Peak identification from ChIP-nexus data.
| Název práce v češtině: | Identifikace vazebných míst v datech z ChIP-nexus |
|---|---|
| Název v anglickém jazyce: | Peak identification from ChIP-nexus data. |
| Klíčová slova: | Interakce protein-DNA, transkripční faktory, ChIP-seq, ChIP-exo, ChIP-nexus, peak callery, Cbf11 |
| Klíčová slova anglicky: | Protein-DNA interactions, transcription factors, ChIP-seq, ChIP-exo, ChIP-nexus, peak callers, Cbf11 |
| Akademický rok vypsání: | 2021/2022 |
| Typ práce: | bakalářská práce |
| Jazyk práce: | angličtina |
| Ústav: | Katedra buněčné biologie (31-151) |
| Vedoucí / školitel: | RNDr. Martin Převorovský, Ph.D. |
| Řešitel: | skrytý - zadáno vedoucím/školitelem |
| Datum přihlášení: | 05.11.2021 |
| Datum zadání: | 05.11.2021 |
| Datum odevzdání elektronické podoby: | 10.05.2022 |
| Datum proběhlé obhajoby: | 02.06.2022 |
| Oponenti: | Mgr. Lenka Gahurová, Ph.D. |
| Předběžná náplň práce |
| To understand the various ways of how gene expression is regulated in the cell, one of the critical requirements is to accurately determine thegenome-wide distribution of chromatin-associated proteins (such astranscription factors ormodified histones).To this end, the chromatin immunoprecipitation technique combined with next-generation sequencing (ChIP-seq) is often used. However, while very informative, ChIP-seq experiments often lack the resolution required to precisely pinpoint the binding sites of the studied protein on DNA. To address these issues, the ChIP-exo and ChIP-nexus methods have been introduced, in which exonuclease treatment of immunoprecipitated protein-DNA complexes helps to more precisely delimit the actual binding site on each DNA fragment.
Peak calling is an analytical step that identifies regions enriched for sequencing read coverage in ChIP experiments (ie, bona-fide binding sites), and numerous peak calling software tools have been created and are used during ChIP-seq analyses. Unfortunately, the availability of reliable peak callers compatible with ChIP-exo/ChIP-nexus data seems to be rather limited. The aims of the proposed BSc thesis project are to: 1) review the currently available approaches and algorithms for peak calling from ChIP-nexus (and closely related methods) data. 2) test the suitability of currently available peak callers for the ChIP-nexus data that is available in the Laboratory of Microbial Genomics. |
| Předběžná náplň práce v anglickém jazyce |
| To understand the various ways of how gene expression is regulated in the cell, one of the critical requirements is to accurately determine thegenome-wide distribution of chromatin-associated proteins (such astranscription factors ormodified histones).To this end, the chromatin immunoprecipitation technique combined with next-generation sequencing (ChIP-seq) is often used. However, while very informative, ChIP-seq experiments often lack the resolution required to precisely pinpoint the binding sites of the studied protein on DNA. To address these issues, the ChIP-exo and ChIP-nexus methods have been introduced, in which exonuclease treatment of immunoprecipitated protein-DNA complexes helps to more precisely delimit the actual binding site on each DNA fragment.
Peak calling is an analytical step that identifies regions enriched for sequencing read coverage in ChIP experiments (ie, bona-fide binding sites), and numerous peak calling software tools have been created and are used during ChIP-seq analyses. Unfortunately, the availability of reliable peak callers compatible with ChIP-exo/ChIP-nexus data seems to be rather limited. The aims of the proposed BSc thesis project are to: 1) review the currently available approaches and algorithms for peak calling from ChIP-nexus (and closely related methods) data. 2) test the suitability of currently available peak callers for the ChIP-nexus data that is available in the Laboratory of Microbial Genomics. |