primirTSS: an R package for identifying cell-specific microRNA transcription start sites

2020 ◽  
Vol 36 (11) ◽  
pp. 3605-3606
Author(s):  
Pumin Li ◽  
Qi Xu ◽  
Xu Hua ◽  
Zhongwei Xie ◽  
Jie Li ◽  
...  
Keyword(s):  
Conservation Score ◽  
R Package ◽  
Supplementary Information ◽  
Transcription Start ◽  
Pol Ii ◽  
Transcription Start Sites ◽  
Web Interfaces ◽  
Multiple Datasets ◽  
R Programming ◽  
Programming Interfaces

Abstract Summary The R/Bioconductor package primirTSS is a fast and convenient tool that allows implementation of the analytical method to identify transcription start sites of microRNAs by integrating ChIP-seq data of H3K4me3 and Pol II. It further ensures the precision by employing the conservation score and sequence features. The tool showed a good performance when using H3K4me3 or Pol II Chip-seq data alone as input, which brings convenience to applications where multiple datasets are hard to acquire. This flexible package is provided with both R-programming interfaces as well as graphical web interfaces. Availability and implementation primirTSS is available at: http://bioconductor.org/packages/primirTSS. The documentation of the package including an accompanying tutorial was deposited at: https://bioconductor.org/packages/release/bioc/vignettes/primirTSS/inst/doc/primirTSS.html. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Pausing sites of RNA polymerase II on actively transcribed genes are enriched in DNA double-stranded breaks

2020 ◽  
Vol 295 (12) ◽  
pp. 3990-4000 ◽  
Author(s):  
Sandeep Singh ◽  
Karol Szlachta ◽  
Arkadi Manukyan ◽  
Heather M. Raimer ◽  
Manikarna Dinda ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Topoisomerase I ◽  
Cell Types ◽  
Dna Breaks ◽  
Transcription Start ◽  
Pol Ii ◽  
Transcription Start Sites

DNA double-stranded breaks (DSBs) are strongly associated with active transcription, and promoter-proximal pausing of RNA polymerase II (Pol II) is a critical step in transcriptional regulation. Mapping the distribution of DSBs along actively expressed genes and identifying the location of DSBs relative to pausing sites can provide mechanistic insights into transcriptional regulation. Using genome-wide DNA break mapping/sequencing techniques at single-nucleotide resolution in human cells, we found that DSBs are preferentially located around transcription start sites of highly transcribed and paused genes and that Pol II promoter-proximal pausing sites are enriched in DSBs. We observed that DSB frequency at pausing sites increases as the strength of pausing increases, regardless of whether the pausing sites are near or far from annotated transcription start sites. Inhibition of topoisomerase I and II by camptothecin and etoposide treatment, respectively, increased DSBs at the pausing sites as the concentrations of drugs increased, demonstrating the involvement of topoisomerases in DSB generation at the pausing sites. DNA breaks generated by topoisomerases are short-lived because of the religation activity of these enzymes, which these drugs inhibit; therefore, the observation of increased DSBs with increasing drug doses at pausing sites indicated active recruitment of topoisomerases to these sites. Furthermore, the enrichment and locations of DSBs at pausing sites were shared among different cell types, suggesting that Pol II promoter-proximal pausing is a common regulatory mechanism. Our findings support a model in which topoisomerases participate in Pol II promoter-proximal pausing and indicated that DSBs at pausing sites contribute to transcriptional activation.

scholarly journals Zipper plot: visualizing transcriptional activity of genomic regions

2016 ◽  
Author(s):  
Francisco Avila Cobos ◽  
Jasper Anckaert ◽  
Pieter-Jan Volders ◽  
Dries Rombaut ◽  
Jo Vandesompele ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Supplementary Information ◽  
Rna Seq ◽  
Transcription Start ◽  
Summary Table ◽  
Transcription Start Sites ◽  
Chip Sequencing ◽  
Statistical Programming ◽  
Transcriptional Units ◽  
Genomic Regions

AbstractSummaryReconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. The Zipper plot is an application that enables users to interrogate putative transcription start sites (TSSs) in relation to various features that are indicative for transcriptional activity. These features are obtained from publicly available datasets including CAGE-sequencing (CAGE-seq), ChIP-sequencing (ChIP-seq) for histone marks and DNasesequencing (DNase-seq). The Zipper plot application requires three input fields (chromosome, genomic coordinate (hg19) of the TSS and strand) and generates a report that includes a detailed summary table, a Zipper plot and several statistics derived from this plot.Availability and ImplementationThe Zipper plot is implemented using the statistical programming language R and is freely available at http://[email protected]; [email protected]; [email protected] informationSupplementary Methods available online.

scholarly journals ReCappable Seq: Comprehensive Determination of Transcription Start Sites derived from all RNA polymerases

2019 ◽  
Author(s):  
Bo Yan ◽  
George Tzertzinis ◽  
Ira Schildkraut ◽  
Laurence Ettwiller
Keyword(s):  
Rna Polymerases ◽  
Transcription Start ◽  
Eukaryotic Transcription ◽  
Pol Ii ◽  
Transcription Start Sites ◽  
Cell Functions ◽  
A Genome ◽  
Wide Scale ◽  
Nucleotide Resolution ◽  
Pol Iii

AbstractMethodologies for determining eukaryotic Transcription Start Sites (TSS) rely on the selection of the 5’ canonical cap structure of Pol-II transcripts and are consequently ignoring entire classes of TSS derived from other RNA polymerases which play critical roles in various cell functions. To overcome this limitation, we developed ReCappable-seq and identified TSS from Pol-ll and non-Pol-II transcripts at nucleotide resolution. Applied to the human transcriptome, ReCappable-seq identifies Pol-II TSS with higher specificity than CAGE and reveals a rich landscape of TSS associated notably with Pol-III transcripts which have been previously not possible to study on a genome-wide scale. Novel TSS consistent with non-Pol-II transcripts can be found in the nuclear and mitochondrial genomes. By identifying TSS derived from all RNA-polymerases, ReCappable-seq reveals distinct epigenetic marks among Pol-lI and non-Pol-II TSS and provides a unique opportunity to concurrently interrogate the regulatory landscape of coding and non-coding RNA.

scholarly journals Ssl2/TFIIH function in transcription start site scanning by RNA Polymerase II in Saccharomyces cerevisiae

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Tingting Zhao ◽  
Irina O Vvedenskaya ◽  
William KM Lai ◽  
Shrabani Basu ◽  
B Franklin Pugh ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Core Promoter ◽  
Interaction Network ◽  
Transcription Start ◽  
Pol Ii ◽  
Transcription Start Sites ◽  
Scanning Rate ◽  
Residue Interaction

In Saccharomyces cerevisiae, RNA Polymerase II (Pol II) selects transcription start sites (TSS) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ~40-120 basepairs downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow.

scholarly journals StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data

2016 ◽  
Author(s):  
Elena D. Stavrovskaya ◽  
Tejasvi Niranjan ◽  
Elana J. Fertig ◽  
Sarah J. Wheelan ◽  
Alexander Favorov ◽  
...  
Keyword(s):  
Partial Correlation ◽  
Reference Genome ◽  
Developmental Trajectories ◽  
Supplementary Information ◽  
Regulation Of Transcription ◽  
Transcription Start ◽  
Genomic Features ◽  
Transcription Start Sites ◽  
Supplementary Material ◽  
Kernel Correlation

AbstractMotivationGenomics features with similar genomewide distributions are generally hypothesized to be functionally related, for example, co-localization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genomewide correlation among genomic features are required.ResultsHere, we propose a method, StereoGene, that rapidly estimates genomewide correlation among pairs of genomic features. These features may represent high throughput data mapped to reference genome or sets of genomic annotations in that reference genome. StereoGene enables correlation of continuous data directly, avoiding the data binarization and subsequent data loss. Correlations are computed among neighboring genomic positions using kernel correlation. Representing the correlation as a function of the genome position, StereoGene outputs the local correlation track as part of the analysis. StereoGene also accounts for confounders such as input DNA by partial correlation. We apply our method to numerous comparisons of ChIP-Seq datasets from the Human Epigenome Atlas and FANTOM CAGE to demonstrate its wide applicability. We observe the changes in the correlation between epigenomic features across developmental trajectories of several tissue types consistent with known biology, and find a novel spatial correlation of CAGE clusters with donor splice sites and with poly(A) sites. These analyses provide examples for the broad applicability of StereoGene for regulatory genomics.AvailabilityThe StereoGene C++ source code, program documentation, Galaxy integration scripts and examples are available from the project homepage http://stereogene.bioinf.fbb.msu.ru/[email protected] informationSupplementary data are available online.

scholarly journals InterMineR: an R package for InterMine databases

2019 ◽  
Vol 35 (17) ◽  
pp. 3206-3207 ◽  
Author(s):  
Konstantinos A Kyritsis ◽  
Bing Wang ◽  
Julie Sullivan ◽  
Rachel Lyne ◽  
Gos Micklem
Keyword(s):  
Data Retrieval ◽  
R Package ◽  
Supplementary Information ◽  
Programming Environment ◽  
Biological Databases ◽  
Statistical Tools ◽  
Bioconductor Project ◽  
Term Enrichment ◽  
R Programming ◽  
Downstream Analysis

Abstract Summary InterMineR is a package designed to provide a flexible interface between the R programming environment and biological databases built using the InterMine platform. The package offers access to the flexible query builder and the library of term enrichment tools of the InterMine framework, as well as interoperability with other Bioconductor packages. This facilitates automation of data retrieval tasks as well as downstream analysis with existing statistical tools in the R environment. Availability and implementation InterMineR is free and open source, released under the LGPL licence and available from the Bioconductor project and Github (https://bioconductor.org/packages/release/bioc/html/InterMineR.html, https://github.com/intermine/interMineR). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals rMSIproc: an R package for mass spectrometry imaging data processing

2020 ◽  
Vol 36 (11) ◽  
pp. 3618-3619 ◽  
Author(s):  
Pere Ràfols ◽  
Bram Heijs ◽  
Esteban del Castillo ◽  
Oscar Yanes ◽  
Liam A McDonnell ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Processing ◽  
Mass Spectrometry Imaging ◽  
R Package ◽  
Supplementary Information ◽  
Imaging Data ◽  
Full Data ◽  
Modern Computer ◽  
Multiple Datasets ◽  
Novel Strategy

Abstract Summary Mass spectrometry imaging (MSI) can reveal biochemical information directly from a tissue section. MSI generates a large quantity of complex spectral data which is still challenging to translate into relevant biochemical information. Here, we present rMSIproc, an open-source R package that implements a full data processing workflow for MSI experiments performed using TOF or FT-based mass spectrometers. The package provides a novel strategy for spectral alignment and recalibration, which allows to process multiple datasets simultaneously. This enables to perform a confident statistical analysis with multiple datasets from one or several experiments. rMSIproc is designed to work with files larger than the computer memory capacity and the algorithms are implemented using a multi-threading strategy. rMSIproc is a powerful tool able to take full advantage of modern computer systems to completely develop the whole MSI potential. Availability and implementation rMSIproc is freely available at https://github.com/prafols/rMSIproc. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq

2021 ◽  
pp. gr.275784.121
Author(s):  
Bo Yan ◽  
George Tzertzinis ◽  
Ira Schildkraut ◽  
Laurence Ettwiller
Keyword(s):  
Noncoding Rna ◽  
Rna Polymerases ◽  
Transcription Start ◽  
Pol Ii ◽  
Transcription Start Sites ◽  
Cell Functions ◽  
Wide Scale ◽  
Nucleotide Resolution ◽  
Pol Iii

Determination of eukaryotic Transcription Start Sites (TSS) has been based on methods that require the cap structure at the 5-prime end of transcripts derived from Pol-II RNA polymerase. Consequently, these methods do not reveal TSS derived from the other RNA polymerases which also play critical roles in various cell functions. To address this limitation, we developed ReCappable-seq which comprehensively identifies TSS for both Pol-lI and non-Pol-II transcripts at single-nucleotide resolution. The method relies on specific enzymatic exchange of 5-prime m7G caps and 5-prime triphosphates with a selectable tag. When applied to human transcriptomes, ReCappable-seq identifies Pol-II TSS that are in agreement with orthogonal methods such as CAGE. Additionally, ReCappable-seq reveals a rich landscape of TSS associated with Pol-III transcripts which have not previously been amenable to study at genome-wide scale. Novel TSS from non-Pol-II transcription can be located in the nuclear and mitochondrial genomes. ReCappable-seq interrogates the regulatory landscape of coding and noncoding RNA concurrently and enables the classification of epigenetic profiles associated with Pol-lI and non-Pol-II TSS.

Μελέτη του ρόλου των επιγενετικών και επιδιορθωτικών μηχανισμών στη ρύθμιση της γονιδιακής έκφρασης

2020 ◽  
Author(s):  
Αναστάσιος Λιάκος
Keyword(s):  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Transcription Start ◽  
Pol Ii ◽  
Transcription Start Sites ◽  
Nucleotide Excision

Τα κύτταρά μας εκτίθενται καθημερινά σε πληθώρα παραγόντων που απειλούν την γονιδιωματική τους ακεραιότητα. Οι βλάβες που προκαλούνται από την υπεριώδη (UV) ακτινοβολία, επιδιορθώνονται από τον μηχανισμό εκτομής βάσης (Nucleotide Excision Repair, NER), ο οποίος αποτελείται από 2 υπό-μονοπάτια: το Global Genome NER (GG-NER), που δρα σε όλο το γονιδίωμα και το Transcription Coupled NER (TC-NER), το οποίο δρα στις ενεργώς μεταγραφόμενες περιοχές, πυροδοτούμενο από το σταμάτημα της RNA πολυμεράσης ΙΙ (Pol II) στις περιοχές των UV επαγόμενων βλαβών, υποδηλώνοντας πως η μεταγραφή μέσω της Pol II διαδραματίζει κομβικό ρόλο στη διατήρηση της γονιδιωματικής ακεραιότητας. Με την εισαγωγή των τεχνολογιών αλληλούχισης νέας γενιάς, βρέθηκε πως τα κύτταρα ανταποκρίνονται στο γενοτοξικό στρες, μέσω μιας πολυεπίπεδης μεταγραφικής αναδιοργάνωσης, η οποία συντελεί στη γρήγορη επιδιόρθωση των UV επαγόμενων βλαβών. Ωστόσο, πολλές λεπτομέρειες του συγκεκριμένου μηχανισμού παρέμειναν αδιευκρίνιστες. Στην παρούσα διατριβή, μελετήθηκε αρχικά η επίδραση της UV ακτινοβολίας στην προσβασιμότητα της χρωματίνης ανθρώπινων ινοβλαστών δέρματος, μέσω της μεθόδου ATAC-seq. Τα αποτελέσματά έδειξαν πως η έκθεση σε UV οδηγεί σε σημαντική αύξηση της προσβασιμότητας της χρωματίνης στις ρυθμιστικές περιοχές του μεταγραφόμενου γονιδιώματος. Η αύξηση αυτή συνάδει με την UV-επαγόμενη απελευθέρωση των μορίων Pol II-ser2P από τις θέσεις παύσης της μεταγραφής πλησίον του υποκινητή, η οποία λαμβάνει χώρα, σε όλες τις ενεργώς μεταγραφόμενες, κωδικές και μη κωδικές, περιοχές του γονιδιώματος. Επιπλέον, πειράματα αλληλούχισης ανοσοκατακρημνισμένης χρωματίνης, σε συνδυασμό με βιοχημικές τεχνικές, έδειξαν ότι τα επίπεδα και η κατανομή της ιστονικής τροποποίησης H3K27ac παραμένουν σταθερά στις περιοχές των σημείων έναρξης της μεταγραφής (Transcription Start Sites, TSS), μετά την έκθεση σε UV. Τα αποτελέσματα αυτά υποδεικνύουν ότι, οι ρυθμιστικές περιοχές των μεταγραφόμενων γονιδιωματικών περιοχών διατηρούν την ενεργότητά τους, μετά από έκθεση σε UV. Ακόμη, βρέθηκε πως η ακτινοβόληση με UV δεν αναστέλλει την πρόσδεση των μορίων Pol II-hypo στις περιοχές TSS των ενεργώς μεταγραφόμενων γενετικών τόπων, αλλά προκαλεί μια γρήγορη μετάβαση των μορίων από το στάδιο μεταγραφικής έναρξης σε αυτό της επιμήκυνσης, οδηγώντας σε μείωση των επιπέδων της Pol II-hypo στους υποκινητές. Διαπιστώθηκε πως η διαδικασία πρόσδεσης-γρήγορης προώθησης λαμβάνει χώρα καθ’ όλη την περιόδο ανάκαμψης των κυττάρων μετά την έκθεση σε UV και επιβεβαιώθηκε πως ταυτόχρονα, τα μόρια Pol II διατηρούν την δυνατότητα να συνθέτουν RNA στις περιοχές πλησίον των TSSs. Επιπλέον, βιοπληροφορική συσχέτιση των δεδομένων μας με δεδομένα αλληλούχισης, τα οποία χαρτογραφούν τα τμήματα του DNA που περιέχουν βλάβες και επιδιορθώνονται μέσω TC-NER, έδειξε πως για την επιτυχή ολοκλήρωση της επιδιόρθωσης και την εξασφάλιση της ακεραιότητας όλου του μεταγραφόμενου γονιδιώματος, απαιτείται συνεχής τροφοδότηση των ενεργών ρυθμιστικών περιοχών, με νέα μόρια Pol II. Συμπερασματικά, η διατήρηση ενεργής κατάστασης της χρωματίνης στα TSS των μεταγραφόμενων κωδικών και μη κωδικών περιοχών μετά την έκθεση σε UV, ευνοεί την πρόσδεση μορίων Pol II και τη γρήγορη προώθησή τους στη φάση επιμήκυνσης, τροφοδοτώντας ένα μεταγραφικό κύμα, το οποίο σαρώνει το ενεργώς μεταγραφόμενο γονιδίωμα, ανιχνεύοντας και επιδιορθώνοντας τις UV επαγόμενες βλάβες. Παράλληλα, μελετήθηκαν οι δυναμικές έναρξης της μεταγραφής μετά από έκθεση σε UV σε ινοβλάστες δέρματος ασθενών CS-B. Βρέθηκε πως η πρόσδεση της Pol II στους υποκινητές των ενεργών γονιδίων δεν αναστέλλεται και πως η τροποποίηση H3K27ac παραμένει σε σταθερά επίπεδα στις περιοχές αυτές. Τα συγκεκριμένα δεδομένα υποδηλώνουν πως η ανικανότητα επανεκκίνησης της μεταγραφής στους ινοβλάστες CS-B, δεν οφείλεται σε μόνιμη αναστολή της μεταγραφικής έναρξης αλλά στην αδυναμία διαχείρισης του σταματήματος της μεταγραφικής επιμήκυνσης στις περιοχές των βλαβών. Τέλος, αρκετά γονίδια σχετιζόμενα με διαδικασίες κυτταρικής ανάπτυξης και διαφοροποίησης, παρουσιάζουν ταυτόχρονα διαφορική έκφραση και στόχευση από την τροποποίηση H3K27me3, συγκρίνοντας μη ακτινοβολημένους φυσιολογικούς και CS-B ινοβλάστες δέρματος. Τα παραπάνω συνδέουν την πρωτεΐνη CSB με τις διαδικασίες της ορθής επιγενετικής ρύθμισης της γονιδιακής έκφρασης.

Sign in / Sign up

Export Citation Format

Share Document