Conserved stem–loop structures in the HIV-1 RNA region containing the A3 3′ splice site and its cis-regulatory element: possible involvement in RNA splicing

The HIV-1 transcript is alternatively spliced to over 30 different mRNAs. Whether RNA secondary structure can influence HIV-1 RNA alternative splicing has not previously been examined. Here we have determined the secondary structure of the HIV-1/BRU RNA segment, containing the alternative A3, A4a, A4b, A4c and A5 3′ splice sites. Site A3, required for tat mRNA production, is contained in the terminal loop of a stem–loop structure (SLS2), which is highly conserved in HIV-1 and related SIVcpz strains. The exon splicing silencer (ESS2) acting on site A3 is located in a long irregular stem–loop structure (SLS3). Two SLS3 domains were protected by nuclear components under splicing condition assays. One contains the A4c branch points and a putative SR protein binding site. The other one is adjacent to ESS2. Unexpectedly, only the 3′ A residue of ESS2 was protected. The suboptimal A3 polypyrimidine tract (PPT) is base paired. Using site-directed mutagenesis and transfection of a mini-HIV-1 cDNA into HeLa cells, we found that, in a wild-type PPT context, a mutation of the A3 downstream sequence that reinforced SLS2 stability decreased site A3 utilization. This was not the case with an optimized PPT. Hence, sequence and secondary structure of the PPT may cooperate in limiting site A3 utilization.

Molecular cytogenetic delineation of a novel critical genomic region in chromosome bands 11q22.3-923.1 in lymphoproliferative disorders.

Aberrations of the long arm of chromosome 11 are among the most common chromosome abnormalities in lymphoproliferative disorders (LPD). Translocations involving BCL1 at 11q13 are strongly associated with mantle cell lymphoma. other nonrandom aberrations, especially deletions and, less frequently, translocations, involving bands 11q21-923 have been identified by chromosome banding analysis. To date, the critical genomic segment and candidate genes involved in these deletions have not been identified. In the present study, we have analyzed tumors from 43 patients with LPD (B-cell chronic lymphocytic leukemia, n = 40; mantle cell lymphoma, n = 3) showing aberrations of bands 11q21-923 by fluorescence in situ hybridization. As probes we used Alu-PCR products from 17 yeast artificial chromosome clones spanning chromosome bands 11q14.3-923.3, including a panel of yeast artificial chromosome clones recognizing a contiguous genomic DNA fragment of approximately 9-10 Mb in bands 11q22.3-923.3. In the 41 tumors exhibiting deletions, we identified a commonly deleted segment in band 11q22.3-923.1; this region is approximately 2-3 Mb in size and contains the genes coding for ATM (ataxia telangiectasia mutated), RDX (radixin), and FDX1 (ferredoxin 1). Furthermore, two translocation break-points were localized to a 1.8-Mb genomic fragment contained within the commonly deleted segment. Thus, we have identified a single critical region of 2-3 Mb in size in which 11q14-923 aberrations in LPD cluster. This provides the basis for the identification of the gene(s) at 11q22.3-923.1 that are involved in the pathogenesis of LPD.

Human semaphorins A(V) and IV reside in the 3p21.3 small cell lung cancer deletion region and demonstrate distinct expression patterns.

Semaphorins and collapsins make up a family of conserved genes that encode nerve growth cone guidance signals. We have identified two additional members of the human semaphorin family [human semaphorin A(V) and human semaphorin IV] in chromosome region 3p21.3, where several small cell lung cancer (SCLC) cell lines exhibit homozygous deletions indicative of a tumor suppressor gene. Human semaphorin A(V) has 86% amino acid homology with murine semaphorin A, whereas semaphorin IV is most closely related to murine semaphorin E, with 50% homology. These semaphorin genes are approximately 70 kb apart flanking two GTP-binding protein genes, GNAI-2 and GNAT-1. In contrast, other human semaphorin gene sequences (human semaphorin III and homologues of murine semaphorins B and C) are not located on chromosome 3. Human semaphorin A(V) is translated in vitro into a 90-kDa protein, which accumulates at the endoplasmic reticulum. The human semaphorin A(V) (3.4-kb mRNA) and IV (3.9- and 2.9-kb mRNAs) genes are expressed abundantly but differentially in a variety of human neural and nonneural tissues. Human semaphorin A(V) was expressed in only 1 out of 23 SCLCs and 7 out of 16 non-SCLCs, whereas semaphorin IV was expressed in 19 out of 23 SCLCs and 13 out of 16 non-SCLCs. Mutational analysis in semaphorin A(V) revealed mutations (germ line in one case) in 3 of 40 lung cancers. Our data suggest the need to determine the function of human semaphorins A(V) and IV in nonneural tissues and their role in the pathogenesis of lung cancer.

Conservation of synteny between the genome of the pufferfish (Fugu rubripes) and the region on human chromosome 14 (14q24.3) associated with familial Alzheimer disease (AD3 locus)

The genome of the pufferfish (Fugu rubripes) (400 Mb) is approximately 7.5 times smaller than the human genome, but it has a similar gene repertoire to that of man. If regions of the two genomes exhibited conservation of gene order (i.e., were syntenic), it should be possible to reduce dramatically the effort required for identification of candidate genes in human disease loci by sequencing syntenic regions of the compact Fugu genome. We have demonstrated that three genes (dihydrolipoamide succinyltransferase, S31iii125, and S20i15), which are linked to FOS in the familial Alzheimer disease focus (AD3) on human chromosome 14, have homologues in the Fugu genome adjacent to Fugu cFOS. The relative gene order of cFOS, S31iii125, and S20i15 was the same in both genomes, but in Fugu these three genes lay within a 12.4-kb region, compared to >600 kb in the human AD3 locus. These results demonstrate the conservation of synteny between the genomes of Fugu and man and highlight the utility of this approach for sequence-based identification of genes in human disease loci.

Yeast artificial chromosome contigs reveal that distal variable-region genes reside at least 3 megabases from the joining regions in the murine immunoglobulin kappa locus.

The immunoglobulin kappa gene locus encodes 95% of the light chains of murine antibody molecules and is thought to contain up to 300 variable (V kappa)-region genes generally considered to comprise 20 families. To delineate the locus we have isolated 29 yeast artificial chromosome genomic clones that form two contigs, span > 3.5 megabases, and contain two known non-immunoglobulin kappa markers. Using PCR primers specific for 19 V kappa gene families and Southern analysis, we have refined the genetically defined order of these V kappa gene families. Of these, V kappa 2 maps at least 3.0 Mb from the joining (J kappa) region and appears to be the most distal V kappa gene segment.

A region of consistent deletion in neuroblastoma maps within human chromosome 1p36.2-36.3.

Deletion of the short arm of human chromosome 1 is the most common cytogenetic abnormality observed in neuroblastoma. To characterize the region of consistent deletion, we performed loss of heterozygosity (LOH) studies on 122 neuroblastoma tumor samples with 30 distal chromosome 1p polymorphisms. LOH was detected in 32 of the 122 tumors (26%). A single region of LOH, marked distally by D1Z2 and proximally by D1S228, was detected in all tumors demonstrating loss. Also, cells from a patient with a constitutional deletion of 1p36, and from a neuroblastoma cell line with a small 1p36 deletion, were analyzed by fluorescence in situ hybridization. Cells from both sources had interstitial deletions of 1p36.2-36.3 which overlapped the consensus region of LOH defined by the tumors. Interstitial deletion in the constitutional case was confirmed by allelic loss studies using the panel of polymorphic markers. Four proposed candidate genes--DAN, ID3 (heir-1), CDC2L1 (p58), and TNFR2--were shown to lie outside of the consensus region of allelic loss, as defined by the above deletions. These results more precisely define the location of a neuroblastoma suppressor gene within 1p36.2-36.3, eliminating 33 centimorgans of proximal 1p36 from consideration. Furthermore, a consensus region of loss, which excludes the four leading candidate genes, was found in all tumors with 1p36 LOH.

Isolation and characterization of a MAGE gene family in the Xp21.3 region.

A human gene with strong homology to the MAGE gene family located in Xq27-qter has been isolated by using exon-trapping of cosmids in the Xp21.3 region. We have mapped and sequenced cDNA and genomic clones corresponding to this gene, MAGE-Xp, and shown that the last exon contains the open reading frame and is present in a minimum of five copies in a 30-kb interval. MAGE-Xp is expressed only in testis and, unlike the Xq27-qter MAGE genes, it is not expressed in any of 12 different tumor tissues tested. However, the gene and predicted protein structure are conserved, suggesting a similar function. MAGE-Xp is located in the 160-kb critical interval defined for the locus involved in sex determination within Xp21 and is 50 kb distal to the DAX-1 gene, which is responsible for X-chromosome-linked adrenal hypoplasia congenita.

Xce haplotypes show modified methylation in a region of the active X chromosome lying 3' to Xist.

During early mammalian embryogenesis, one of the two X chromosomes in somatic cells of the female becomes inactivated through a process that is thought to depend on a unique initiator region, the X-chromosome inactivation center (Xic). The recently characterized Xist sequence (X-inactive-specific transcript) is thought to be a possible candidate for Xic. In mice a further genetic element, the X chromosome-controlling element (Xce), is also known to influence the choice of which of the two X chromosomes is inactivated. We report that a region of the mouse X chromosome lying 15 kb distal to Xist contains several sites that show hypermethylation specifically associated with the active X chromosome. Analysis of this region in various Xce strains has revealed a correlation between the strength of the Xce allele carried and the methylation status of this region. We propose that such a region could be involved in the initial stages of the inactivation process and in particular in the choice of which of the two X chromosomes present in a female cell will be inactivated.

Hamburg Region, Germany, 1878 (Image 3 of 4) (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: [Topographische Karte 1:25 000] : Niendorf (933). It was published by Konig[liche] Preuss[ische] Landes-Aufnahme in 1878. Scale 1:25,000. This layer is image 3 of 4 total images of the four sheet source map, representing the northwest portion of the map. Covers the Hamburg region, Germany. Map in German.The image inside the map neatline is georeferenced to the surface of the earth and fit to the Deutsches Hauptdreiecksnetz (DHDN) 3-degree Gauss-Kruger Zone 3 coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as roads, railroads and stations, drainage, built-up areas and selected buildings, ground cover, gardens, docks, wharves, and more. Relief shown by contours and spot heights. Depths shown by soundings.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Punjab Region, India & Pakistan, 1869 (Image 3 of 4) (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: The Punjab and its dependencies with portions of the North West Provinces and Afghanistan, 1869. It was published by Survey of India in 1875. Scale 1:1,013,760. This layer is image 3 of 4 total images of the four sheet source map, representing the southwest portion of the map. Covers the Punjab region, India and Pakistan.The image inside the map neatline is georeferenced to the surface of the earth and fit to the Asia North Lambert Conformal Conic coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, roads, railroads, cities and other human settlements, territorial and administrative boundaries, shoreline features, and more. Relief shown by shading and spot heights.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Central America & Caribbean Region, 1803 (Image 3 of 4) (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Chart of the West Indies and Spanish Dominions in North America, by A. Arrowsmith ; Jones, Smith & Co., sc. Beaufort Buildgs., Strand. It was published June 1st, 1803, by A. Arrowsmith, No. 24 Rathbone Place. Scale [ca. 1:2,775,525]. This layer is image 3 of 4 total images of the four sheet source map, representing the southwest portion fo the map. Covers primarily Central America and the Caribbean region.The image inside the map neatline is georeferenced to the surface of the earth and fit to the World Miller Cylindrical projected coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, cities and other human settlements, territorial boundaries, shoreline features, roads, mines, and more. Relief shown by hachures, depths shown by soundings. Includes notes.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Mosul Region, Iraq, 1855 (Image 1 of 3) (Raster Image)

This layer is a georeferenced raster image of the historic paper map set entitled: Vestiges of Assyria, by Felix Jones ; aided in the field operations by J.M. Hyslop ; engraved by J. & C. Walker. Map 1 entitled: Ichnographic sketch of the remains of ancient Nineveh with the enceinte of modern Mosul of Arab M.S.S. and the [Mespila] of the Anabasis. It was published by John Walker in 1855. Scale [ca. 1:12,000]. This layer is image 1 of 3 total images of the six sheet source map, representing the Mosul region Iraq. Map chiefly in English. Some place names given also in Arabic. This datalayer is compiled from two images of the six sheet source map that have been stitched together using image editing software to create a single image.The image inside the map neatline is georeferenced to the surface of the earth and fit to the European Datum 1950 TM42 (Transverse Mercator, Central Meridian 42) coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as ancient city ruins, drainage, canals, cities, villages, and other human settlements, roads, fortifications, selected buildings, and more. Relief shown by hachures.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Mosul Region, Iraq, 1855 (Image 2 of 3) (Raster Image)

This layer is a georeferenced raster image of the historic paper map set entitled: Vestiges of Assyria, by Felix Jones ; aided in the field operations by J.M. Hyslop ; engraved by J. & C. Walker. Map 2 entitled: Positions and plan of the ancient cities of Nimrūd and Selamiyeh, the former identical with the [Larissa] of Xenophon, perhaps the Calah of Genesis and ... of the cuneiform inscriptions. It was published by John Walker in 1855. Scale [ca. 1:12,000]. This layer is image 2 of 3 total images of the six sheet source map, representing the Mosul region Iraq. Map chiefly in English. Some place names given also in Arabic. This datalayer is compiled from two images of the six sheet source map that have been stitched together using image editing software to create a single image.The image inside the map neatline is georeferenced to the surface of the earth and fit to the European Datum 1950 TM42 (Transverse Mercator, Central Meridian 42) coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as ancient city ruins, drainage, canals, cities, villages, and other human settlements, roads, fortifications, selected buildings, and more. Relief shown by hachures.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Mosul Region, Iraq, 1855 (Image 3 of 3) (Raster Image)

This layer is a georeferenced raster image of the historic paper map set entitled: Vestiges of Assyria, by Felix Jones ; aided in the field operations by J.M. Hyslop ; engraved by J. & C. Walker. Map 3 entitled: Map of the country included in the angle formed by the river Tigris & the Upper Zab shewing the disposition of the various ancient sites in the vicinity of Nineveh. It was published by John Walker in 1855. Scale [ca. 1:75,000]. This layer is image 3 of 3 total images of the six sheet source map, representing the Mosul region Iraq at a scale of [ca. 1:75,000]. Map chiefly in English. Some place names given also in Arabic. This datalayer is compiled from two images of the six sheet source map that have been stitched together using image editing software to create a single image.The image inside the map neatline is georeferenced to the surface of the earth and fit to the European Datum 1950 TM42 (Transverse Mercator, Central Meridian 42) coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as ancient city ruins, drainage, canals, cities, villages, and other human settlements, roads, fortifications, selected buildings, and more. Relief shown by hachures.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

Amsterdam Region, the Netherlands, 1749 (Image 1 of 3) (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Kaarte van alle de dykpligtige en eenige waalpligtige landen behorende onder het Hoogreemraadschap van den Zeeburg en Diemerdyk, J. Wandelaar, delin. et sculpsit. It was published in 1749. Scale [ca. 1:6,000]. This layer is image 1 of 3 total images of the three sheet source map, representing the northern portion of the map. Covers the region east of Amsterdam, the Netherlands including portions of Gemeente Amsterdam, Gemeente Diemen, Gemeente Muiden, and Gemeente Weesp. Map in Dutch.The image inside the map neatline is georeferenced to the surface of the earth and fit to the RD_New (Rijksdriehoekstelsel), GCS Amersfoort coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as drainage, canals, cities and other human settlements, administrative boundaries, roads, propery boundaries with names of landowners, selected buildings and built-up areas, fortification, dikes, dams, windmills, shoreline features, and more. Relief shown by hachures. Depths shown by soundings.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.