic Acid - genetics; RNA, Helminth - chemistry; RNA, Helminth - genetics; RNA, Helminth - metabolism; RNA, Small Nuclear - chemistry; RNA, Small Nuclear - genetics; RNA, Small Nuclear - metabolism; Scaffold or matrix attachment regions; Sequence Alignment; Small molecular weight RNA; Repetitive DNA; Scaffold or matrix attachment regions; Clustered repeats; Nuclear matrix proteins; Entamoeba; Small molecular weight RNA
• ISSN: 0166-6851; 1872-9428
• DOI: 10.1016/S0166-6851(02)00244-X

We have isolated two DNA elements-Eh MRS1 and Eh MRS2-from Entamoeba histolytica, which contain the eukaryotic consensus Scaffold/Matrix Attachment Region (S/MAR) bipartite recognition sequences. Both these sequences bind to high salt extractable nuclear proteins and insoluble nuclear matrix proteins in E. histolytica HM1:IMSS, suggesting that the predicted S/MAR recognition sequences may indeed function as scaffold attachment regions in E. histolytica. Sequence analysis shows that Eh MRS1 and Eh MRS2 contain internal tandem repeats ranging from units of 8–11 bp and are themselves present as independent arrays of tandemly repeating units of approximately 1100 bp each. Eh MRS1 and Eh MRS2 are localised on different chromosomes in E. histolytica HM1:IMSS. Both Eh MRS1 and Eh MRS2 also code for small molecular weight RNAs of unknown function. Thus, two unique sequences-Eh MRS1 and Eh MRS2-demonstrate very similar properties, suggesting that they belong to a superfamily of genomic elements, which may function as scaffold or matrix attachment sites in Entamoeba.