Endogenous Retroviral promoter of the Human gene

Kim Tae Hyung

http://www.primate.or.kr

Oct 02,2004

MPL

Origin of a substantial fraction of human regulatory sequences from transposable elements

King Jordan 1, Igor B. Rogozin1, Galina V. Glazko2 and Eugene V. Koonin1

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A/Room N511M, 8600 Rockville Pike, Bethesda, MD 20894, USA2 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; http://zlab.bu.edu/~mfrith/HPD.html)

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 : 38LTR : 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. GENE LTR ERV Tissue TYPE

1

NT_004487.16 NCF2 LTR27 TSS_GT

NT_004487.16 PLAC3 MER41 TSS

NT_004686.16 GBP5 LTR12 HERV9 TSS

NT_004836.15 SMYD3 LTR8 TSS_GT

NT_019273.16 CHIA LTR66 HERVL TSS_GT

NT_037485.3 MAN1C1 MER52 TSS

3

NT_005612.14 SIAT1 MER21 TSS_GT

NT_005612.14 ZNF80 pTR5 TSS

NT_022517.16 CCBP2 MER39 TSS_GT

5

NT_006713.13 ARSB LTR37 TSS

NT_023148.12 FIS LTR12 HERV9 TSS

NT_078018.1 BIRC1 MER21 TSS_GT

6 NT_007592.13 ZNF323 LTR18 HERVL TSS_GT

7

NT_007819.14 NUDT1 LTR1 TSS_GT

NT_030008.6 ABCA13 LTR12 HERV9 TSS_GT

NT_079596.1 NOS3 LTR10 HERVI TSS

8

NT_008046.14 HHLA1 LTR7 HERVH TSS

NT_008127.15 HSJ001348 LTR43 TSS

NT_008183.17 RPESP MER9 TSS

NT_078037.2 CA1 MER74 TSS_GT

9 NT_008470.16 BAAT MER11 TSS

11NT_009237.16 NOV1 LTR18 HERVL TSS_GT

NT_033899.6 PRDM10 LTR52 TSS

12NT_009759.15 GALNT8 LTR14 HERVK TSS

NT_029419.10 CPM MER39 TSS_GT

13 NT_009952.14 G30 MER57 TSS_GT

NT_026437.10 TCL6 MER4 TSS

15NT_010194.16 CYP19A1 MER21 TSS_GT

NT_010274.15 SV2B MER39 TSS_GT

16NT_010393.14 OTOA LTR45 TSS_GT

NT_037887.3 MSLN MER54 TSS_GT

17NT_010755.14 GSDML LTR7 HERVH TSS

NT_010799.14 CCL15 MER50 TSS

19 NT_011109.15 FPRL2 LTR54 TSS

20NT_011387.8 HSPC072 MLT2 TSS_GT

NT_011387.8 NSFL1C LTR10 HERVI TSS

21 NT_011512.9 DSCR8 LTR9 TSS

The consequences of LTR-derived promoters in the HESAS