Large-Scale Transcriptional Activity in Chromosomes 21 and 22

By Philipp Kapranov, S. Cawley, J. Drenkow, S. Bekiranov, R. Strausberg, S. P. Fodor, Thomas R. Gingeras. Science, 2002

877 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/93a5488a5742b2f2b0c90dc68b520165764a0d21

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In Molecular Biology

Citations in the corpus

A bivalent chromatin structure marks key developmental genes in embryonic stem cells. (2006, methodology): “They contain approximately 1.3 million probe pairs, each consisting of perfect match (PM) and single base mismatch (MM) 25-mer oligonucleotides, designed to interrogate the unique sequence in these regions at approximately 30 base intervals (Kapranov et al., 2002).”
Global transcription in pluripotent embryonic stem cells. (2008, methodology): “A total of 192 chips were used for the whole experiment, and composite graphs combining the three biological replica were generated for each time point using standard Affymetrix pipeline (Kampa et al., 2004; Kapranov et al., 2002).”
Computational methods for transcriptome annotation and quantification using RNA-seq (2011, background): “Alternative strategies, such as genome-wide tiling arrays, allowed for the identification of transcribed regions at a larger and more cost-efficient scale but with limited resolutio”
Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene (2004, neutral): “The nine probes used were antisense oligonucleotides corresponding to the following positions relative to the SER3 ATG:2650 to2724 (1),2467 to2541 (2),2341 to2415 (3),2217 to2291 (4), 2118 to2192 (5),þ39 to236 (6),þ223 toþ149 (7),þ530 toþ456 (8),þ891 toþ817 (9).”
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007, neutral): “Successful RACE reactions (%) Index TF 5' RACE 3' RACE 5' and 3' RACE 5' or 3' RACE Transcription on both strands No transcript detected Exonic 20 19 (95) 19 (95) 16 (80) 20 (100) 19 (95) 0 (0) Intronic 90 71 (79) 77 (86) 66 (73) 79 (88) 65 (72) 11 (12) Intergenic 90 62 (69) 65 (72) 44 (49) 77 (86) ”
Transcriptional and Post-transcriptional Gene Regulation by Long Non-coding RNA (2017, background): “22, has indicated that 94% of probes detect transcripts outside of known exons [6], while another study suggests that 49% of transcribed nucleotides are outside of any annotated gene [20].”
Complete sequencing and characterization of 21,243 full-length human cDNAs (2004, background): “Although some of these cDNAs might be cloning artifacts, recent evidence indicates that unexpectedly large populations of non-protein-coding transcripts exist in mammalian cell”
A comprehensive comparison of comparative RNA structure prediction approaches (2004, background): “The number of non-coding RNAs (ncRNA) in humans remains a mystery, but progress in this direction suggests the number of ncRNAs produced is comparable to the number of proteins [4-6].”