scholarly journals Dissecting chronic myeloid leukaemia overlapping transcriptome with TIF-Seq2

2019 ◽  
Author(s):  
Jingwen Wang ◽  
Bingnan Li ◽  
Sueli Marques ◽  
Lars M. Steinmetz ◽  
Wu Wei ◽  
...  
Keyword(s):  
Chronic Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Human Cell Line ◽  
Transcription Unit ◽  
List Type ◽  
Rna Seq ◽  
Rna Molecules ◽  
Long Read ◽  
Overlapping Transcription ◽  
Nucleotide Resolution

ABSTRACTEukaryotic transcriptomes are complex involving thousands of overlapping transcripts. The interleaved nature of the transcriptome limits our ability to identify regulatory regions and, in some cases, can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptome, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5’ and 3’ ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identify thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-seq, we accurately defined boundaries of lowly expressed unannotated and read-though transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explore transcription regulation among the overlapping units and investigate their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription unit. Our work shows that, by paring the 5’ and 3’ end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitates accurate assignment of promoters to genes and easily identify transcriptionally fused genes.Key pointsStudy of TSS-PAS co-occurrence allows dissecting complex overlapping transcription units.Partially overlapping transcription units in human commonly use PAS within the first 2Kb.TIF-Seq2 facilitates the identification of lowly expressed and transcriptionally fused genes.

scholarly journals TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes

2020 ◽  
Vol 48 (18) ◽  
pp. e104-e104 ◽  
Author(s):  
Jingwen Wang ◽  
Bingnan Li ◽  
Sueli Marques ◽  
Lars M Steinmetz ◽  
Wu Wei ◽  
...  
Keyword(s):  
Human Cell Line ◽  
Rna Seq ◽  
Single Nucleotide ◽  
Rna Molecules ◽  
Unannotated Transcript ◽  
Long Read ◽  
Nucleotide Resolution ◽  
Overlapping Transcripts ◽  
Single Nucleotide Resolution ◽  
Leukaemia Patient

Abstract Eukaryotic transcriptomes are complex, involving thousands of overlapping transcripts. The interleaved nature of the transcriptomes limits our ability to identify regulatory regions, and in some cases can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptomes, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5′ and 3′ ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identified thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-Seq, we accurately defined boundaries of lowly expressed unannotated and read-through transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explored transcription regulation among overlapping units and investigated their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription units. Our work shows that, by paring the 5′ and 3′ end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitate accurate assignment of promoters to genes and easily identify transcriptionally fused genes.

scholarly journals isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ruijiao Xin ◽  
Yan Gao ◽  
Yuan Gao ◽  
Robert Wang ◽  
Kathryn E. Kadash-Edmondson ◽  
...  
Keyword(s):  
Rolling Circle Amplification ◽  
Circular Rna ◽  
Human Cell Line ◽  
Full Length ◽  
Circular Rnas ◽  
Rna Seq ◽  
Short Read ◽  
Rolling Circle ◽  
Rna Molecules ◽  
Long Read

AbstractCircular RNAs (circRNAs) have emerged as an important class of functional RNA molecules. Short-read RNA sequencing (RNA-seq) is a widely used strategy to identify circRNAs. However, an inherent limitation of short-read RNA-seq is that it does not experimentally determine the full-length sequences and exact exonic compositions of circRNAs. Here, we report isoCirc, a strategy for sequencing full-length circRNA isoforms, using rolling circle amplification followed by nanopore long-read sequencing. We describe an integrated computational pipeline to reliably characterize full-length circRNA isoforms using isoCirc data. Using isoCirc, we generate a comprehensive catalog of 107,147 full-length circRNA isoforms across 12 human tissues and one human cell line (HEK293), including 40,628 isoforms ≥500 nt in length. We identify widespread alternative splicing events within the internal part of circRNAs, including 720 retained intron events corresponding to a class of exon-intron circRNAs (EIciRNAs). Collectively, isoCirc and the companion dataset provide a useful strategy and resource for studying circRNAs in human transcriptomes.

Haematological Disease Pattern at Specialized HOPD - A study in Bangabandhu Sheikh Mujib Medical University

2018 ◽  
Vol 2 (02) ◽  
pp. 39-41
Author(s):  
Md. Rafiquzzaman Khan ◽  
Arifur Rahman ◽  
Khaza Amirul Islam ◽  
AQM Ashraful Haque ◽  
Masuda Begum
Keyword(s):  
Iron Deficiency ◽  
Chronic Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Iron Deficiency Anaemia ◽  
Beta Thalassemia ◽  
Female Ratio ◽  
Deficiency Anaemia ◽  
Beta Thalassaemia ◽  
Hb E ◽  
Medical University

The aim of this retrospective observational study was to observe the pattern and frequency of haematological disorders among the patients attending in the specialized Haematology outpatient Department (HOPD) in Bangabandhu Sheikh Mujib Medical University. Consecutive 201 patients over the period of one year were enrolled. Their age ranged from 01 to 72 years with a mean age of 36.76 years. Most of the patients (34.3%) were in between the ages of 31 to 45 years followed by 16 to 30 years (27.9%). Male to female ratio was 0.65. Iron deficiency anaemia is the most common (24.9%) followed by chronic myeloid leukaemia (11.9%), Hb E beta thalassaemia (9.5%), idiopathic thrombocytopenic purpura (9.5%), beta thalassaemia trait (7.0%), Hb E trait (5.5 %), aplastic anaemia (5.0%), multiple myeloma (3.5%), acute lymphoblastic leukaemia (3.0%). Acute myeloid leukaemia, autoimmune haemolytic anaemia, chronic lymphocytic leukaemia, anaemia of chronic disease, non-Hodgkin lymphoma, polycythaemia, beta thalassemia major and alpha thalassemia was 2.5%, 2.5%, 2.0%, 1.5%, 1.5%, 1.5%, 1.0% and 1.0%, respectively. In the present study, we observed that iron deficiency anaemia the most common non-malignant disease and chronic myeloid leukaemia is the common haematological malignancy.

Chronic Myeloid Leukaemia

2017 ◽  
Vol 1 (01) ◽  
pp. 16-22
Author(s):  
Mohiuddin Ahmed Khan ◽  
Mafruh Akter ◽  
Muhammad Kamruzzaman
Keyword(s):  
Chronic Myeloid Leukaemia ◽  
Myeloid Leukaemia

TKI dose reduction can effectively maintain major molecular remission in patients with chronic myeloid leukaemia

2020 ◽  
Author(s):  
Simone Claudiani ◽  
Jane F. Apperley ◽  
Richard Szydlo ◽  
Afzal Khan ◽  
George Nesr ◽  
...  
Keyword(s):  
Chronic Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Dose Reduction ◽  
Molecular Remission

CHRONIC MYELOID LEUKÆMIA: A STUDY OF 86 PATIENTS

1959 ◽  
Vol 2 (3) ◽  
pp. 75-84
Author(s):  
C. K. Hamblt ◽  
T. I. Robertson
Keyword(s):  
Chronic Myeloid Leukaemia ◽  
Myeloid Leukaemia

Extramedullary pericardial haematopoiesis as a presenting feature of chronic myeloid leukaemia

2021 ◽  
Author(s):  
Louisa Shackleton ◽  
Julie McCarthy ◽  
Vitaliy Mykytiv
Keyword(s):  
Chronic Myeloid Leukaemia ◽  
Myeloid Leukaemia
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