Journal: BMC Evolutionary Biology

Article Title: Evolution of motif variants and positional bias of the cyclic-AMP response element

doi: 10.1186/1471-2148-7-S1-S15

Figure Lengend Snippet: Summary of TSS-SRs from 9 species

Article Snippet: Gallus gallus , galGal2 , RefSeq Genes , 1,692.

Techniques:

Journal: PLoS Biology

Article Title: Distinct Genomic Integration of MLV and SIV Vectors in Primate Hematopoietic Stem and Progenitor Cells

doi: 10.1371/journal.pbio.0020423

Figure Lengend Snippet: Shown are integrations that landed within RefSeq gene introns (arrows) in comparison to in silico-generated integration sites (bars). Black indicates MLV and gray indicates SIV. * p < 0.0001 by a Chi 2 test.

Article Snippet: We correlated the 760 integration sites (432 for MLV and 328 for SIV) that unequivocally mapped to a unique position in the genome to the locations of annotated genes, using the UCSC Genome Browser Reference Sequence (RefSeq) Genes track, which displays the positions of National Center for Biotechnology Information mRNA Reference Sequences ( ).

Techniques: Comparison, In Silico, Generated

Journal: PLoS Biology

Article Title: Distinct Genomic Integration of MLV and SIV Vectors in Primate Hematopoietic Stem and Progenitor Cells

doi: 10.1371/journal.pbio.0020423

Figure Lengend Snippet: (A) Distribution of MLV and SIV integration sites relative to gene density within a 1-Mbp window compared to in silico-generated random integration sites. Each bar corresponds to the percentage of integration sites within the corresponding gene density region. (B) Location of MLV and SIV integration sites and gene density on human Chromosome 6. MLV and SIV integrations were aligned to Chromosome 6 (obtained from the UCSC custom annotation track feature) and shown in relation to RefSeq gene density (blue). 73% of the SIV integration events are within the 20-Mbp unique ridge of Chromosome 6, compared to 29% for MLV. Distance between thick black bars is 20 Mbp; centromere is represented by the black circle.

Article Snippet: We correlated the 760 integration sites (432 for MLV and 328 for SIV) that unequivocally mapped to a unique position in the genome to the locations of annotated genes, using the UCSC Genome Browser Reference Sequence (RefSeq) Genes track, which displays the positions of National Center for Biotechnology Information mRNA Reference Sequences ( ).

Techniques: In Silico, Generated

Journal: Endocrinology

Article Title: Sex-Biased lncRNAs Inversely Correlate With Sex-Opposite Gene Coexpression Networks in Diversity Outbred Mouse Liver

doi: 10.1210/en.2018-00949

Figure Lengend Snippet: Mouse liver–expressed lncRNAs. (A) Pipeline used for discovery of 15,558 liver-expressed lncRNAs, based on Melia et al. (22), except only gene structures whose exons overlap protein-coding gene exons transcribed in the same direction were removed. Of the 15,558 lncRNAs, 13,343 did not overlap any protein-coding gene and, therefore, were designated intergenic; 1,966 lncRNAs were designated antisense on the basis of their overlap with the antisense strand of a protein-coding gene; and 249 lncRNAs were designated intragenic (i.e., they were transcribed in the same direction as an overlapping protein-coding gene, but without any exonic region overlap). Data characterizing the 15,558 liver-expressed lncRNAs are presented in Supplemental Table 2A (44). (B) Principal component analysis of 186 RNA-seq samples used to discover liver-expressed lncRNAs. The first principal component separates the livers by the age of the mice from young to old (right to left; ages are indicated on the right). (C–G) Examples of sex-specific lncRNAs discovered in this study. Gene structures of lncRNAs are shown in green. Shown are wig files based on sequencing reads for male and female nuclear RNA-seq samples. (C) Intergenic lncRNA showing strong female-biased gene expression. (D, E) Intergenic lncRNAs showing strong male-biased gene expression. Additional details about these two lncRNAs are shown in Table 2 and Supplemental Fig. 2 (44). (F) Female-specific lncRNA, ncRNA_inter_chr15_12684, that is transcribed on the reverse strand and overlaps ncRNA_inter_chr15_12685, which is transcribed on the forward strand. Corresponds to RefSeq noncoding gene 9030619P08Rik. (G) Male-specific, antisense lncRNA, ncRNA_as_chr3_2800, that is transcribed on the reverse strand and overlaps Pde5a, which is transcribed on the forward strand. chr, chromosome; Ed, embryonic day; F, forward strand; FPR, false-positive rate; inter, intergenic; ncRNA, noncoding RNA; ORF, open reading frame; PC, principal component; R, reverse strand; RefSeq, National Center for Biotechnology Information Reference Sequence database.

Article Snippet: Corresponds to RefSeq noncoding gene 9030619P08Rik. (G) Male-specific, antisense lncRNA, ncRNA_as_chr3_2800, that is transcribed on the reverse strand and overlaps Pde5a , which is transcribed on the forward strand. chr, chromosome; Ed, embryonic day; F, forward strand; FPR, false-positive rate; inter, intergenic; ncRNA, noncoding RNA; ORF, open reading frame; PC, principal component; R, reverse strand; RefSeq, National Center for Biotechnology Information Reference Sequence database.

Techniques: RNA Sequencing, Sequencing, Gene Expression