Abstract

1. Cerebellum Cerebellum Salivary gland Salivary gland Skeletal muscle Skeletal muscle Bone marrow Bone marrow Adrenal gland Adrenal gland Whole brain Whole brain Spinal cord Spinal cord Marker Marker Fetal brain Fetal brain Fetal liver Fetal liver Prostate Prostate Thymus Thyroid Trachea Thymus Thyroid Trachea Placenta Placenta Heart Heart Lung Kidney Liver Marker Uterus Testis Kidney Liver Lung Marker Testis Uterus Abstract SFTPB Gene Structure Other region SINE 13% 16% LINE 20% ARMD event and evolutionary aspect of the SFTPB gene SFTPB Gene Expression in Various Tissues of Human S 419 bp NM_000542.2 New Transcript Gene-related Sequence HERV element 8% 36% DNA element Pseudogene Coding sequence 3% 1% 3% Integration lineage of HERV-H LTR and AluSx in the SFTPB gene AS Marker HU CH RH OR GO TA JM NM RL SFTPB Gene Expression in Various Tissues of Rhesus monkey GI Cerebrum Stomach Pancreas Cerebellum Heart Adrenal gland Salivary gland Urine bladder Duodenum Marker Kidney Trachea Liver Gullet Jejunum Cecum Lung Marker Rectum Tongue Ileum Testis Spleen Colon 638 bp Marker Cerebrum Stomach Pancreas Cerebellum Adrenal gland Heart Salivary gland Urine bladder Duodenum Marker CH HU Kidney Trachea Liver Gullet Jejunum Cecum GO RH Lung OR TA JM NM RL Marker Rectum Tongue Testis Spleen Colon Ileum GI 763 bp 392 bp AluSg AluJ AluSx LTR7B SFTPB Gene Expression in Various Tissues of New World monkeys ARMD event ? AluSg vs AluSx AluJ AluSx LTR7B Alternative splicing ARMD event Insertion of TEs Evolutionary Investigation of SFTPB Gene: Exonization, Alu Recombination-mediated Deletion, and Alternative Splicing Ja-Rang Lee1, Jae-Won Huh1,2, Dae-Soo Kim3, Hong-Seok Ha1, Kung Ahn1, Yun-Ji Kim1, Kyu-Tae Chang2, and Heui-Soo Kim1,* 1 Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea 2 National Primate Research Center (NPRC), KRIBB, Ochang, Chungbuk 363-883, Republic of Korea 3 Korea Bioinformation Center, KRIBB, Daejeon 305-806, Korea Results & Discussion The SFTPB (surfactant, pulmonary-associated protein B) gene on human chromosome 2p11.2 encodes an amphipathic surfactant protein essential for lung function and homeostasis after birth. The SFTPB gene has been investigated to have transcript variants related with transposable elements (LTR7B and AluSx). We investigated the evolutionary aspect and molecular characterization of SFTPB gene using genomic DNAs and RNAs from various primate samples. LTR7B and AluSx elements within the SFTPB gene have been integrated into ancestor genome before the divergence of simian and prosimian. Alu recombination-mediated deletion (ARMD) event has been occurred after the divergence of New World monkeys and Old World monkeys in SFTPB gene 3’ UTR region. Transcript variants (306 bp and 463 bp) were newly identified by comparative RT-PCR analysis. Original transcript (419 bp) shows ubiquitous expression in various tissues and TE fusion transcript (841 bp) shows the lung specific expression in human. Taken together, integration event of LTR7B and AluSx on SFTPB gene seem to cause a lineage specific exonization event via general exonization event (New World monkeys and prosimian), ARMD event (Old World monkeys and hominoids), and alternative splicing (human) during the primate evolution. Chr. 2 2p11.2 638 bp NM_198843.1 AS2 S1 11_A 10 1 2 AS2 NM_000542.2 S1 638 bp 11_B 1 2 10 S AS 841 bp NM_198843.1 New Transcript 841 bp 463 bp 419 bp 306 bp G3PDH 120 bp G3PDH 120 bp Introduction 463 bp 419 bp 306 bp G3PDH 120 bp G3PDH 120 bp Marker Marker Marker Marker Cerebellum Brain Cerebellum Cerebellum Kidney Heart Kidney Kidney Kidney Heart Heart Heart Lung Uterus Liver Liver Lung Lung Lung Uterus 463 bp 419 bp 306 bp 306 bp G3PDH 120 bp G3PDH 120 bp G3PDH 120 bp G3PDH 120 bp Materials & Methods http://www.primate.or.kr/HESAS/ Bioinformatics Genomic DNA of various primate and human cDNA of various tissues of human, rhesus monkey & marmoset Genomic DNA & cDNA Human, Rhesus monkey & Marmoset(30 cycle) ; Various tissues RT-PCR 30 cycle; 94 ℃- 40 sec, 56 ℃- 30 sec, 72 ℃- 40 sec Qiaquick Gel-extraction, Promega T-easy Vector, EcoR-I(DH5α) PCR & Cloning of PCR product References Genome Information Lab. 1. Han, K., Lee J., Meyer, T. J., Wang, J., Sen, S. K., Srikanta, D., Liang, P. & Batzer, M. A. (2007). Alu recombination-mediated structural deletions in the chimpanzee genome. PLoS Genet.3, 1939-1949. 2. Clark JC, Wert SE, Bachurski CJ, Stahlman MT, Stripp BR, Weaver TE, Whitsett JA. 1995. Targeted disruption of the surfactant protein B gene disrupts surfactant homeostasis, causing respiratory failure in newborn mice. Proc. Natl. Acad. Sci. USA. 92: 7794-7798.