Takayuki Nojima

Transcription is a highly dynamic process. Consequently, we have developed native elongating transcript sequencing technology for mammalian chromatin (mNET-seq), which generates single-nucleotide resolution, nascent transcription profiles. Nascent RNA was detected in the active site of RNA polymerase II (Pol II) along with associated RNA processing intermediates. In particular, we detected 5'splice site cleavage by the spliceosome, showing that cleaved upstream exon transcripts are associated wi

Numerous long intervening noncoding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNAs, their synthesis and turnover remain poorly characterized. Here, we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, includ

Extensive tracts of the mammalian genome that lack protein-coding function are still transcribed into long noncoding RNA. While these lncRNAs are generally short lived, length restricted, and non-polyadenylated, how their expression is distinguished from protein-coding genes remains enigmatic. Surprisingly, depletion of the ubiquitous Pol-II-associated transcription elongation factor SPT6 promotes a redistribution of H3K36me3 histone marks from active protein coding to lncRNA genes, which correl

The highly intronic nature of protein coding genes in mammals necessitates a co-transcriptional splicing mechanism as revealed by mNET-seq analysis. Immunoprecipitation of MNase-digested chromatin with antibodies against RNA polymerase II (Pol II) shows that active spliceosomes (both snRNA and proteins) are complexed to Pol II S5P CTD during elongation and co-transcriptional splicing. Notably, elongating Pol II-spliceosome complexes form strong interactions with nascent transcripts, resulting in

A clinicopathologic study of 46 patients with periosteal chondroma and 14 patients with periosteal chondrosarcoma revealed that periosteal chondroma tended to affect younger patients and that the lesion was usually smaller. Radiographically, the typical periosteal chondroma was a small, well-marginated tumor on the outer surface of a long bone. Erosion of the cortical surface and marginal buttresses were usually present. Periosteal chondrosarcoma had a more aggressive appearance and was seen as

Mammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly because of technical limitations in purifying authentic nascent transcripts. We present a new approach to characterize nascent RNA, called polymerase intact nascent transcript (POINT) technology. This three-pronged methodology maps nascent RNA 5' ends (POINT-5), establishes the kinetics of co-transcrip

RNA export factor (REF) is a component of the exon junction complex (EJC) that is deposited on mRNA in a splicing-dependent manner, and targets spliced mRNA for export. In this study, analysis of the RNA-binding protein complexes revealed that REF associates with β-globin mRNA at the region other than the EJC deposition site. Comparison between RNA polymerase II and T7 transcription and further analysis showed that the deposition of REF apart from the EJC is dependent on the 5′ cap structure, bu

Viruses use alternative splicing to produce a broad series of proteins from small genomes by utilizing the cellular splicing machinery. Since viruses use cellular RNA binding proteins for viral RNA processing, it is presumable that the splicing of cellular pre-mRNAs is affected by viral infection. Here, we showed that herpes simplex virus type 2 (HSV-2) modifies the expression of promyelocytic leukemia (PML) isoforms by altering pre-mRNA splicing. Using a newly developed virus-sensitive splicing

Specimens of a synovial sarcoma from the left thigh of a 60-year-old woman and cells from the tumor transplanted into nude mice were examined morphologically and immunohistochemically, and the karyotype was analyzed. Immunohistochemically, cells of both the parent tumor and the transplanted tumor were positive for vimentin and cytokeratin. The multicystic features of the parent tumor were not reproduced in the mice. On ultrastructural examination, the parent tumor cells were found to have dilate

We present a case of chordoid glioma involving the third ventricle in a 42-year-old woman. CT and MR showed a homogeneously enhancing mass occupying the third ventricle, with a cystic component. Chordoid glioma should be included in the differential diagnosis of uncommon masses of the third ventricle in middle-aged women.

CDK9 is a kinase critical for the productive transcription of protein-coding genes by RNA polymerase II (pol II). As part of P-TEFb, CDK9 phosphorylates the carboxyl-terminal domain (CTD) of pol II and elongation factors, which allows pol II to elongate past the early elongation checkpoint (EEC) encountered soon after initiation. We show that, in addition to halting pol II at the EEC, loss of CDK9 activity causes premature termination of transcription across the last exon, loss of polyadenylatio

percent in patients with multiple osteochondromatosis (Matsuno et al. 1988). It is sometimes difficult to distinguish malignant transformation in an osteo- chondroma from other malignant tumors occurring on the surface of bone. Since the dedifferentiated chondrosarcoma (DCS) was described in detail by Dahlin and Beabout (1971), it has been given considerable attention because of its characteristic histologic features and high malignancy. DCS occurs in approximately 10 percent of the patients who