Endogenous Retroviral promoter of the Human gene Kim Tae Hyung Oct 02,2004 MPL

Origin of a substantial fraction of human regulatory sequences from transposable elements King Jordan 1, Igor B. Rogozin 1, Galina V. Glazko 2 and Eugene V. Koonin 1 1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A/Room N511M, Rockville Pike, Bethesda, MD 20894, USA 2 Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, 328 Mueller Lab, University Park, PA 16802, USA Generally, we are interested in understanding the evolution of life. Specifically, to obtain glimpses of such understanding, we employ existing and new methods of computational biology to perform research in three main directions. i) Empirical comparative and evolutionary genomics - comparison of prokaryotic and eukaryotic genomes with the aim of predicting gene functions, constructing evolutionary scenarios for particular gene families and functional categories, and deciphering general evolutionary trends. One of the evolutionary phenomena we are particularly interested in is horizontal gene transfer between diverse organisms. One of the products of this research direction is the database of Clusters of Orthologous Groups of proteins (COGs). ii) Exploitation of genome comparisons, particularly those between relatively close genomes, for addressing fundmanetal issue of evolutionary biology such as the nature of adaptation and selection in different categories of genes. iii) Classification and evolutionary analysis of protein domains and domain architectures. An important dimension in this type of research is discovery of "new" domains that are shared by many diverse proteins but have not been defined previously. Principal Research Interests

Types of alternative splicing events

Transposable element (TE)-derived sequences in human regulatory regions The Human Promoter Database (HPD;

Transposable elements (TEs) in human regulatory sequences

Transposable element (TE)-derived cis-regulatory elements

Sequence alignment of the -globin locus and a mammalian apparent long terminal repeat (LTR)-retrotransposon (MaLR)

The types and consequences of alternative promoters

Proposed mechanisms that could lead to creation of alternative promoters

Selected human and rodent genes with alternative promoters

Promoter activity of the ENDRB LTR

Tissue specific 97 kb

MID1

Functional analysis of alternative MID1 promoters

Antisense and RNAi

Experimental analysis of alternative splicing

Analysis of expressed pattern by providing ERV-derived promoter in the HESAS

Total : 135 Internal : 38 LTR : 97 Known Gene : 48 LTR-derived : 37 Internal : 11 Unknown Gene: 87 (LOCXXX, FLJXXXX, MGCXXXX,….) The statistic about ERV-derived promoter in the HESAS

CHR.ACC.GENELTRERVTissueTYPE 1 NT_ NCF2LTR27TSS_GT NT_ PLAC3MER41TSS NT_ GBP5LTR12HERV9TSS NT_ SMYD3LTR8TSS_GT NT_ CHIALTR66HERVLTSS_GT NT_ MAN1C1MER52TSS 3 NT_ SIAT1MER21TSS_GT NT_ ZNF80pTR5TSS NT_ CCBP2MER39TSS_GT 5 NT_ ARSBLTR37TSS NT_ FISLTR12HERV9TSS NT_ BIRC1MER21TSS_GT 6NT_ ZNF323LTR18HERVLTSS_GT 7 NT_ NUDT1LTR1TSS_GT NT_ ABCA13LTR12HERV9TSS_GT NT_ NOS3LTR10HERVITSS 8 NT_ HHLA1LTR7HERVHTSS NT_ HSJ001348LTR43TSS NT_ RPESPMER9TSS NT_ CA1MER74TSS_GT 9NT_ BAATMER11TSS 11 NT_ NOV1LTR18HERVLTSS_GT NT_ PRDM10LTR52TSS 12 NT_ GALNT8LTR14HERVKTSS NT_ CPMMER39TSS_GT 13NT_ G30MER57TSS_GT NT_ TCL6MER4TSS 15 NT_ CYP19A1MER21TSS_GT NT_ SV2BMER39TSS_GT 16 NT_ OTOALTR45TSS_GT NT_ MSLNMER54TSS_GT 17 NT_ GSDMLLTR7HERVHTSS NT_ CCL15MER50TSS 19NT_ FPRL2LTR54TSS 20 NT_ HSPC072MLT2TSS_GT NT_ NSFL1CLTR10HERVITSS 21NT_ DSCR8LTR9TSS The consequences of LTR-derived promoters in the HESAS